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Open AccessArticle Towards a Cognitive Radar: Canada’s Third-Generation High Frequency Surface Wave Radar (HFSWR) for Surveillance of the 200 Nautical Mile Exclusive Economic Zone

by Anthony Ponsford, Rick McKerracher, Zhen Ding, Peter Moo and Derek Yee

Sensors 2017, 17(7), 1588; doi:10.3390/s17071588

Received: 21 April 2017 / Revised: 19 June 2017 / Accepted: 29 June 2017 / Published: 7 July 2017

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Abstract

Canada’s third-generation HFSWR forms the foundation of a maritime domain awareness system that provides enforcement agencies with real-time persistent surveillance out to and beyond the 200 nautical mile exclusive economic zone (EEZ). Cognitive sense-and-adapt technology and dynamic spectrum management ensures robust and resilient

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Canada’s third-generation HFSWR forms the foundation of a maritime domain awareness system that provides enforcement agencies with real-time persistent surveillance out to and beyond the 200 nautical mile exclusive economic zone (EEZ). Cognitive sense-and-adapt technology and dynamic spectrum management ensures robust and resilient operation in the highly congested High Frequency (HF) band. Dynamic spectrum access enables the system to simultaneously operate on two frequencies on a non-interference and non-protected basis, without impacting other spectrum users. Sense-and-adapt technologies ensure that the system instantaneously switches to a new vacant channel on the detection of another user or unwanted jamming signal. Adaptive signal processing techniques mitigate against electrical noise, interference and clutter. Sense-and-adapt techniques applied at the detector and tracker stages maximize the probability of track initiation whilst minimizing the probability of false or otherwise erroneous track data. Full article

(This article belongs to the Special Issue Marine Sensing)

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Open AccessArticle Public Support for Electronic Cigarette Regulation in Hong Kong: A Population-Based Cross-Sectional Study

by Yee Tak Derek Cheung, Man Ping Wang, Sai Yin Ho, Nan Jiang, Antonio Kwong, Vienna Lai and Tai Hing Lam

Int. J. Environ. Res. Public Health 2017, 14(7), 709; doi:10.3390/ijerph14070709

Received: 15 May 2017 / Revised: 27 June 2017 / Accepted: 28 June 2017 / Published: 30 June 2017

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Abstract

This study aimed to gauge the Hong Kong’s public support towards new e-cigarette regulation, and examine the associated factors of the support. We conducted a two-stage, randomized cross-sectional telephone-based survey to assess the public support towards the banning of e-cigarette promotion and advertisement,

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This study aimed to gauge the Hong Kong’s public support towards new e-cigarette regulation, and examine the associated factors of the support. We conducted a two-stage, randomized cross-sectional telephone-based survey to assess the public support towards the banning of e-cigarette promotion and advertisement, its use in smoke-free venues, the sale to people aged under 18, and regulating the sale of nicotine-free e-cigarettes. Adults (aged 15 years or above) who were never smoking (n = 1706), ex-smoking (n = 1712) or currently smoking (n = 1834) were included. Over half (57.8%) supported all the four regulations. Banning of e-cigarette promotion and advertisement (71.7%) received slightly less support than the other three regulations (banning of e-cigarette use in smoke-free venues (81.5%); banning of e-cigarette sale to minors (93.9%); sale restriction of nicotine-free e-cigarettes (80.9%)). Current smokers, and perceiving e-cigarettes as less harmful than traditional cigarettes or not knowing the harmfulness, were associated with a lower level of support. Our findings showed a strong public support for further regulation of e-cigarettes in Hong Kong. Current stringent measures on tobacco and e-cigarettes, and media reports on the harmfulness of e-cigarettes may underpin the strong support for the regulation. Full article

(This article belongs to the Section Global Health)

Open AccessArticle Influence of Stratigraphic Conditions on the Deformation Characteristics of Oil/Gas Wells Piercing Longwall Pillars and Mining Optimization

by Shun Liang, Derek Elsworth, Xuehai Fu, Xuehua Li and Qiangling Yao

Energies 2017, 10(6), 775; doi:10.3390/en10060775

Received: 18 April 2017 / Revised: 26 May 2017 / Accepted: 31 May 2017 / Published: 3 June 2017

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Abstract

Hydrocarbon wells drilled vertically through longwall coal pillars are vulnerable to severe deformation and potential failure as a result of underground coal mining. The lithology of the host rocks play a critical role in well stability. In this study, a two dimensional finite

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Hydrocarbon wells drilled vertically through longwall coal pillars are vulnerable to severe deformation and potential failure as a result of underground coal mining. The lithology of the host rocks play a critical role in well stability. In this study, a two dimensional finite element method is employed to investigate the horizontal shear offset, vertical delamination, and compression at the weak interface between neighboring soft and stiff layers after the sequential extraction of longwall panels flanking the protective coal pillar. The influence of stratigraphic conditions, including the single rock layer thickness (SRLT), seam mining height (SMH), and seam dip angle (SDA), on deformation of hydrocarbon wells is explored. An optimization of mining sequence along strike and for panel advance direction along dip is also performed. Finally, some recommendations regarding coal mining and peripheral support measures are suggested. Full article

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Open AccessArticle Horticultural Loss Generated by Wholesalers: A Case Study of the Canning Vale Fruit and Vegetable Markets in Western Australia

by Purabi R. Ghosh, Derek Fawcett, Devindri Perera, Shashi B. Sharma and Gerrard E. J. Poinern

Horticulturae 2017, 3(2), 34; doi:10.3390/horticulturae3020034

Received: 6 April 2017 / Revised: 9 May 2017 / Accepted: 20 May 2017 / Published: 25 May 2017

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Abstract

In today’s economic climate, businesses need to efficiently manage their finite resources to maintain long-term sustainable growth, productivity, and profits. However, food loss produces large unacceptable economic losses, environmental degradation, and impacts on humanity globally. Its cost in Australia is estimated to be

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In today’s economic climate, businesses need to efficiently manage their finite resources to maintain long-term sustainable growth, productivity, and profits. However, food loss produces large unacceptable economic losses, environmental degradation, and impacts on humanity globally. Its cost in Australia is estimated to be around AUS$8 billion each year, but knowledge of its extent within the food value chain from farm to fork is very limited. The present study examines food loss by wholesalers. A survey questionnaire was prepared and distributed; 35 wholesalers and processors replied and their responses to 10 targeted questions on produce volumes, amounts handled, reasons for food loss, and innovations applied or being considered to reduce and utilize food loss were analyzed. Reported food loss was estimated to be 180 kg per week per primary wholesaler and 30 kg per secondary wholesaler, or around 286 tonnes per year. Participants ranked “over supply” and “no market demand” as the main causes for food loss. The study found that improving grading guidelines has the potential to significantly reduce food loss levels and improve profit margins. Full article

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Open AccessFeature PaperArticle “Modern Nature”: Derek Jarman’s Garden

by Melissa Zeiger

Humanities 2017, 6(2), 22; doi:10.3390/h6020022

Received: 14 February 2017 / Accepted: 5 April 2017 / Published: 12 April 2017

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Abstract

The queer filmmaker, artist, activist, and gardener, Derek Jarman, when diagnosed with AIDS in 1986, turned to what may seem like an unlikely form of political and aesthetic expression. His eventually world-famous garden allowed him symbolically and aesthetically to address the political issues

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The queer filmmaker, artist, activist, and gardener, Derek Jarman, when diagnosed with AIDS in 1986, turned to what may seem like an unlikely form of political and aesthetic expression. His eventually world-famous garden allowed him symbolically and aesthetically to address the political issues with which he had always passionately concerned himself: environmental degradation, nuclear expansion, homophobia, consumer culture, and AIDS. Each of these issues entailed a crisis of political response in the late twentieth century, and in the garden, Jarman addresses this crisis on a number of levels, but always as elements of a terminal condition without any prospect of a “cure.” Using literary analysis to examine the garden and Jarman’s writing about it, in addition to a cultural studies perspective to place these topics in a broad context, this essay undertakes a study of the garden’s codes and effects. Consulting Sarah Ensor and Eve Kosofsky Sedgwick, both of whom describe terminality as a temporality with its own powers and ways of being, I focus on Jarman’s efforts in what he acknowledges as a damaged, post-natural landscape. Rather than seeing crisis only as a moment of emergency, Jarman imagines other more reflective responses to crisis that, I argue, complement more interventionist approaches. Full article

(This article belongs to the Special Issue Gender in Times of Crisis: A Multidisciplinary Conversation)

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Open AccessBrief Report Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency

by Maxime Junior Jean, Derek Power, Weili Kong, Huachao Huang, Netty Santoso and Jian Zhu

Viruses 2017, 9(4), 67; doi:10.3390/v9040067

Received: 13 February 2017 / Revised: 19 March 2017 / Accepted: 24 March 2017 / Published: 1 April 2017

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Abstract

Human immunodeficiency virus type 1 (HIV-1) Tat is a virus-encoded trans-activator that plays a central role in viral transcription. We used our recently developed parallel analysis of in vitro translated open reading frames (ORFs) (PLATO) approach to identify host proteins that associate with

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Human immunodeficiency virus type 1 (HIV-1) Tat is a virus-encoded trans-activator that plays a central role in viral transcription. We used our recently developed parallel analysis of in vitro translated open reading frames (ORFs) (PLATO) approach to identify host proteins that associate with HIV-1 Tat. From this proteomic assay, we identify 89 Tat-associated proteins (TAPs). We combine our results with other datasets of Tat or long terminal repeat (LTR)-associated proteins. For some of these proteins (NAT10, TINP1, XRCC5, SIN3A), we confirm their strong association with Tat. These TAPs also suppress Tat-mediated HIV-1 transcription. Removing suppression of HIV-1 transcription benefits the reversal of post-integrated, latent HIV-1 proviruses. We demonstrate that these transcriptionally suppressing TAPs contribute to HIV-1 latency in Jurkat latency (J-LAT) cells. Therefore, our proteomic analysis highlights the previously unappreciated TAPs that play a role in maintaining HIV-1 latency and can be further studied as potential pharmacological targets for the “shock and kill” HIV-1 cure strategy. Full article

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Open AccessArticle Improving Suicide Prevention in Dutch Regions by Creating Local Suicide Prevention Action Networks (SUPRANET): A Study Protocol

by Renske Gilissen, Derek De Beurs, Jan Mokkenstorm, Saskia Mérelle, Gé Donker, Sanne Terpstra, Carla Derijck, The SUPRANET (Suicide Prevention Action Network) Research Group and Gerdien Franx

Int. J. Environ. Res. Public Health 2017, 14(4), 349; doi:10.3390/ijerph14040349

Received: 30 January 2017 / Revised: 16 March 2017 / Accepted: 22 March 2017 / Published: 28 March 2017

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Abstract

The European Alliance against Depression (EAAD) program is to be introduced in The Netherlands from 2017 onwards. This program to combat suicide consists of interventions on four levels: (1) increasing the awareness of suicide by local media campaigns; (2) training local gatekeepers, such

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The European Alliance against Depression (EAAD) program is to be introduced in The Netherlands from 2017 onwards. This program to combat suicide consists of interventions on four levels: (1) increasing the awareness of suicide by local media campaigns; (2) training local gatekeepers, such as teachers or police officers; (3) targeting high-risk persons in the community; and (4) training and support of professionals in primary care settings. The implementation starts in seven Dutch pilot regions. Each region is designated as a Suicide Prevention Action NETwork (SUPRANET). This paper describes the SUPRANET program components and the evaluation of its feasibility and impact. The findings will be used to facilitate the national implementation of EAAD in The Netherlands and to add new findings to the existing literature on EAAD. Full article

(This article belongs to the Special Issue From Understanding Suicide Risk to Preventing Suicide)

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Open AccessReview Human T Cell Memory: A Dynamic View

by Derek C. Macallan, José A. M. Borghans and Becca Asquith

Vaccines 2017, 5(1), 5; doi:10.3390/vaccines5010005

Received: 18 July 2016 / Revised: 3 November 2016 / Accepted: 17 January 2017 / Published: 4 February 2017

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Abstract

Long-term T cell-mediated protection depends upon the formation of a pool of memory cells to protect against future pathogen challenge. In this review we argue that looking at T cell memory from a dynamic viewpoint can help in understanding how memory populations are

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Long-term T cell-mediated protection depends upon the formation of a pool of memory cells to protect against future pathogen challenge. In this review we argue that looking at T cell memory from a dynamic viewpoint can help in understanding how memory populations are maintained following pathogen exposure or vaccination. For example, a dynamic view resolves the apparent paradox between the relatively short lifespans of individual memory cells and very long-lived immunological memory by focussing on the persistence of clonal populations, rather than individual cells. Clonal survival is achieved by balancing proliferation, death and differentiation rates within and between identifiable phenotypic pools; such pools correspond broadly to sequential stages in the linear differentiation pathway. Each pool has its own characteristic kinetics, but only when considered as a population; single cells exhibit considerable heterogeneity. In humans, we tend to concentrate on circulating cells, but memory T cells in non-lymphoid tissues and bone marrow are increasingly recognised as critical for immune defence; their kinetics, however, remain largely unexplored. Considering vaccination from this viewpoint shifts the focus from the size of the primary response to the survival of the clone and enables identification of critical system pinch-points and opportunities to improve vaccine efficacy. Full article

(This article belongs to the Special Issue T Cell Memory to Vaccination)

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Open AccessArticle Prelamin A Accumulation Attenuates Rac1 Activity and Increases the Intrinsic Migrational Persistence of Aged Vascular Smooth Muscle Cells

by Lauren J. Porter, Mark R. Holt, Daniel Soong, Catherine M. Shanahan and Derek T. Warren

Cells 2016, 5(4), 41; doi:10.3390/cells5040041

Received: 15 September 2016 / Revised: 10 November 2016 / Accepted: 11 November 2016 / Published: 15 November 2016

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Abstract

Vascular smooth muscle cell (VSMC) motility is essential during both physiological and pathological vessel remodeling. Although ageing has emerged as a major risk factor in the development of cardiovascular disease, our understanding of the impact of ageing on VSMC motility remains limited. Prelamin

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Vascular smooth muscle cell (VSMC) motility is essential during both physiological and pathological vessel remodeling. Although ageing has emerged as a major risk factor in the development of cardiovascular disease, our understanding of the impact of ageing on VSMC motility remains limited. Prelamin A accumulation is known to drive VSMC ageing and we show that presenescent VSMCs, that have accumulated prelamin A, display increased focal adhesion dynamics, augmented migrational velocity/persistence and attenuated Rac1 activity. Importantly, prelamin A accumulation in proliferative VSMCs, induced by depletion of the prelamin A processing enzyme FACE1, recapitulated the focal adhesion, migrational persistence and Rac1 phenotypes observed in presenescent VSMCs. Moreover, lamin A/C-depleted VSMCs also display reduced Rac1 activity, suggesting that prelamin A influences Rac1 activity by interfering with lamin A/C function at the nuclear envelope. Taken together, these data demonstrate that lamin A/C maintains Rac1 activity in VSMCs and prelamin A disrupts lamin A/C function to reduce Rac1 activity and induce migrational persistence during VSMC ageing. Full article

(This article belongs to the collection Lamins and Laminopathies)

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Open AccessArticle Wearable IMU for Shoulder Injury Prevention in Overhead Sports

by Samir A. Rawashdeh, Derek A. Rafeldt and Timothy L. Uhl

Sensors 2016, 16(11), 1847; doi:10.3390/s16111847

Received: 11 August 2016 / Revised: 21 October 2016 / Accepted: 26 October 2016 / Published: 3 November 2016

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Abstract

Body-worn inertial sensors have enabled motion capture outside of the laboratory setting. In this work, an inertial measurement unit was attached to the upper arm to track and discriminate between shoulder motion gestures in order to help prevent shoulder over-use injuries in athletics

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Body-worn inertial sensors have enabled motion capture outside of the laboratory setting. In this work, an inertial measurement unit was attached to the upper arm to track and discriminate between shoulder motion gestures in order to help prevent shoulder over-use injuries in athletics through real-time preventative feedback. We present a detection and classification approach that can be used to count the number of times certain motion gestures occur. The application presented involves tracking baseball throws and volleyball serves, which are common overhead movements that can lead to shoulder and elbow overuse injuries. Eleven subjects are recruited to collect training, testing, and randomized validation data, which include throws, serves, and seven other exercises that serve as a large null class of similar movements, which is analogous to a realistic usage scenario and requires a robust estimator. Full article

(This article belongs to the collection Sensors for Globalized Healthy Living and Wellbeing)

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Open AccessCommunication A Proof-of-Concept Study: Simple and Effective Detection of P and T Waves in Arrhythmic ECG Signals

by Mohamed Elgendi, Marianna Meo and Derek Abbott

Bioengineering 2016, 3(4), 26; doi:10.3390/bioengineering3040026

Received: 1 September 2016 / Revised: 12 October 2016 / Accepted: 14 October 2016 / Published: 17 October 2016

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Abstract

A robust and numerically-efficient method based on two moving average filters, followed by a dynamic event-related threshold, has been developed to detect P and T waves in electrocardiogram (ECG) signals as a proof-of-concept. Detection of P and T waves is affected by the

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A robust and numerically-efficient method based on two moving average filters, followed by a dynamic event-related threshold, has been developed to detect P and T waves in electrocardiogram (ECG) signals as a proof-of-concept. Detection of P and T waves is affected by the quality and abnormalities in ECG recordings; the proposed method can detect P and T waves simultaneously through a unique algorithm despite these challenges. The algorithm was tested on arrhythmic ECG signals extracted from the MIT-BIH arrhythmia database with 21,702 beats. These signals typically suffer from: (1) non-stationary effects; (2) low signal-to-noise ratio; (3) premature atrial complexes; (4) premature ventricular complexes; (5) left bundle branch blocks; and (6) right bundle branch blocks. Interestingly, our algorithm obtained a sensitivity of 98.05% and a positive predictivity of 97.11% for P waves, and a sensitivity of 99.86% and a positive predictivity of 99.65% for T waves. These results, combined with the simplicity of the method, demonstrate that an efficient and simple algorithm can suit portable, wearable, and battery-operated ECG devices. Full article

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Open AccessArticle Additive Manufacture of Three Dimensional Nanocomposite Based Objects through Multiphoton Fabrication

by Yaan Liu, Qin Hu, Fan Zhang, Christopher Tuck, Derek Irvine, Richard Hague, Yinfeng He, Marco Simonelli, Graham A. Rance, Emily F. Smith and Ricky D. Wildman

Polymers 2016, 8(9), 325; doi:10.3390/polym8090325

Received: 25 May 2016 / Revised: 27 July 2016 / Accepted: 4 August 2016 / Published: 1 September 2016

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Abstract

Three-dimensional structures prepared from a gold-polymer composite formulation have been fabricated using multiphoton lithography. In this process, gold nanoparticles were simultaneously formed through photoreduction whilst polymerisation of two possible monomers was promoted. The monomers, trimethylopropane triacrylate (TMPTA) and pentaerythritol triacrylate (PETA) were mixed

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Three-dimensional structures prepared from a gold-polymer composite formulation have been fabricated using multiphoton lithography. In this process, gold nanoparticles were simultaneously formed through photoreduction whilst polymerisation of two possible monomers was promoted. The monomers, trimethylopropane triacrylate (TMPTA) and pentaerythritol triacrylate (PETA) were mixed with a gold salt, but it was found that the addition of a ruthenium(II) complex enhanced both the geometrical uniformity and integrity of the polymerised/reduced material, enabling the first production of 3D gold-polymer structures by single step multiphoton lithography. Full article

(This article belongs to the Special Issue Three-Dimensional Structures: Fabrication and Application)

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Open AccessArticle P2Y₁₂ Inhibitor Pre-Treatment in Non-ST-Elevation Acute Coronary Syndrome: A Decision-Analytic Model

by James Gunton, Trent Hartshorne, Jeremy Langrish, Anthony Chuang and Derek Chew

J. Clin. Med. 2016, 5(8), 72; doi:10.3390/jcm5080072

Received: 4 February 2016 / Revised: 7 August 2016 / Accepted: 11 August 2016 / Published: 17 August 2016

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Abstract

Current guidelines recommend initiation of a P2Y₁₂ inhibitor for all patients with non-ST-elevation acute coronary syndrome (NSTE-ACS) at the time of diagnosis (pre-treatment); however, there are no randomized trials directly comparing pre-treatment with initiation at the time of angiography to support this

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Current guidelines recommend initiation of a P2Y₁₂ inhibitor for all patients with non-ST-elevation acute coronary syndrome (NSTE-ACS) at the time of diagnosis (pre-treatment); however, there are no randomized trials directly comparing pre-treatment with initiation at the time of angiography to support this practice. We explore clinical and institutional parameters potentially associated with benefit with this strategy in a decision-analytic model based on available evidence from randomised trials. A decision analysis model was constructed comparing three P2Y₁₂ inhibitors in addition to aspirin in patients with NSTE-ACS. Based on clinical trial data, the cumulative probability of 30 day mortality, myocardial infarction (MI) and major bleeding were determined, and used to calculate the net clinical benefit (NCB) with and without pre-treatment. Sensitivity analysis was performed to assess the relationship between NCB and baseline ischemic risk, bleeding risk, time to angiography and local surgical revascularization rates. Pre-treatment with ticagrelor and clopidogrel was associated with a greater than 50% likelihood of providing a >1% increase in 30 day NCB when baseline estimated ischemic risk exceeds 11% and 14%, respectively. Prasugrel pre-treatment did not achieve a greater than 50% probability of an increase in NCB regardless of baseline ischemic risk. Institutional surgical revascularization rates and time to coronary angiography did not correlate with the likelihood of benefit from P2Y₁₂ pre-treatment. In conclusion, pre-treatment with P2Y₁₂ inhibition is unlikely to be beneficial to the majority of patients presenting with NSTE-ACS. A tailored assessment of each patient’s individual ischemic and bleeding risk may identify those likely to benefit. Full article

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Open AccessArticle Adsorption and Oxidation Investigations over Pt/Al₂O₃ Catalyst: A Microcalorimetric Study

by Oana Mihai, Derek Creaser and Louise Olsson

Catalysts 2016, 6(5), 73; doi:10.3390/catal6050073

Received: 11 February 2016 / Revised: 27 April 2016 / Accepted: 5 May 2016 / Published: 17 May 2016

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Abstract

The differential adsorption heats of oxygen and NO, as well as catalytic oxidation behavior during NO oxidation and NO₂ dissociation reactions over supported Pt-catalysts, were investigated by microcalorimetric measurements. The average heat of adsorption (∆H) of oxygen ranged from 310 kJ/mol at

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The differential adsorption heats of oxygen and NO, as well as catalytic oxidation behavior during NO oxidation and NO₂ dissociation reactions over supported Pt-catalysts, were investigated by microcalorimetric measurements. The average heat of adsorption (∆H) of oxygen ranged from 310 kJ/mol at 200 °C to 289 kJ/mol at 400 °C. Over this temperature range formation of platinum oxides and coverage dependence caused variations in the apparent heat of adsorption. NO heat of adsorption from 50 to 150 °C was near constant with an average value of 202 kJ/mol over the temperature range. Full article

(This article belongs to the Special Issue Automotive Emission Control Catalysts)

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Open AccessArticle Integrating Limiting-Factors Analysis with Process-Based Restoration to Improve Recovery of Endangered Salmonids in the Pacific Northwest, USA

by Derek B. Booth, Jenna G. Scholz, Timothy J. Beechie and Stephen C. Ralph

Water 2016, 8(5), 174; doi:10.3390/w8050174

Received: 1 February 2016 / Revised: 14 March 2016 / Accepted: 6 April 2016 / Published: 28 April 2016

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Abstract

Two approaches to ecological restoration planning, limiting-factors analysis and process-based restoration, are employed in efforts to recover endangered salmonid species throughout the Pacific Northwest of North America. Limiting-factors analysis seeks to identify physical limitations to fish production that may be addressed by habitat

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Two approaches to ecological restoration planning, limiting-factors analysis and process-based restoration, are employed in efforts to recover endangered salmonid species throughout the Pacific Northwest of North America. Limiting-factors analysis seeks to identify physical limitations to fish production that may be addressed by habitat restoration; it is known as the “Field of Dreams” hypothesis (i.e., if you build it, they will come). Process-based restoration, in contrast, assumes that protection and/or restoration of watershed-scale processes will best achieve self-sustaining habitat features that support salmon populations. Two case studies from the Columbia River basin (northwestern USA) display current efforts to integrate these two restoration approaches to improve salmonid populations. Although these examples both identify site-specific habitat features to construct, they also recognize the importance of supporting key watershed processes to achieve restoration goals. The challenge in advancing the practice of restoration planning is not in simply acknowledging the conceptual benefits of process-based restoration while maintaining a traditional focus on enumerating site-specific conditions and identifying habitat-construction projects, but rather in following process-based guidance during recovery planning and, ultimately, through implementation of on-the-ground actions. We encourage a realignment of the restoration community to truly embrace a process-based, multi-scalar view of the riverine landscape. Full article

(This article belongs to the Special Issue Stream Ecosystems and Restoration: Linking Bioassessments to Improved Planning and Design Strategies)

Open AccessReview Dendritic Cells in Oncolytic Virus-Based Anti-Cancer Therapy

by Youra Kim, Derek R. Clements, Andra M. Sterea, Hyun Woo Jang, Shashi A. Gujar and Patrick W. K. Lee

Viruses 2015, 7(12), 6506-6525; doi:10.3390/v7122953

Received: 9 September 2015 / Revised: 10 November 2015 / Accepted: 27 November 2015 / Published: 9 December 2015

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Abstract

Dendritic cells (DCs) are specialized antigen-presenting cells that have a notable role in the initiation and regulation of innate and adaptive immune responses. In the context of cancer, appropriately activated DCs can induce anti-tumor immunity by activating innate immune cells and tumor-specific lymphocytes

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Dendritic cells (DCs) are specialized antigen-presenting cells that have a notable role in the initiation and regulation of innate and adaptive immune responses. In the context of cancer, appropriately activated DCs can induce anti-tumor immunity by activating innate immune cells and tumor-specific lymphocytes that target cancer cells. However, the tumor microenvironment (TME) imposes different mechanisms that facilitate the impairment of DC functions, such as inefficient antigen presentation or polarization into immunosuppressive DCs. These tumor-associated DCs thus fail to initiate tumor-specific immunity, and indirectly support tumor progression. Hence, there is increasing interest in identifying interventions that can overturn DC impairment within the TME. Many reports thus far have studied oncolytic viruses (OVs), viruses that preferentially target and kill cancer cells, for their capacity to enhance DC-mediated anti-tumor effects. Herein, we describe the general characteristics of DCs, focusing on their role in innate and adaptive immunity in the context of the TME. We also examine how DC-OV interaction affects DC recruitment, OV delivery, and anti-tumor immunity activation. Understanding these roles of DCs in the TME and OV infection is critical in devising strategies to further harness the anti-tumor effects of both DCs and OVs, ultimately enhancing the efficacy of OV-based oncotherapy. Full article

(This article belongs to the Special Issue Oncolytic Viruses)

Open AccessArticle Molecular Differentiated Initiator Reactivity in the Synthesis of Poly(caprolactone)-Based Hydrophobic Homopolymer and Amphiphilic Core Corona Star Polymers

by Eileen Deng, Nam T. Nguyen, Frédéric Hild, Ian E. Hamilton, Georgios Dimitrakis, Samuel W. Kingman, Phei-Li Lau and Derek J. Irvine

Molecules 2015, 20(11), 20131-20145; doi:10.3390/molecules201119681

Received: 7 October 2015 / Revised: 26 October 2015 / Accepted: 27 October 2015 / Published: 9 November 2015

Abstract

Macromolecules that possess three-dimensional, branched molecular structures are of great interest because they exhibit significantly differentiated application performance compared to conventional linear (straight chain) polymers. This paper reports the synthesis of 3- and 4-arm star branched polymers via ring opening polymerisation (ROP) utilising

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Macromolecules that possess three-dimensional, branched molecular structures are of great interest because they exhibit significantly differentiated application performance compared to conventional linear (straight chain) polymers. This paper reports the synthesis of 3- and 4-arm star branched polymers via ring opening polymerisation (ROP) utilising multi-functional hydroxyl initiators and Sn(Oct)₂asprecatalyst. The structures produced include mono-functional hydrophobic and multi-functional amphiphilic core corona stars. The characteristics of the synthetic process were shown to be principally dependent upon the physical/dielectric properties of the initiators used. ROP’s using initiators that were more available to become directly involved with the Sn(Oct)₂ in the “in-situ” formation of the true catalytic species were observed to require shorter reaction times. Use of microwave heating (MWH) in homopolymer star synthesis reduced reaction times compared to conventional heating (CH) equivalents, this was attributed to an increased rate of “in-situ” catalyst formation. However, in amphiphilic core corona star formation, the MWH polymerisations exhibited slower propagation rates than CH equivalents. This was attributed to macro-structuring within the reaction medium, which reduced the potential for reaction. It was concluded that CH experiments were less affected by this macro-structuring because it was disrupted by the thermal currents/gradients caused by the conductive/convective heating mechanisms. These gradients are much reduced/absent with MWH because it selectively heats specific species simultaneously throughout the entire volume of the reaction medium. These partitioning problems were overcome by introducing additional quantities of the species that had been determined to selectively heat. Full article

(This article belongs to the Special Issue Microwave-Assisted Organic Synthesis)

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Open AccessReview Green Synthesis of Metallic Nanoparticles via Biological Entities

by Monaliben Shah, Derek Fawcett, Shashi Sharma, Suraj Kumar Tripathy and Gérrard Eddy Jai Poinern

Materials 2015, 8(11), 7278-7308; doi:10.3390/ma8115377

Received: 4 August 2015 / Accepted: 21 October 2015 / Published: 29 October 2015

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Abstract

Nanotechnology is the creation, manipulation and use of materials at the nanometre size scale (1 to 100 nm). At this size scale there are significant differences in many material properties that are normally not seen in the same materials at larger scales. Although

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Nanotechnology is the creation, manipulation and use of materials at the nanometre size scale (1 to 100 nm). At this size scale there are significant differences in many material properties that are normally not seen in the same materials at larger scales. Although nanoscale materials can be produced using a variety of traditional physical and chemical processes, it is now possible to biologically synthesize materials via environment-friendly green chemistry based techniques. In recent years, the convergence between nanotechnology and biology has created the new field of nanobiotechnology that incorporates the use of biological entities such as actinomycetes algae, bacteria, fungi, viruses, yeasts, and plants in a number of biochemical and biophysical processes. The biological synthesis via nanobiotechnology processes have a significant potential to boost nanoparticles production without the use of harsh, toxic, and expensive chemicals commonly used in conventional physical and chemical processes. The aim of this review is to provide an overview of recent trends in synthesizing nanoparticles via biological entities and their potential applications. Full article

(This article belongs to the Section Manufacturing Processes and Systems)

Open AccessArticle Towards Investigating Global Warming Impact on Human Health Using Derivatives of Photoplethysmogram Signals

by Mohamed Elgendi, Ian Norton, Matt Brearley, Richard R. Fletcher, Derek Abbott, Nigel H. Lovell and Dale Schuurmans

Int. J. Environ. Res. Public Health 2015, 12(10), 12776-12791; doi:10.3390/ijerph121012776

Received: 11 August 2015 / Revised: 29 September 2015 / Accepted: 8 October 2015 / Published: 14 October 2015

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Abstract

Recent clinical studies show that the contour of the photoplethysmogram (PPG) wave contains valuable information for characterizing cardiovascular activity. However, analyzing the PPG wave contour is difficult; therefore, researchers have applied first or higher order derivatives to emphasize and conveniently quantify subtle changes

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Recent clinical studies show that the contour of the photoplethysmogram (PPG) wave contains valuable information for characterizing cardiovascular activity. However, analyzing the PPG wave contour is difficult; therefore, researchers have applied first or higher order derivatives to emphasize and conveniently quantify subtle changes in the filtered PPG contour. Our hypothesis is that analyzing the whole PPG recording rather than each PPG wave contour or on a beat-by-beat basis can detect heat-stressed subjects and that, consequently, we will be able to investigate the impact of global warming on human health. Here, we explore the most suitable derivative order for heat stress assessment based on the energy and entropy of the whole PPG recording. The results of our study indicate that the use of the entropy of the seventh derivative of the filtered PPG signal shows promising results in detecting heat stress using 20-second recordings, with an overall accuracy of 71.6%. Moreover, the combination of the entropy of the seventh derivative of the filtered PPG signal with the root mean square of successive differences, or RMSSD (a traditional heart rate variability index of heat stress), improved the detection of heat stress to 88.9% accuracy. Full article

Open AccessArticle On Time Domain Analysis of Photoplethysmogram Signals for Monitoring Heat Stress

by Mohamed Elgendi, Rich Fletcher, Ian Norton, Matt Brearley, Derek Abbott, Nigel H. Lovell and Dale Schuurmans

Sensors 2015, 15(10), 24716-24734; doi:10.3390/s151024716

Received: 23 June 2015 / Revised: 14 September 2015 / Accepted: 21 September 2015 / Published: 25 September 2015

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Abstract

There are a limited number of studies on heat stress dynamics during exercise using the photoplethysmogram (PPG) and its second derivative (APG). However, we investigate the most suitable index from short PPG signal recordings for heat stress assessment. The APG waveform consists of

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There are a limited number of studies on heat stress dynamics during exercise using the photoplethysmogram (PPG) and its second derivative (APG). However, we investigate the most suitable index from short PPG signal recordings for heat stress assessment. The APG waveform consists of a, b, c and d waves in systole and an e wave in diastole. Our preliminary results indicate that the use of the energy of aa area, derived from PPG signals measured from emergency responders in tropical conditions, is promising in determining the heat stress level using 20-s recordings. After examining 14 time domain features using leave-one-out cross-validation, we found that the aa energy extracted from PPG signals is the most informative feature for classifying heat-stressed subjects, with an overall accuracy of 79%. Moreover, the combination of the aa energy with the traditional heart rate variability index of heat stress (i.e., the square root of the mean of the squares of the successive aa intervals) improved the heat stress detection to an overall accuracy of 83%. Full article

(This article belongs to the Section Biosensors)

Open AccessArticle Capability of Spaceborne Hyperspectral EnMAP Mission for Mapping Fractional Cover for Soil Erosion Modeling

by Sarah Malec, Derek Rogge, Uta Heiden, Arturo Sanchez-Azofeifa, Martin Bachmann and Martin Wegmann

Remote Sens. 2015, 7(9), 11776-11800; doi:10.3390/rs70911776

Received: 29 May 2015 / Revised: 7 September 2015 / Accepted: 8 September 2015 / Published: 15 September 2015

Cited by 5 | Viewed by 998 | PDF Full-text (26324 KB) | HTML Full-text | XML Full-text

Abstract

Soil erosion can be linked to relative fractional cover of photosynthetic-active vegetation (PV), non-photosynthetic-active vegetation (NPV) and bare soil (BS), which can be integrated into erosion models as the cover-management C-factor. This study investigates the capability of EnMAP imagery to map fractional cover

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Soil erosion can be linked to relative fractional cover of photosynthetic-active vegetation (PV), non-photosynthetic-active vegetation (NPV) and bare soil (BS), which can be integrated into erosion models as the cover-management C-factor. This study investigates the capability of EnMAP imagery to map fractional cover in a region near San Jose, Costa Rica, characterized by spatially extensive coffee plantations and grazing in a mountainous terrain. Simulated EnMAP imagery is based on airborne hyperspectral HyMap data. Fractional cover estimates are derived in an automated fashion by extracting image endmembers to be used with a Multiple End-member Spectral Mixture Analysis approach. The C-factor is calculated based on the fractional cover estimates determined independently for EnMAP and HyMap. Results demonstrate that with EnMAP imagery it is possible to extract quality endmember classes with important spectral features related to PV, NPV and soil, and be able to estimate relative cover fractions. This spectral information is critical to separate BS and NPV which greatly can impact the C-factor derivation. From a regional perspective, we can use EnMAP to provide good fractional cover estimates that can be integrated into soil erosion modeling. Full article

(This article belongs to the Special Issue The Environmental Mapping and Analysis Program (EnMAP) Mission: Preparing for Its Scientific Exploitation)

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Open AccessArticle Chemical Composition of Apricot Pit Shells and Effect of Hot-Water Extraction

by Derek B. Corbett, Neil Kohan, Grazielle Machado, Chengyan Jing, Aditi Nagardeolekar and Biljana M. Bujanovic

Energies 2015, 8(9), 9640-9654; doi:10.3390/en8099640

Received: 25 May 2015 / Revised: 1 August 2015 / Accepted: 20 August 2015 / Published: 3 September 2015

Cited by 5 | Viewed by 868 | PDF Full-text (581 KB) | HTML Full-text | XML Full-text

Abstract

Agricultural residues, such as corn stover, wheat straw, and nut shells show promise as feedstocks for lignocellulosic biorefinery due to their relatively high polysaccharide content and low or no nutritional value for human consumption. Apricot pit shells (APS) were studied in this work

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Agricultural residues, such as corn stover, wheat straw, and nut shells show promise as feedstocks for lignocellulosic biorefinery due to their relatively high polysaccharide content and low or no nutritional value for human consumption. Apricot pit shells (APS) were studied in this work to assess their potential for use in a biorefinery. Hot water extraction (HWE; 160 °C, 2 h), proposed to remove easily accessible hemicelluloses, was performed to evaluate the susceptibility of APS to this mild pretreatment process. The chemical composition of APS before and after HWE (EAPS) was analyzed by standard methods and ¹H-NMR. A low yield of the remaining HW-extracted APS (~59%) indicated that APS are highly susceptible to this pretreatment method. ¹H-NMR analysis of EAPS revealed that ~77% of xylan present in raw APS was removed along with ~24% of lignin. The energy of combustion of APS was measured before and after HWE showing a slight increase due to HWE (1.61% increase). Near infrared radiation spectroscopy (NIRS), proposed as a quick non-invasive method of biomass analysis, was performed. NIRS corroborated results of traditional analysis and ¹H-NMR. Determination of antioxidizing activity (AOA) of APS extracts was also undertaken. AOA of organic APS extracts were shown to be more than 20 times higher than that of a synthetic antioxidizing agent. Full article

(This article belongs to the Special Issue Bioenergy and Biorefining)

Open AccessArticle The Effect of Agile Workspace and Remote Working on Experiences of Privacy, Crowding and Satisfaction

by Trevor Keeling, Derek Clements-Croome and Etienne Roesch

Buildings 2015, 5(3), 880-898; doi:10.3390/buildings5030880

Received: 15 June 2015 / Revised: 8 July 2015 / Accepted: 30 July 2015 / Published: 7 August 2015

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Abstract

Occupant density is an important and basic metric of space use efficiency. It affects user experience of privacy, crowding and satisfaction. The effect of agile working has been two fold. Firstly, offices have an increasing range of workspace settings such as break out

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Occupant density is an important and basic metric of space use efficiency. It affects user experience of privacy, crowding and satisfaction. The effect of agile working has been two fold. Firstly, offices have an increasing range of workspace settings such as break out space, collaborative space and contemplative space in contrast to the traditional workspace settings of assigned desks and formal meeting rooms. Secondly, office workers have become increasingly mobile as they are able to work from a greater variety of locations both in and out of their main place of work. This study asks whether workers who occupy agile workspaces and those with greater mobility experience privacy differently from workers with more conventional offices and work patterns. The experience of privacy can be considered in terms of retreat from people, control of information flow and control of interactions. Our results show that agile workspaces improve the ability to control information compared with open plan offices. It was also found that highly mobile workers are more sensitive to the negative effects of interacting with people. From this a taxonomy of offices is defined in terms of the features that contribute to the experience of privacy. Full article

(This article belongs to the Special Issue The Impacts of the Building Environment on Health and Well-Being)

Open AccessArticle Fast T Wave Detection Calibrated by Clinical Knowledge with Annotation of P and T Waves

by Mohamed Elgendi, Bjoern Eskofier and Derek Abbott

Sensors 2015, 15(7), 17693-17714; doi:10.3390/s150717693

Received: 1 June 2015 / Revised: 8 July 2015 / Accepted: 10 July 2015 / Published: 21 July 2015

Cited by 6 | Viewed by 1280 | PDF Full-text (1460 KB) | HTML Full-text | XML Full-text

Abstract

Background: There are limited studies on the automatic detection of T waves in arrhythmic electrocardiogram (ECG) signals. This is perhaps because there is no available arrhythmia dataset with annotated T waves. There is a growing need to develop numerically-efficient algorithms that can accommodate

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Background: There are limited studies on the automatic detection of T waves in arrhythmic electrocardiogram (ECG) signals. This is perhaps because there is no available arrhythmia dataset with annotated T waves. There is a growing need to develop numerically-efficient algorithms that can accommodate the new trend of battery-driven ECG devices. Moreover, there is also a need to analyze long-term recorded signals in a reliable and time-efficient manner, therefore improving the diagnostic ability of mobile devices and point-of-care technologies. Methods: Here, the T wave annotation of the well-known MIT-BIH arrhythmia database is discussed and provided. Moreover, a simple fast method for detecting T waves is introduced. A typical T wave detection method has been reduced to a basic approach consisting of two moving averages and dynamic thresholds. The dynamic thresholds were calibrated using four clinically known types of sinus node response to atrial premature depolarization (compensation, reset, interpolation, and reentry). Results: The determination of T wave peaks is performed and the proposed algorithm is evaluated on two well-known databases, the QT and MIT-BIH Arrhythmia databases. The detector obtained a sensitivity of 97.14% and a positive predictivity of 99.29% over the first lead of the validation databases (total of 221,186 beats). Conclusions: We present a simple yet very reliable T wave detection algorithm that can be potentially implemented on mobile battery-driven devices. In contrast to complex methods, it can be easily implemented in a digital filter design. Full article

(This article belongs to the Section Physical Sensors)

Open AccessArticle 3D-Printed ABS and PLA Scaffolds for Cartilage and Nucleus Pulposus Tissue Regeneration

by Derek H. Rosenzweig, Eric Carelli, Thomas Steffen, Peter Jarzem and Lisbet Haglund

Int. J. Mol. Sci. 2015, 16(7), 15118-15135; doi:10.3390/ijms160715118

Received: 25 April 2015 / Revised: 3 June 2015 / Accepted: 30 June 2015 / Published: 3 July 2015

Cited by 30 | Viewed by 2047 | PDF Full-text (3172 KB) | HTML Full-text | XML Full-text

Abstract

Painful degeneration of soft tissues accounts for high socioeconomic costs. Tissue engineering aims to provide biomimetics recapitulating native tissues. Biocompatible thermoplastics for 3D printing can generate high-resolution structures resembling tissue extracellular matrix. Large-pore 3D-printed acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA) scaffolds

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Painful degeneration of soft tissues accounts for high socioeconomic costs. Tissue engineering aims to provide biomimetics recapitulating native tissues. Biocompatible thermoplastics for 3D printing can generate high-resolution structures resembling tissue extracellular matrix. Large-pore 3D-printed acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA) scaffolds were compared for cell ingrowth, viability, and tissue generation. Primary articular chondrocytes and nucleus pulposus (NP) cells were cultured on ABS and PLA scaffolds for three weeks. Both cell types proliferated well, showed high viability, and produced ample amounts of proteoglycan and collagen type II on both scaffolds. NP generated more matrix than chondrocytes; however, no difference was observed between scaffold types. Mechanical testing revealed sustained scaffold stability. This study demonstrates that chondrocytes and NP cells can proliferate on both ABS and PLA scaffolds printed with a simplistic, inexpensive desktop 3D printer. Moreover, NP cells produced more proteoglycan than chondrocytes, irrespective of thermoplastic type, indicating that cells maintain individual phenotype over the three-week culture period. Future scaffold designs covering larger pore sizes and better mimicking native tissue structure combined with more flexible or resorbable materials may provide implantable constructs with the proper structure, function, and cellularity necessary for potential cartilage and disc tissue repair in vivo. Full article

(This article belongs to the Special Issue Biomaterials for Tissue Engineering)

Open AccessArticle From Public to Private Standards for Tropical Commodities: A Century of Global Discourse on Land Governance on the Forest Frontier

by Derek Byerlee and Ximena Rueda

Forests 2015, 6(4), 1301-1324; doi:10.3390/f6041301

Received: 11 September 2014 / Revised: 11 September 2014 / Accepted: 1 April 2015 / Published: 21 April 2015

Abstract

Globalization and commodity exports have a long history in affecting land use changes and land rights on the tropical forest frontier. This paper reviews a century of social and environmental discourse around land issues for four commodities grown in the humid tropics—rubber, cocoa,

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Globalization and commodity exports have a long history in affecting land use changes and land rights on the tropical forest frontier. This paper reviews a century of social and environmental discourse around land issues for four commodities grown in the humid tropics—rubber, cocoa, oil palm and bananas. States have exercised sovereign rights over land and forest resources and the outcomes for deforestation and land rights of existing users have been quite varied depending on local institutional contexts and political economy. In the current period of globalization, as land use changes associated with tropical commodities have accelerated, land issues are now at center stage in the global discourse. However, efforts to protect forests and the rights of local communities and indigenous groups continue to be ad hoc and codification of minimum standards and their implementation remains a work in progress. Given a widespread failure of state directed policies and institutions to curb deforestation and protect land rights, the private sector, with the exception of the rubber industry, is emphasizing voluntary standards to certify sustainability of their products. This is an important step but expectations that they will effectively address concerns about the impact of tropical commodities expansion might be too high, given their voluntary nature, demand constraints, and the challenge of including smallholders. It is also doubtful that private standards can more than partially compensate for long standing weaknesses in land governance and institutions on the forest frontier. Full article

(This article belongs to the Special Issue Governing Forest Landscapes: Challenges and Ways Forward)

Open AccessArticle Predictive Risk of Radiation Induced Cerebral Necrosis in Pediatric Brain Cancer Patients after VMAT Versus Proton Therapy

by Derek Freund, Rui Zhang, Mary Sanders and Wayne Newhauser

Cancers 2015, 7(2), 617-630; doi:10.3390/cancers7020617

Received: 1 January 2015 / Revised: 16 March 2015 / Accepted: 25 March 2015 / Published: 10 April 2015

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Abstract

Cancer of the brain and central nervous system (CNS) is the second most common of all pediatric cancers. Treatment of many of these cancers includes radiation therapy of which radiation induced cerebral necrosis (RICN) can be a severe and potentially devastating side effect.

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Cancer of the brain and central nervous system (CNS) is the second most common of all pediatric cancers. Treatment of many of these cancers includes radiation therapy of which radiation induced cerebral necrosis (RICN) can be a severe and potentially devastating side effect. Risk factors for RICN include brain volume irradiated, the dose given per fraction and total dose. Thirteen pediatric patients were selected for this study to determine the difference in predicted risk of RICN when treating with volumetric modulated arc therapy (VMAT) compared to passively scattered proton therapy (PSPT) and intensity modulated proton therapy (IMPT). Plans were compared on the basis of dosimetric endpoints in the planned treatment volume (PTV) and brain and a radiobiological endpoint of RICN calculated using the Lyman-Kutcher-Burman probit model. Uncertainty tests were performed to determine if the predicted risk of necrosis was sensitive to positional errors, proton range errors and selection of risk models. Both PSPT and IMPT plans resulted in a significant increase in the maximum dose to the brain, a significant reduction in the total brain volume irradiated to low doses, and a significant lower predicted risk of necrosis compared with the VMAT plans. The findings of this study were upheld by the uncertainty analysis. Full article

(This article belongs to the Special Issue Proton Therapy for Cancer)

Open AccessReview The Origin and Evolution of Ribonucleotide Reduction

by Daniel Lundin, Gustav Berggren, Derek T. Logan and Britt-Marie Sjöberg

Life 2015, 5(1), 604-636; doi:10.3390/life5010604

Received: 15 January 2015 / Revised: 4 February 2015 / Accepted: 6 February 2015 / Published: 27 February 2015

Abstract

Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a

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Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA- to DNA-encoded genomes. While it is entirely possible that a different pathway was later replaced with the modern mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA + protein world and suggest a model for a prototypical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to modern RNRs, the urRNR, which diversified into the modern three classes. Since the initial radical generation differs between the three modern classes, it is difficult to establish how it was generated in the urRNR. Here we suggest a model that is similar to the B₁₂-dependent mechanism in modern class II RNRs. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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Open AccessReview Host Antimicrobial Peptides in Bacterial Homeostasis and Pathogenesis of Disease

by Derek R. Heimlich, Alistair Harrison and Kevin M. Mason

Antibiotics 2014, 3(4), 645-676; doi:10.3390/antibiotics3040645

Received: 29 September 2014 / Revised: 5 November 2014 / Accepted: 5 November 2014 / Published: 17 November 2014

Cited by 3 | Viewed by 2080 | PDF Full-text (1294 KB) | HTML Full-text | XML Full-text

Abstract

Innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. Bacteria that enter these sites must counter host responses for colonization.

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Innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. Bacteria that enter these sites must counter host responses for colonization. From the host’s perspective, the innate immune system works expeditiously to minimize the bacterial threat before colonization and subsequent dysbiosis. The multifactorial nature of disease further challenges predictions of how each independent variable influences bacterial pathogenesis. From bacterial colonization to infection and through disease, the microenvironments of the host are in constant flux as bacterial and host factors contribute to changes at the host-pathogen interface, with the host attempting to eradicate bacteria and the bacteria fighting to maintain residency. A key component of this innate host response towards bacterial infection is the production of antimicrobial peptides (AMPs). As an early component of the host response, AMPs modulate bacterial load and prevent establishment of infection. Under quiescent conditions, some AMPs are constitutively expressed by the epithelium. Bacterial infection can subsequently induce production of other AMPs in an effort to maintain sterility, or to restrict colonization. As demonstrated in various studies, the absence of a single AMP can influence pathogenesis, highlighting the importance of AMP concentration in maintaining homeostasis. Yet, AMPs can increase bacterial virulence through the co-opting of the peptides or alteration of bacterial virulence gene expression. Further, bacterial factors used to subvert AMPs can modify host microenvironments and alter colonization of the residential flora that principally maintain homeostasis. Thus, the dynamic interplay between host defense peptides and bacterial factors produced to quell peptide activity play a critical role in the progression and outcome of disease. Full article

(This article belongs to the Special Issue Antimicrobial Peptides) Printed Edition available

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Open AccessArticle Low-Frequency High-Magnitude Mechanical Strain of Articular Chondrocytes Activates p38 MAPK and Induces Phenotypic Changes Associated with Osteoarthritis and Pain

by Derek H. Rosenzweig, Thomas M. Quinn and Lisbet Haglund

Int. J. Mol. Sci. 2014, 15(8), 14427-14441; doi:10.3390/ijms150814427

Received: 14 April 2014 / Revised: 12 August 2014 / Accepted: 14 August 2014 / Published: 19 August 2014

Cited by 8 | Viewed by 1380 | PDF Full-text (3922 KB) | HTML Full-text | XML Full-text

Abstract

Osteoarthritis (OA) is a debilitating joint disorder resulting from an incompletely understood combination of mechanical, biological, and biochemical processes. OA is often accompanied by inflammation and pain, whereby cytokines associated with chronic OA can up-regulate expression of neurotrophic factors such as nerve growth

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Osteoarthritis (OA) is a debilitating joint disorder resulting from an incompletely understood combination of mechanical, biological, and biochemical processes. OA is often accompanied by inflammation and pain, whereby cytokines associated with chronic OA can up-regulate expression of neurotrophic factors such as nerve growth factor (NGF). Several studies suggest a role for cytokines and NGF in OA pain, however the effects of changing mechanical properties in OA tissue on chondrocyte metabolism remain unclear. Here, we used high-extension silicone rubber membranes to examine if high mechanical strain (HMS) of primary articular chondrocytes increases inflammatory gene expression and promotes neurotrophic factor release. HMS cultured chondrocytes displayed up-regulated NGF, TNFα and ADAMTS4 gene expression while decreasing TLR2 expression, as compared to static controls. HMS culture increased p38 MAPK activity compared to static controls. Conditioned medium from HMS dynamic cultures, but not static cultures, induced significant neurite sprouting in PC12 cells. The increased neurite sprouting was accompanied by consistent increases in PC12 cell death. Low-frequency high-magnitude mechanical strain of primary articular chondrocytes in vitro drives factor secretion associated with degenerative joint disease and joint pain. This study provides evidence for a direct link between cellular strain, secretory factors, neo-innervation, and pain in OA pathology. Full article

(This article belongs to the Special Issue The Chondrocyte Phenotype in Cartilage Biology)

Open AccessArticle Limit Cycles in Nonlinear Systems with Fractional Order Plants

by Derek P. Atherton, Nusret Tan, Celaleddin Yeroglu, Gürkan Kavuran and Ali Yüce

Machines 2014, 2(3), 176-201; doi:10.3390/machines2030176

Received: 31 March 2014 / Revised: 9 June 2014 / Accepted: 1 July 2014 / Published: 17 July 2014

Cited by 4 | Viewed by 1533 | PDF Full-text (817 KB) | HTML Full-text | XML Full-text

Abstract

In recent years, there has been considerable interest in the study of feedback systems containing processes whose dynamics are best described by fractional order derivatives. Various situations have been cited for describing heat flow and aspects of bioengineering, where such models are believed

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In recent years, there has been considerable interest in the study of feedback systems containing processes whose dynamics are best described by fractional order derivatives. Various situations have been cited for describing heat flow and aspects of bioengineering, where such models are believed to be superior. In many situations these feedback systems are not linear and information on their stability and the possibility of the existence of limit cycles is required. This paper presents new results for determining limit cycles using the approximate describing function method and an exact method when the nonlinearity is a relay characteristic. Full article

(This article belongs to the Special Issue Advances in Control Engineering)

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Open AccessArticle Pre-Hospital ECG E-Transmission for Patients with Suspected Myocardial Infarction in the Highlands of Scotland

by Gordon F. Rushworth, Charlie Bloe, H. Lesley Diack, Rachel Reilly, Calum Murray, Derek Stewart and Stephen J. Leslie

Int. J. Environ. Res. Public Health 2014, 11(2), 2346-2360; doi:10.3390/ijerph110202346

Received: 16 December 2013 / Revised: 29 January 2014 / Accepted: 13 February 2014 / Published: 21 February 2014

Cited by 4 | Viewed by 2054 | PDF Full-text (386 KB) | HTML Full-text | XML Full-text

Abstract

Patients with ST elevation myocardial infarction (STEMI) require prompt treatment, best done by primary percutaneous coronary intervention (PPCI). However, for patients unable to receive PPCI, immediate pre-hospital thrombolysis (PHT) is the best alternative. Evidence indicates that diagnostic and management support for staff increases

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Patients with ST elevation myocardial infarction (STEMI) require prompt treatment, best done by primary percutaneous coronary intervention (PPCI). However, for patients unable to receive PPCI, immediate pre-hospital thrombolysis (PHT) is the best alternative. Evidence indicates that diagnostic and management support for staff increases the use of PHT. This study aimed to describe the patient demographics and management of patients, to determine any potential inter-area differences in referral rates to the ECG e-transmission service and to explore the views and experiences of key staff involved in ECG e-transmission within NHS Highland. Data from 2,025 patient episodes of ECG e-transmission identified a statistically significant geographical variation in ECG e-transmission and PHT delivery. Scottish Ambulance Service (SAS) staff were more likely than GPs to deliver PHT overall, however, GPs were more likely to deliver in remote areas. Interviews with six Cardiac Care Unit (CCU) nurses and six SAS staff highlighted their positive views of ECG e-transmission, citing perceived benefits to patients and interprofessional relationships. Poor access to network signal was noted to be a barrier to engaging in the system. This study has demonstrated that a specialist triage service based on e-transmission of ECGs in patients with suspected STEMI can be implemented in a diverse geographical setting. Work is needed to ensure equity of the service for all patients. Full article

(This article belongs to the Special Issue Advances in Telehealthcare)

Open AccessArticle The Effect of Exogenous Zinc Concentration on the Responsiveness of MC3T3-E1 Pre-Osteoblasts to Surface Microtopography: Part II (Differentiation)

by Kathryn Dorst, Derek Rammelkamp, Michael Hadjiargyrou and Yizhi Meng

Materials 2014, 7(2), 1097-1112; doi:10.3390/ma7021097

Received: 20 December 2013 / Revised: 24 January 2014 / Accepted: 28 January 2014 / Published: 11 February 2014

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Abstract

Osseointegration of bone implants is a vital part of the recovery process. Numerous studies have shown that micropatterned geometries can promote cell-substrate associations and strengthen the bond between tissue and the implanted material. As demonstrated previously, exogenous zinc levels can influence the responsiveness

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Osseointegration of bone implants is a vital part of the recovery process. Numerous studies have shown that micropatterned geometries can promote cell-substrate associations and strengthen the bond between tissue and the implanted material. As demonstrated previously, exogenous zinc levels can influence the responsiveness of pre-osteoblasts to micropatterns and modify their migratory behavior. In this study, we sought to determine the effect of exogenous zinc on differentiation of osteoblasts cultured on micropatterned vs. planar substrates. Levels of activated metalloproteinase-2 (MMP-2) and transforming growth factor-beta 1 (TGF-β1), as well as early stage differentiation marker alkaline phosphatase, were altered with the addition of zinc. These results suggest that exogenous zinc concentration and micropatterning may interdependently modulate osteoblast differentiation. Full article

(This article belongs to the Special Issue Biocompatibility of Materials 2013)

Open AccessArticle The Effect of Exogenous Zinc Concentration on the Responsiveness of MC3T3-E1 Pre-Osteoblasts to Surface Microtopography: Part I (Migration)

by Kathryn Dorst, Derek Rammelkamp, Michael Hadjiargyrou, Dilip Gersappe and Yizhi Meng

Materials 2013, 6(12), 5517-5532; doi:10.3390/ma6125517

Received: 21 October 2013 / Revised: 11 November 2013 / Accepted: 21 November 2013 / Published: 27 November 2013

Abstract

Initial cell-surface interactions are guided by the material properties of substrate topography. To examine if these interactions are also modulated by the presence of zinc, we seeded murine pre-osteoblasts (MC3T3-E1, subclone 4) on micropatterned polydimethylsiloxane (PDMS) containing wide (20 µm width, 30 µm

[...] Read more.

Initial cell-surface interactions are guided by the material properties of substrate topography. To examine if these interactions are also modulated by the presence of zinc, we seeded murine pre-osteoblasts (MC3T3-E1, subclone 4) on micropatterned polydimethylsiloxane (PDMS) containing wide (20 µm width, 30 µm pitch, 2 µm height) or narrow (2 µm width, 10 µm pitch, 2 µm height) ridges, with flat PDMS and tissue culture polystyrene (TC) as controls. Zinc concentration was adjusted to mimic deficient (0.23 µM), serum-level (3.6 µM), and zinc-rich (50 µM) conditions. Significant differences were observed in regard to cell morphology, motility, and contact guidance. We found that cells exhibited distinct anisotropic migration on the wide PDMS patterns under either zinc-deprived (0.23 µM) or serum-level zinc conditions (3.6 µM). However, this effect was absent in a zinc-rich environment (50 µM). These results suggest that the contact guidance of pre-osteoblasts may be partly influenced by trace metals in the microenvironment of the extracellular matrix. Full article

(This article belongs to the Special Issue Biocompatibility of Materials 2013)

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Open AccessReview Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data

by Lingyang Xu, Yali Hou, Derek M. Bickhart, Jiuzhou Song and George E. Liu

Microarrays 2013, 2(3), 171-185; doi:10.3390/microarrays2030171

Received: 2 May 2013 / Revised: 4 June 2013 / Accepted: 5 June 2013 / Published: 25 June 2013

Cited by 13 | Viewed by 3346 | PDF Full-text (183 KB) | HTML Full-text | XML Full-text

Abstract

Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized

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Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed. Full article

(This article belongs to the Special Issue Copy-Number-Variation Microarrays in Basic Research and Clinical Applications)

Open AccessArticle Comparison Study of Oral Iron Preparations Using a Human Intestinal Model

by Mohammed Gulrez ZARIWALA, Satyanarayana SOMAVARAPU, Sebastien FARNAUD and Derek RENSHAW

Sci. Pharm. 2013, 81(4), 1123-1140; doi:10.3797/scipharm.1304-03

Received: 4 April 2013 / Accepted: 21 June 2013 / Published: 21 June 2013

Cited by 4 | Viewed by 130 | PDF Full-text (330 KB)

Abstract

Iron deficiency and related iron deficiency anaemia (IDA) are the most prevalent nutritional disorders worldwide. The standard treatment involves supple-mentation with solid or liquid iron supplement preparations, usually based on a ferrous salt such as ferrous sulphate, ferrous fumarate, or ferrous gluconate. In

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Iron deficiency and related iron deficiency anaemia (IDA) are the most prevalent nutritional disorders worldwide. The standard treatment involves supple-mentation with solid or liquid iron supplement preparations, usually based on a ferrous salt such as ferrous sulphate, ferrous fumarate, or ferrous gluconate. In the present study, we compared iron uptake and absorption from various solid and liquid iron supplement preparations currently available in the United Kingdom using the well-characterised human epithelial adenocarcinoma cell line Caco-2. Intracellular ferritin protein formation by the Caco-2 cell was con-sidered an indicator of cellular iron uptake and absorption. We investigated the effects of formulation ingredients at a defined pH on iron uptake and absorption, and designed a novel two-stage dissolution-absorption protocol that mimicked physiological conditions. Our experiments revealed wide variations in the rate of dissolution between the various solid iron preparations. Conventional-release ferrous iron tablets dissolved rapidly (48 ± 4 mins to 64 ± 4 mins), whereas modified-released tablets and capsules took significantly longer to undergo complete dissolution (274 ± 8 to 256 ± 8 mins). Among the solid iron prepa-rations, ferrous sulphate conventional-release tablets demonstrated the highest iron absorption, whereas modified-release ferrous preparations demonstrated uniformly low iron absorption, as compared to the control (P < 0.05). Taken together, our results demonstrate that there are wide-ranging variations in dissolution times and iron uptake from oral iron preparations, with the physical characteristics of the preparation as well as the form of iron playing a key role. Full article

Open AccessReview Mechanisms Underlying Auditory Hallucinations—Understanding Perception without Stimulus

by Derek K. Tracy and Sukhwinder S. Shergill

Brain Sci. 2013, 3(2), 642-669; doi:10.3390/brainsci3020642

Received: 21 March 2013 / Revised: 7 April 2013 / Accepted: 18 April 2013 / Published: 26 April 2013

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Abstract

Auditory verbal hallucinations (AVH) are a common phenomenon, occurring in the “healthy” population as well as in several mental illnesses, most notably schizophrenia. Current thinking supports a spectrum conceptualisation of AVH: several neurocognitive hypotheses of AVH have been proposed, including the “feed-forward” model

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Auditory verbal hallucinations (AVH) are a common phenomenon, occurring in the “healthy” population as well as in several mental illnesses, most notably schizophrenia. Current thinking supports a spectrum conceptualisation of AVH: several neurocognitive hypotheses of AVH have been proposed, including the “feed-forward” model of failure to provide appropriate information to somatosensory cortices so that stimuli appear unbidden, and an “aberrant memory model” implicating deficient memory processes. Neuroimaging and connectivity studies are in broad agreement with these with a general dysconnectivity between frontotemporal regions involved in language, memory and salience properties. Disappointingly many AVH remain resistant to standard treatments and persist for many years. There is a need to develop novel therapies to augment existing pharmacological and psychological therapies: transcranial magnetic stimulation has emerged as a potential treatment, though more recent clinical data has been less encouraging. Our understanding of AVH remains incomplete though much progress has been made in recent years. We herein provide a broad overview and review of this. Full article

(This article belongs to the Special Issue Brain and Language)

Open AccessArticle The Influence of Fish Length on Tissue Mercury Dynamics: Implications for Natural Resource Management and Human Health Risk

by Dana K. Sackett, W. Gregory Cope, James A. Rice and D. Derek Aday

Int. J. Environ. Res. Public Health 2013, 10(2), 638-659; doi:10.3390/ijerph10020638

Received: 21 December 2012 / Revised: 25 January 2013 / Accepted: 28 January 2013 / Published: 6 February 2013

Cited by 8 | Viewed by 2123 | PDF Full-text (711 KB) | HTML Full-text | XML Full-text

Abstract

Consumption of fish has well-known human health benefits, though some fish may contain elevated levels of mercury (Hg) that are especially harmful to developing children. Fish length is most often the basis for establishing fishery harvest regulations that determine which fish will ultimately

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Consumption of fish has well-known human health benefits, though some fish may contain elevated levels of mercury (Hg) that are especially harmful to developing children. Fish length is most often the basis for establishing fishery harvest regulations that determine which fish will ultimately be consumed by humans. It is, therefore, essential to quantify the relationship between fish length and Hg accumulation in regard to harvest regulations for effective fishery and public health policy. We examined this relationship for three sportfish from six lakes across North Carolina, USA. Bluegill (Lepomis macrochirus) had the lowest Hg levels and only the very largest fish in the most contaminated site exceeded the US Environmental Protection Agency (USEPA) Hg screening level. Black crappie (Pomoxis nigromaculatus) had an intermediate level of Hg and larger individuals exceeded the USEPA screening level; however, they tended not to exceed this level before reaching the harvest length limit. Largemouth bass (Micropterus salmoides) exceeded the USEPA screening level at sizes below the fishery length limit in two lakes, leaving only higher risk fish for anglers to harvest and consume. Removing the effects of fish age and trophic position, we found strong positive correlations between Hg and fish length for largemouth bass and black crappie. We suggest public health officials and wildlife managers collaborate to structure fishery regulations and length-based fish consumption advisories that protect consumers from Hg exposure and communicate the relative risk of fish consumption. Full article

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Open AccessArticle Mineralization Content Alters Osteogenic Responses of Bone Marrow Stromal Cells on Hydroxyapatite/Polycaprolactone Composite Nanofiber Scaffolds

by Timothy T. Ruckh, Derek A. Carroll, Justin R. Weaver and Ketul C. Popat

J. Funct. Biomater. 2012, 3(4), 776-798; doi:10.3390/jfb3040776

Received: 20 June 2012 / Revised: 25 September 2012 / Accepted: 24 October 2012 / Published: 14 November 2012

Cited by 4 | Viewed by 2196 | PDF Full-text (11348 KB) | HTML Full-text | XML Full-text

Abstract

Synthetic tissue scaffolds have a high potential impact for patients experiencing osteogenesis imperfecta. Using electrospinning, tissue scaffolds composed of hydroxyapatite/polycaprolactone (HAp/PCL) composite nanofibers were fabricated with two different HAp concentrations—1% and 10% of the solid scaffold weight. After physico-chemical scaffold characterization, rat

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Synthetic tissue scaffolds have a high potential impact for patients experiencing osteogenesis imperfecta. Using electrospinning, tissue scaffolds composed of hydroxyapatite/polycaprolactone (HAp/PCL) composite nanofibers were fabricated with two different HAp concentrations—1% and 10% of the solid scaffold weight. After physico-chemical scaffold characterization, rat bone marrow stromal cells were cultured on the composite scaffolds in maintenance medium and then in osteogenic medium. Quantitative PCR, colorimetric assays, immunofluorescent labeling, and electron microscopy measured osteogenic cell responses to the HAp/PCL scaffolds. In maintenance conditions, both Hap/PCL scaffolds and control scaffolds supported cell colonization through seven days with minor differences. In osteogenic conditions, the 10% HAp scaffolds exhibited significantly increased ALP assay levels at week 3, consistent with previous reports. However, qPCR analysis demonstrated an overall decrease in bone matrix-associated genes on Hap/PCL scaffolds. Osteopontin and osteocalcin immunofluorescent microscopy revealed a trend that both mineralized scaffolds had greater amounts of both proteins, though qPCR results indicated the opposite trend for osteopontin. Additionally, type I collagen expression decreased on HAp scaffolds. These results indicate that cells are sensitive to minor changes in mineral content within nanofibers, even at just 1% w/w, and elucidating the sensing mechanism may lead to optimized osteogenic scaffold designs. Full article

(This article belongs to the Special Issue Biocompatibility of Biomaterials)

Open AccessReview Responses of Cryptofaunal Species Richness and Trophic Potential to Coral Reef Habitat Degradation

by Ian C. Enochs and Derek P. Manzello

Diversity 2012, 4(1), 94-104; doi:10.3390/d4010094

Received: 17 November 2011 / Revised: 7 February 2012 / Accepted: 10 February 2012 / Published: 15 February 2012

Cited by 4 | Viewed by 2552 | PDF Full-text (563 KB) | HTML Full-text | XML Full-text

Abstract

Coral reefs are declining worldwide as a result of many anthropogenic disturbances. This trend is alarming because coral reefs are hotspots of marine biodiversity and considered the ‘rainforests of the sea. As in the rainforest, much of the diversity on a coral reef

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Coral reefs are declining worldwide as a result of many anthropogenic disturbances. This trend is alarming because coral reefs are hotspots of marine biodiversity and considered the ‘rainforests of the sea. As in the rainforest, much of the diversity on a coral reef is cryptic, remaining hidden among the cracks and crevices of structural taxa. Although the cryptofauna make up the majority of a reef’s metazoan biodiversity, we know little about their basic ecology or how these communities respond to reef degradation. Emerging research shows that the species richness of the motile cryptofauna is higher among dead (framework) vs. live coral substrates and, surprisingly, increases within successively more eroded reef framework structures, ultimately reaching a maximum in dead coral rubble. Consequently, the paradigm that abundant live coral is the apex of reef diversity needs to be clarified. This provides guarded optimism amidst alarming reports of declines in live coral cover and the impending doom of coral reefs, as motile cryptic biodiversity should persist independent of live coral cover. Granted, the maintenance of this high species richness is contingent on the presence of reef rubble, which will eventually be lost due to physical, chemical, and biological erosion if not replenished by live coral calcification and mortality. The trophic potential of a reef, as inferred from the abundance of cryptic organisms, is highest on live coral. Among dead framework substrates, however, the density of cryptofauna reaches a peak at intermediate levels of degradation. In summary, the response of the motile cryptofauna, and thus a large fraction of the reef’s biodiversity, to reef degradation is more complex and nuanced than currently thought; such that species richness may be less sensitive than overall trophic function. Full article

(This article belongs to the Special Issue Coral Reef Diversity: Climate Change and Coral Reef Degradation)

Open AccessArticle The Influence of Synthesis Parameters on Particle Size and Photoluminescence Characteristics of Ligand Capped Tb³⁺:LaF₃

by Kyle Gipson, Courtney Kucera, Derek Stadther, Kathryn Stevens, John Ballato and Phil Brown

Polymers 2011, 3(4), 2039-2052; doi:10.3390/polym3042039

Received: 11 October 2011 / Revised: 11 November 2011 / Accepted: 17 November 2011 / Published: 29 November 2011

Cited by 6 | Viewed by 2186 | PDF Full-text (815 KB) | HTML Full-text | XML Full-text

Abstract

Organic ligand surface-treated Tb³⁺:LaF₃ was synthesized in water and methanol for subsequent incorporation into polymethyl methacrylate (PMMA) via solution-precipitation chemistry in order to produce optically active polymer nanocomposites. Nanoparticle agglomerate diameters ranged from 388 ± 188 nm when synthesized in

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Organic ligand surface-treated Tb³⁺:LaF₃ was synthesized in water and methanol for subsequent incorporation into polymethyl methacrylate (PMMA) via solution-precipitation chemistry in order to produce optically active polymer nanocomposites. Nanoparticle agglomerate diameters ranged from 388 ± 188 nm when synthesized in water and 37 ± 2 nm when synthesized in methanol. Suspension stability is paramount for producing optically transparent materials. Methanol nanoparticle synthesized at a pH of 3 exhibited the smallest agglomerate size. Optical spectroscopy, dynamic light scattering, transmission electron microscopy, scanning transmission electron microscopy, and zeta potential analysis were used to characterize the particles synthesized. Full article

(This article belongs to the Special Issue Polymers for Optical Applications)

Open AccessArticle A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity

by Derek Peršoh, Alfons R. Weig and Gerhard Rambold

Microarrays 2012, 1(1), 25-41; doi:10.3390/microarrays1010025

Received: 1 September 2011 / Revised: 14 October 2011 / Accepted: 17 October 2011 / Published: 31 October 2011

Cited by 7 | Viewed by 3027 | PDF Full-text (252 KB) | HTML Full-text | XML Full-text

Abstract

A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation)

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A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory. Full article

Open AccessArticle Temporal Stability of the Velodyne HDL-64E S2 Scanner for High Accuracy Scanning Applications

by Craig Glennie and Derek D. Lichti

Remote Sens. 2011, 3(3), 539-553; doi:10.3390/rs3030539

Received: 10 February 2011 / Revised: 5 March 2011 / Accepted: 8 March 2011 / Published: 14 March 2011

Cited by 28 | Viewed by 4149 | PDF Full-text (670 KB) | HTML Full-text | XML Full-text

Abstract

The temporal stability and static calibration and analysis of the Velodyne HDL‑64E S2 scanning LiDAR system is discussed and analyzed. The mathematical model for measurements for the HDL-64E S2 scanner is updated to include misalignments between the angular encoder and scanner axis of

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The temporal stability and static calibration and analysis of the Velodyne HDL‑64E S2 scanning LiDAR system is discussed and analyzed. The mathematical model for measurements for the HDL-64E S2 scanner is updated to include misalignments between the angular encoder and scanner axis of rotation, which are found to be a marginally significant source of error. It is reported that the horizontal and vertical laser offsets cannot reliably be obtained with the current calibration model due to their high correlation with the horizontal and vertical offsets. By analyzing observations from two separate HDL-64E S2 scanners it was found that the temporal stability of the horizontal angle offset is near the quantization level of the encoder, but the vertical angular offset, distance offset and distance scale are slightly larger than expected. This is felt to be due to long term variations in the scanner range, whose root cause is as of yet unidentified. Nevertheless, a temporally averaged calibration dataset for each of the scanners resulted in a 25% improvement in the 3D planar misclosure residual RMSE over the standard factory calibration model. Full article

(This article belongs to the Special Issue Terrestrial Laser Scanning)

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Open AccessArticle Quantification of the Variability of Continuous Glucose Monitoring Data

by Edward Aboufadel, Robert Castellano and Derek Olson

Algorithms 2011, 4(1), 16-27; doi:10.3390/a4010016

Received: 4 January 2011 / Revised: 20 January 2011 / Accepted: 12 February 2011 / Published: 15 February 2011

Cited by 1 | Viewed by 4181 | PDF Full-text (335 KB) | HTML Full-text | XML Full-text

Abstract

Several measurements are used to describe the behavior of a diabetic patient’s blood glucose. We describe a new, wavelet-based algorithm that indicates a new measurement called a PLA index could be used to quantify the variability or predictability of blood glucose. This wavelet-based

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Several measurements are used to describe the behavior of a diabetic patient’s blood glucose. We describe a new, wavelet-based algorithm that indicates a new measurement called a PLA index could be used to quantify the variability or predictability of blood glucose. This wavelet-based approach emphasizes the shape of a blood glucose graph. Using continuous glucose monitors (CGMs), this measurement could become a new tool to classify patients based on their blood glucose behavior and may become a new method in the management of diabetes. Full article

Open AccessReview The Carbon and Global Warming Potential Impacts of Organic Farming: Does It Have a Significant Role in an Energy Constrained World?

by Derek H. Lynch, Rod MacRae and Ralph C. Martin

Sustainability 2011, 3(2), 322-362; doi:10.3390/su3020322

Received: 2 December 2010 / Revised: 19 January 2011 / Accepted: 24 January 2011 / Published: 28 January 2011

Cited by 43 | Viewed by 7847 | PDF Full-text (468 KB) | HTML Full-text | XML Full-text

Abstract

About 130 studies were analyzed to compare farm-level energy use and global warming potential (GWP) of organic and conventional production sectors. Cross cutting issues such as tillage, compost, soil carbon sequestration and energy offsets were also reviewed. Finally, we contrasted E and GWP

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About 130 studies were analyzed to compare farm-level energy use and global warming potential (GWP) of organic and conventional production sectors. Cross cutting issues such as tillage, compost, soil carbon sequestration and energy offsets were also reviewed. Finally, we contrasted E and GWP data from the wider food system. We concluded that the evidence strongly favours organic farming with respect to whole-farm energy use and energy efficiency both on a per hectare and per farm product basis, with the possible exception of poultry and fruit sectors. For GWP, evidence is insufficient except in a few sectors, with results per ha more consistently favouring organic farming than GWP per unit product. Tillage was consistently a negligible contributor to farm E use and additional tillage on organic farms does not appear to significantly deplete soil C. Energy offsets, biogas, energy crops and residues have a more limited role on organic farms compared to conventional ones, because of the nutrient and soil building uses of soil organic matter, and the high demand for organic foods in human markets. If farm E use represents 35% of total food chain E use, improvements shown of 20% or more in E efficiency through organic farm management would reduce food-chain E use by 7% or more. Among other food supply chain stages, wholesale/retail (including cooling and packaging) and processing often each contribute 30% or more to total food system E. Thus, additional improvements can be obtained with reduced processing, whole foods and food waste minimization. Full article

(This article belongs to the Special Issue Energy Sustainability after Global Fossil Energy Depletion)

Open AccessArticle An O(n)-Round Strategy for the Magnus-Derek Game

by Zhivko Nedev

Algorithms 2010, 3(3), 244-254; doi:10.3390/a3030244

Received: 8 June 2010 / Revised: 6 July 2010 / Accepted: 8 July 2010 / Published: 15 July 2010

Cited by 2 | Viewed by 4347 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text

Abstract

We analyze further the Magnus-Derek game, a two-player game played on a round table with n positions. The players jointly control the movement of a token. One player, Magnus, aims to maximize the number of positions visited while minimizing the number of rounds.

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We analyze further the Magnus-Derek game, a two-player game played on a round table with n positions. The players jointly control the movement of a token. One player, Magnus, aims to maximize the number of positions visited while minimizing the number of rounds. The other player, Derek, attempts to minimize the number of visited positions. We present a new strategy for Magnus that succeeds in visiting the maximal number of positions in 3(n – 1) rounds, which is the optimal number of rounds up to a constant factor. Full article

(This article belongs to the Special Issue Algorithmic Game Theory)

Open AccessReview Novel Anti-Infective Compounds from Marine Bacteria

by Hafizur Rahman, Brian Austin, Wilfrid J. Mitchell, Peter C. Morris, Derek J. Jamieson, David R. Adams, Andrew Mearns Spragg and Michael Schweizer

Mar. Drugs 2010, 8(3), 498-518; doi:10.3390/md8030498

Received: 3 February 2010 / Revised: 1 March 2010 / Accepted: 2 March 2010 / Published: 5 March 2010

Cited by 65 | Viewed by 10324 | PDF Full-text (277 KB) | HTML Full-text | XML Full-text

Abstract

As a result of the continuous evolution of microbial pathogens towards antibiotic-resistance, there have been demands for the development of new and effective antimicrobial compounds. Since the 1960s, the scientific literature has accumulated many publications about novel pharmaceutical compounds produced by a diverse

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As a result of the continuous evolution of microbial pathogens towards antibiotic-resistance, there have been demands for the development of new and effective antimicrobial compounds. Since the 1960s, the scientific literature has accumulated many publications about novel pharmaceutical compounds produced by a diverse range of marine bacteria. Indeed, marine micro-organisms continue to be a productive and successful focus for natural products research, with many newly isolated compounds possessing potentially valuable pharmacological activities. In this regard, the marine environment will undoubtedly prove to be an increasingly important source of novel antimicrobial metabolites, and selective or targeted approaches are already enabling the recovery of a significant number of antibiotic-producing micro-organisms. The aim of this review is to consider advances made in the discovery of new secondary metabolites derived from marine bacteria, and in particular those effective against the so called “superbugs”, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant enterococci (VRE), which are largely responsible for the increase in numbers of hospital acquired, i.e., nosocomial, infections. Full article

(This article belongs to the Special Issue Marine Anti-infective Agents)

Open AccessArticle Antioxidant Properties and Neuroprotective Capacity of Strawberry Tree Fruit (Arbutus unedo)

by Sofia Fortalezas, Lucélia Tavares, Rui Pimpão, Meenu Tyagi, Vera Pontes, Paula M. Alves, Gordon McDougall, Derek Stewart, Ricardo B. Ferreira and Cláudia N. Santos

Nutrients 2010, 2(2), 214-229; doi:10.3390/nu2020214

Received: 16 December 2009 / Accepted: 9 February 2010 / Published: 21 February 2010

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Abstract

Berries contain significant amounts of phytochemicals, including polyphenols, which are reported to reduce cancer risk, coronary heart disease and other degenerative diseases. These effects are mainly attributed to the antioxidant capacity of polyphenols found in berries. Strawberry tree (Arbutus unedo) berries

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Berries contain significant amounts of phytochemicals, including polyphenols, which are reported to reduce cancer risk, coronary heart disease and other degenerative diseases. These effects are mainly attributed to the antioxidant capacity of polyphenols found in berries. Strawberry tree (Arbutus unedo) berries are used in folk medicine but seldom eaten as fresh fruits. Their phenolic profile and antioxidant capacity reveal a high potential, but they are not well characterized as a “health promoting food”. The aim of this study was to assess the antioxidant properties of the edible strawberry tree fruit in vitro and in a neurodegeneration cell model. Raspberry (Rubus idaeus), a well documented health-promoting fruit, was used as a control for comparison purposes. A. unedo yielded a similar content in polyphenols and a slightly lower value of total antioxidant capacity in comparison to R. idaeus. Although the chemically-measured antioxidant activity was similar between both fruits, R. idaeus increased neuroblastoma survival in a neurodegeneration cell model by 36.6% whereas A. unedo extracts caused no effect on neuroblastoma viability. These results clearly demonstrate that a promising level of chemically-determined antioxidant activity of a plant extract is not necessarily correlated with biological significance, as assessed by the effect of A. unedo fruit in a neurodegeneration cell model. Full article

(This article belongs to the Special Issue Foodomics 2009)

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