Search Results (15)

Background/Objectives: Clinical surveillance of infectious diseases caused by viruses, such as SARS-CoV-2, is important for effective intervention and preventing potential epidemics or pandemics. The development of cost-effective whole genome sequencing technologies has facilitated worldwide efforts to sequence viral genomes. The array of sequence data generated across the globe offers diverse opportunities to study SARS-CoV-2 evolutionary dynamics and serves as a foundation for different research questions in the future. Even though bioinformatics tools are rapidly developed for accessing and analyzing large-scale data from public repositories, surveillance labs lack streamlined pipelines to handle high sample volumes and efficiently identify mutations for variant reporting with minimal computational expertise. Methods: We have developed a SARS-CoV-2 mutational analysis pipeline using Workflow Description Language (WDL), which is open-source and combines various steps in an analysis workflow with human-readable syntax. Thus, users with minimal informatics background can easily adapt the workflow while creating a local data repository within their institution. The pipeline processes input FASTA files and quality control files from Ion Torrent S5, performs clade and variant assignments, integrates patient metadata, and stores the results into a REDCap database. Results: In this framework, REDCap acts as the core data backbone for run-level tracking and result storage. To further enhance the utility of our REDCap-based data capture system, we have developed an intuitive interactive dashboard. This interface seamlessly connects with the REDCap data sources, providing real-time monitoring, interactive visualization, and the ability to create a consolidated variant report. Conclusions: Our overall approach streamlines processes in managing complex genomic data and offers easy adaptation to empower other molecular labs. Full article

Sediment management is fundamental for managing mountain watercourses and their upslope catchment. A multidisciplinary approach—not limited to the discipline of hydraulics—is necessary for investigating the alterations in sediment transport along the watercourse by detecting those reaches dominated by erosion and deposition processes, by quantifying the sediment volume change, by assessing the functionality of the existing torrent control structures, and by delimitating the riparian vegetation patches. To pursue these goals, specific continuous monitoring is essential, despite being extremely rare in mountain catchments. The present study proposed an integrated approach to determine the hydro-morphological–sedimentological–ecological state of a mountain watercourse though field- and desk-based analyses. Such an integral approach includes a rainfall–runoff model, a morphological change analysis and the application of empirical formulations for estimating peak discharge, mobilizable sediment/large wood volume and watercourse hydraulic capacity, at reach and catchment scales. The procedure was tested on the Upper Adda River catchment (North Italy). The results identified where and with what priority maintenance and monitoring activities must be carried out, considering sediment regime, torrent control structures and vegetation. This study is an example of how it is possible to enhance all existing information through successive qualitative and quantitative approximations and to concentrate new resources (human and economic) on specific gaps, for drafting a scientifically robust and practical sediment management plan. Full article

Over the past two decades, rapid climate change has severely impacted people’s lives globally, affecting their safety and sustainability. Water, a vital human resource, has been severely affected, with drought and high temperatures leading to desertification, the drying up of rivers and lakes, spontaneous fires in forests, and massive floods and torrents due to melting ice and rising sea and ocean surface water levels. The expected impacts of climate change on the Nile, Egypt’s primary water source, are significant. These impacts can vary across regions, depending on factors like local climate, socio-economic dynamics, topography, and environmental nature. Upper Egypt, characterized by arid and semi-arid regions, faces water scarcity and socio-economic development challenges. Climate change exacerbates these issues, posing significant threats to the region’s ecological sustainability and socio-economic development. Therefore, it is crucial to address these impacts to ensure the Nile’s continued vitality and sustainability. The study aims to analyze the climate change data over the past few decades, analyze its characteristics, and model its effects on Upper Egypt’s water sources. The study expected a big decrease in the water resources of the Nile. While what is currently occurring in terms of fluctuating rainfall rates between scarcity and severity contradicts the results of those studies, that is the best evidence of the need for further research and studies to obtain more reliable and consistent results with the reality that it may help decision-makers to develop scenarios to manage climate change effectively, preventing or reducing negative effects, and finding suitable alternatives. Studies predict a 10% decrease in Nile revenue at Aswan High Dam Lake by 2095, with some predicting a 30% increase. This lack of credibility underscores the need for more comprehensive studies. Full article

Multiple sclerosis (MS) arises from a complex interplay between host genetic factors and environmental components, with the gut microbiota emerging as a key area of investigation. In the current study, we used ion torrent sequencing to delve into the bacteriome (bacterial microbiota) and mycobiome (fungal microbiota) of people with MS (pwMS), and compared them to healthy controls (HC). Through principal coordinate, diversity, and abundance analyses, as well as clustering and cross-kingdom microbial correlation assessments, we uncovered significant differences in the microbial profiles between pwMS and HC. Elevated levels of the fungus Torulaspora and the bacterial family Enterobacteriaceae were observed in pwMS, whereas beneficial bacterial taxa, such as Prevotelladaceae and Dialister, were reduced. Notably, clustering analysis revealed overlapping patterns in the bacteriome and mycobiome data for 74% of the participants, with weakened cross-kingdom interactions evident in the altered microbiota of pwMS. Our findings highlight the dysbiosis of both bacterial and fungal microbiota in MS, characterized by shifts in biodiversity and composition. Furthermore, the distinct disease-associated pattern of fungi–bacteria interactions suggests that fungi, in addition to bacteria, contribute to the pathogenesis of MS. Overall, our study sheds light on the intricate microbial dynamics underlying MS, paving the way for further investigation into the potential therapeutic targeting of the gut microbiota in MS management. Full article

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. The study aimed to identify the antimicrobial resistance and accessory genes, the clonal relatedness, and the evolutionary dynamics of selected CRKP isolates recovered in an adult and pediatric intensive care unit of a tertiary hospital in Greece. Methods: Twenty-four CRKP isolates recovered during 2018–2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST, and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed using various bioinformatics software. Results: The isolates belonged to eight sequence types: 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM, and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16, and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323, and ST39 were classified into distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs. Conclusions: The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates. Full article

The development of methodologies for analyzing the evolution and pressures exerted on the river channel network is one of the main concerns of researchers today. The assessment of natural or artificial changes of river channels and beds plays an important role in environmental protection, but also in the implementation of integrated water resource management plans. Given the episodic and dynamic nature of river bank and bed erosion, along with the difficulty of reaching certain reaches, a methodological approach that uses aerial imagery, initially from satellite sources and afterwards from unmanned aerial vehicles, is proposed. This approach was utilized in a perennial river in Romania but also in an ephemeral torrent channel in Greece, in order to test the prevalent types of hydrographic network in the Mediterranean and Black Sea region. The methodology used was able to identify the location and the volume of the bed material extracted and the time frame in which it occurred. These encouraging results showcase an accurate but also relevantly low-cost monitoring method for illegal anthropogenic activities that can be easily adopted by the responsible authorities. The adoption of the method will contribute to the more efficient monitoring of river protection, by accurately and timely identifying areas of illegal river bed extraction that will enable authorities to enforce European Union and national legislation. Full article

Current commercial software tools implement turbulence models on computational fluid dynamics (CFD) techniques and combine them with fluid-structural interaction (FSI) techniques. There are currently a great variety of turbulence methods that are worth investigating through a comparative study in order to delineate their behavior on scaffolds used in tissue engineering and bone regeneration. Additive manufacturing (AM) offers the opportunity to obtain three-dimensional printed scaffolds (3D scaffolds) that are designed respecting morphologies and that are typically used for the fused deposition model (FDM). These are typically made using biocompatible and biodegradable materials, such as polyetherimide (PEI), ULTEM 1010 biocompatible and polylactic acid (PLA). Starting from our own geometric model, simulations were carried out applying a series of turbulence models which have been proposed due to a variety of properties, such as permeability, speed regime, pressures, depressions and stiffness, that in turn are subject to boundary conditions based on a blood torrent. The obtained results revealed that the detached eddy simulation (DES) model shows better performance for the use of 3D scaffolds in its normal operating regime. Finally, although the results do not present relevant differences between the two materials used in the comparison, the prototypes simulated in PEI ULTEM 1010 do not allow their manufacture in FDM for the required pore size. The printed 3D scaffolds of PLA reveal an elastic behavior and a rigidity that are similar to other prototypes of ceramic composition. Prototypes made of PLA reveal unpredictable variability in pore and layer size which are very similar to cell growth itself and difficult to keep constant. Full article

Snow gliding, a slow movement downhill of snow cover, is complex to forecast and model and yet is extremely important, because it drives snowpack dynamics in the pre-avalanching phase. Despite recent interest in this process and the development of some studies therein, this phenomenon is poorly understood and represents a major point of uncertainty for avalanche forecasting. This study presents a data-driven, physically based, time-dependent 1D model, Poli-Glide, able to predict the slow movement of snowpacks along a flow line at the daily scale. The objective of the work was to create a useful snow gliding model, requiring few, relatively easily available input data, by (i) modeling snowpack evolution from measured precipitation and air temperature, (ii) evaluating the rate and extent of movement of the snowpack in the gliding phase, and (iii) assessing fracture (i.e., avalanching) timing. Such a model could be then used to provide hazard assessment in areas subject to gliding, thereby, and subsequent avalanching. To do so, some simplifying assumptions were introduced, namely that (i) negligible traction stress occurs within soil, (ii) water percolation into snow occurs at a fixed rate, and (iii) the micro topography of soil is schematized according to a sinusoidal function in the absence of soil erosion. The proposed model was then applied to the “Torrent des Marais-Mont de La Saxe” site in Aosta Valley, monitored during the winters of 2010 and 2011, featuring different weather conditions. The results showed an acceptable capacity of the model to reproduce snowpack deformation patterns and the final snowpack’s displacement. Correlation analysis based upon observed glide rates further confirmed dependence against the chosen variables, thus witnessing the goodness of the model. The results could be a valuable starting point for future research aimed at including more complex parameterizations of the different processes that affect gliding. Full article

Little is known about the dynamic of HIV-1 shedding and resistance profiles in the female genital reservoir after antiretroviral therapy (ART) initiation in resource-limited countries (RLCs), which is critical for evaluating the residual sexual HIV-1 transmission risk. The present study aimed to evaluate the efficacy of 1 year duration ART at blood and genital levels in females newly diagnosed for HIV-1 from three centers in Bamako, Mali. Seventy-eight consenting females were enrolled at the time of their HIV-1 infection diagnosis. HIV-1 RNA loads (Abbott Real-Time HIV-1 assay) were tested in blood and cervicovaginal fluids (CVF) before and 12 months after ART initiation. Primary and acquired resistances to ART were evaluated by Viroseq^TM HIV-1 genotyping assay. The vaginal microbiota was analyzed using IonTorrent^TM NGS technology (Thermo Fisher Scientific). Proportions of primary drug resistance mutations in blood and CVF were 13.4% and 25%, respectively. Discrepant profiles were observed in 25% of paired blood/CVF samples. The acquired resistance rate was 3.1% in blood. At month 12, undetectable HIV-1 RNA load was reached in 84.6% and 75% of blood and CVF samples, respectively. A vaginal dysbiosis was associated with HIV RNA shedding. Our findings emphasize the need of reinforcing education to improve retention in care system, as well as the necessity of regular virological monitoring before and during ART and of implementing vaginal dysbiosis diagnosis and treatment in RLCs. Full article

The spatial and temporal scale of flash flood occurrence provides limited opportunities for observations and measurements using conventional monitoring networks, turning the focus to event-based, post-disaster studies. Post-flood surveys exploit field evidence to make indirect discharge estimations, aiming to improve our understanding of hydrological response dynamics under extreme meteorological forcing. However, discharge estimations are associated with demanding fieldwork aiming to record in small timeframes delicate data and data prone-to-be-lost and achieve the desired accuracy in measurements to minimize various uncertainties of the process. In this work, we explore the potential of unmanned aerial systems (UAS) technology, in combination with the Structure for Motion (SfM) and optical granulometry techniques in peak discharge estimations. We compare the results of the UAS-aided discharge estimations to estimates derived from differential Global Navigation Satellite System (d-GNSS) surveys and hydrologic modelling. The application in the catchment of the Soures torrent in Greece, after a catastrophic flood, shows that the UAS-aided method determined peak discharge with accuracy, providing very similar values compared to the ones estimated by the established traditional approach. The technique proved to be particularly effective, providing flexibility in terms of resources and timing, although there are certain limitations to its applicability, related mostly to the optical granulometry as well as the condition of the channel. The application highlighted important advantages and certain weaknesses of these emerging tools in indirect discharge estimations, which we discuss in detail. Full article

Viticulture is globally an important economic activity, and grapevine microbiomes hold a significant role in influencing yield and quality. Earlier studies showed that cultivar and agronomic management affect grapevine microbiome structure and, potentially, the quality of the end product. While microbial dynamics and ecology were established on some grapevine tissues, i.e., leaves and grapes, there is less knowledge deciphering microbiomes on other tissues, i.e., barks and buds. Moreover, although the impact on the microbiome of the so-called “vitivinicultural terroir” is well established, there are limited data considering microbiomes of genetically diverse cultivars within the same environment. Our study aims to explore microbiome diversity on bud and bark tissues of 37 different grapevine cultivars under the same environment and agronomic management. We targeted the V2-9 regions of the 16S rRNA gene of the microbiomes in bark and buds at the onset of new vegetation and bud expansion using Ion Torrent sequencing technology. Our results show that these tissues display high bacterial diversity regardless of cultivars’ use. Proteobacteria, Bacteroidetes, and Actinobacteria were the most prevalent among 11 detected phyla. The genotype of the cultivar seems to affect bacterial diversity and structure (p < 0.001) within the same environment. Our approach highlights the efficiency of high-throughput sequencing to unfold microbiomes of several grapevine parts that could be an important source of microbial inoculation and an important molecular fingerprint of the wine and grape end products. Full article

With the extensive use of peer-to-peer applications in recent years, the network traffic becomes more dynamic and less predictable, which leads to the decline of network resource utilization and the degradation of network performance. Aiming towards the above problems, we explore how to strengthen the cooperation between peer-to-peer applications and networks, making the application adjust its own traffic mode according to current network traffic status to enhance the stability of network traffic. We improve two key algorithms of peer selection and choking/unchoking in the protocol and introduce traffic relaxation to characterize traffic state while taking the current most popular peer-to-peer application (bit torrent protocol) as an example. In our improved method, peers are selected probabilistically according their traffic relaxation, and the double-parameter selection problem that simultaneously considers the traffic relaxation and transfer rate of peers is also solved. Finally, we conduct simulation experiments in two real network typologies with real traffic matrix data and different sizes of bit torrent swarms; the experimental results show that our method can significantly improve the stability of the network traffic without sacrificing or even improving the performance of the bit torrent protocol when compared with original BT protocol. Full article

The design of countermeasure works to mitigate landslide risk needs to deal with the multiple unknowns that are linked with soil properties, distribution and rheology. Most of the time, the degree of definition of all these elements is low. Through landslide monitoring, it is possible to acquire signals from the landslide that carry synthetic information about its dynamic. Thus, if it is possible to define a model that is able to link the landslide displacements with the triggering factors and to predict them consistently, that model may be used to evaluate the effect of a countermeasure work directly, bypassing the geomechanical uncertainty. In this paper, an example application of this approach is described. The displacements of a landslide located in North East Italy are connected with the water discharge of the small stream the crosses the landslide body. A countermeasure work that intercepts the discharge of the torrent is expected to reduce the landslide displacements of approximately 70%, with lower costs of construction and smaller impacts on the environment and landscape with respect of other types of structural mitigation works such as slope reprofiling and large retaining walls. Full article

Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps’ semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields. Full article

Cardiac dynamics are traditionally linked to a left ventricle, right ventricle, and septum morphology, a topography that differs from the heart’s five-century-old anatomic description of containing a helix and circumferential wrap architectural configuration. Torrent Guasp’s helical ventricular myocardial band (HVMB) defines this anatomy and its structure, and explains why the heart’s six dynamic actions of narrowing, shortening, lengthening, widening, twisting, and uncoiling happen. The described structural findings will raise questions about deductions guiding “accepted cardiac mechanics”, and their functional aspects will challenge and overturn them. These suppositions include the LV, RV, and septum description, timing of mitral valve opening, isovolumic relaxation period, reasons for torsion/twisting, untwisting, reasons for longitudinal and circumferential strain, echocardiographic sub segmentation, resynchronization, RV function dynamics, diastolic dysfunction’s cause, and unrecognized septum impairment. Torrent Guasp’s revolutionary contributions may alter future understanding of the diagnosis and treatment of cardiac disease. Full article