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Methods and Protocols, Volume 5, Issue 3

2022 June - 18 articles

Cover Story: We present BiGAMi, a bi-objective genetic algorithm fitness function for feature selection in microbial datasets to train high-performing phenotype classifiers. The proposed fitness function allowed us to build classifiers that outperformed the baseline performance established by the original studies by eliminating 97.68% to 99.96% features of the original dataset. Identifying the minimal subset of the most predictive features for a classification task allows the use of simpler machine learning models and subsequently increases the interpretability of classification results. Applying this feature selection approach to novel diseases is expected to quickly identify the microbes most relevant to a specific condition. View this paper
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Articles (18)

  • Article
  • Open Access
11 Citations
3,330 Views
18 Pages

Combined Use of Non-Invasive and Micro-Invasive Analytical Investigations to Understand the State of Conservation and the Causes of Degradation of I Tesori del Mare (1901) by Plinio Nomellini

  • Andrea Macchia,
  • Chiara Biribicchi,
  • Laura Rivaroli,
  • Hélène Aureli,
  • Eleonora Cerafogli,
  • Irene Angela Colasanti,
  • Paola Carnazza,
  • Giuseppe Demasi and
  • Mauro Francesco La Russa

In this study, the investigation of the oil painting on canvas I Tesori del Mare made by Plinio Nomellini in 1901 is presented. The aim of the research was threefold: the examination of the state of conservation in view of the restoration treatment,...

  • Protocol
  • Open Access
17 Citations
3,843 Views
12 Pages

Equine Oviductal Organoid Generation and Cryopreservation

  • Riley E. Thompson,
  • Mindy A. Meyers,
  • D. N. Rao Veeramachaneni,
  • Budhan S. Pukazhenthi and
  • Fiona K. Hollinshead

Organoids are a type of three-dimensional (3D) cell culture that more closely mimic the in vivo environment and can be maintained in the long term. To date, oviductal organoids have only been reported in laboratory mice, women, and cattle. Equine ovi...

  • Protocol
  • Open Access
3,056 Views
17 Pages

Congenital heart defects (CHD) are the most common type of birth defects. Several human case studies and genetically altered animal models have identified abnormalities in the development of ventricular conduction system (VCS) in the heart. While cel...

  • Article
  • Open Access
13 Citations
4,495 Views
16 Pages

Discriminant Analysis PCA-LDA Assisted Surface-Enhanced Raman Spectroscopy for Direct Identification of Malaria-Infected Red Blood Cells

  • Gunganist Kongklad,
  • Ratchapak Chitaree,
  • Tana Taechalertpaisarn,
  • Nathinee Panvisavas and
  • Noppadon Nuntawong

Various methods for detecting malaria have been developed in recent years, each with its own set of advantages. These methods include microscopic, antigen-based, and molecular-based analysis of blood samples. This study aimed to develop a new, altern...

  • Protocol
  • Open Access
2 Citations
3,904 Views
22 Pages

Hospitalised patients with extreme obesity have poorer healthcare outcomes compared to normal weight patients. How hospital services are coordinated and delivered to meet the care needs of patients with extreme obesity is not well understood. The aim...

  • Protocol
  • Open Access
1 Citations
2,832 Views
5 Pages

Clinical Considerations and Outcomes for Spine Surgery Patients with a History of Transplant: A Systematic Scoping Review Protocol

  • Roshini Kalagara,
  • Zerubabbel K. Asfaw,
  • Matthew T. Carr,
  • Addison Quinones,
  • Lisa Genadry,
  • Zaid Nakadar,
  • Anzila Haris,
  • Alexander J. Schupper,
  • Jonathan S. Gal and
  • Tanvir F. Choudhri

Spine surgery patients with a history of organ transplantation are a complex population due to their unique anesthetic considerations, immunologic profiles, drug interactions, and potential organ dysfunction. It is common for these patients to develo...

  • Communication
  • Open Access
3 Citations
3,695 Views
8 Pages

Microneedle Array Technique for the Longitudinal Extraction of Interstitial Fluid without Hair Removal

  • Robert M. Taylor,
  • Abdul-Mehdi S. Ali,
  • Yiliang Zhu,
  • Alicia M. Bolt and
  • Justin T. Baca

Interstitial fluid (ISF) bathes the cells and tissues and is in constant exchange with blood. As an exchange medium for waste, nutrients, exosomes, and signaling molecules, ISF is recognized as a plentiful source of biomolecules. Many basic and pre-c...

  • Article
  • Open Access
22 Citations
4,637 Views
14 Pages

Human Activity Recognition (HAR) is increasingly used in a variety of applications, including health care, fitness tracking, and rehabilitation. To reduce the impact on the user’s daily activities, wearable technologies have been advanced throu...

  • Protocol
  • Open Access
6 Citations
7,172 Views
10 Pages

Genome editing using the CRISPR/Cas9 system is one of the trendiest methodologies in the scientific community. Many genome editing approaches require recombinant Streptococcus pyogenes Cas9 (SpCas9) at some point during their application, for instanc...

  • Article
  • Open Access
1 Citations
4,072 Views
14 Pages

In order to improve a recently established cell-based assay to assess the potency of botulinum neurotoxin, neuroblastoma-derived SiMa cells and induced pluripotent stem-cells (iPSC) were modified to incorporate the coding sequence of a reporter lucif...

  • Article
  • Open Access
6 Citations
4,722 Views
15 Pages

BiGAMi: Bi-Objective Genetic Algorithm Fitness Function for Feature Selection on Microbiome Datasets

  • Mike Leske,
  • Francesca Bottacini,
  • Haithem Afli and
  • Bruno G. N. Andrade

The relationship between the host and the microbiome, or the assemblage of microorganisms (including bacteria, archaea, fungi, and viruses), has been proven crucial for its health and disease development. The high dimensionality of microbiome dataset...

  • Article
  • Open Access
1 Citations
3,945 Views
16 Pages

A Polarized Raman Spectroscopic Method for Advanced Analyses of the Osteon Lamellar Structure of Human Bone

  • Giuseppe Pezzotti,
  • Eiji Ishimura,
  • Ryosuke Inai,
  • Wenliang Zhu,
  • Taigi Honma,
  • Nobuhiko Sugano,
  • Wataru Ando,
  • Ugo Pazzaglia and
  • Elia Marin

Raman spectroscopy has recently been used for quantitative analyses of cortical bone tissue and related materials, such as dentin and enamel. While those analyses have proven useful as potential diagnostic tools, the Raman spectrum of bone encrypts a...

  • Article
  • Open Access
5 Citations
10,777 Views
14 Pages

Anti-Inflammatory Diet for Women with Interstitial Cystitis/Bladder Pain Syndrome: The AID-IC Pilot Study

  • Barbara Gordon,
  • Cynthia Blanton,
  • Rebekah Ramsey,
  • Andrea Jeffery,
  • Laura Richey and
  • Rachel Hulse

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic condition characterized by pelvic pain coupled with urinary frequency and urgency. The underlying cause of IC/BPS is unknown; there is no cure. Dietary components exacerbate symptoms....

  • Protocol
  • Open Access
2 Citations
4,395 Views
6 Pages

Methodologies and MR Parameters in Quantitative Magnetic Resonance Neurography: A Scoping Review Protocol

  • Fabian Balsiger,
  • Benedikt Wagner,
  • Johann M. E. Jende,
  • Benjamin Marty,
  • Martin Bendszus,
  • Olivier Scheidegger and
  • Felix T. Kurz

Magnetic resonance neurography (MRN), the MR imaging of peripheral nerves, is clinically used for assessing and monitoring peripheral neuropathies based on qualitative, weighted MR imaging. Recently, quantitative MRN has been increasingly reported wi...

  • Article
  • Open Access
6 Citations
5,311 Views
16 Pages

Aquaculture, a mass supplier of seafood, relies on plastic materials that may contain the endocrine disruptors bisphenol-A (BPA) and tert-octylphenol (t-OCT). These pollutants present toxicity to Artemia, the live aquaculture feed, and are transferre...

  • Article
  • Open Access
29 Citations
6,111 Views
16 Pages

In-Situ Comparative Study of Eucalyptus, Basil, Cloves, Thyme, Pine Tree, and Tea Tree Essential Oil Biocide Efficacy

  • Andrea Macchia,
  • Hélène Aureli,
  • Fernanda Prestileo,
  • Federico Ortenzi,
  • Shaila Sellathurai,
  • Antonella Docci,
  • Eleonora Cerafogli,
  • Irene Angela Colasanti,
  • Michela Ricca and
  • Mauro Francesco La Russa

Bio-colonization is a dynamic and multiphasic process headed by microorganisms. Conventional treatments to process affected stone materials include chemical biocides, whose formulations are mainly composed of quaternary ammonium salts(QAs), reported...

  • Protocol
  • Open Access
2 Citations
4,181 Views
12 Pages

An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus

  • Simon Bourdareau,
  • Olivier Godfroy,
  • Josselin Gueno,
  • Delphine Scornet,
  • Susana M. Coelho,
  • Leila Tirichine and
  • J. Mark Cock

The brown algae are an important but understudied group of multicellular marine organisms. A number of genetic and genomic tools have been developed for the model brown alga Ectocarpus; this includes, most recently, chromatin immunoprecipitation meth...

  • Brief Report
  • Open Access
4 Citations
3,896 Views
9 Pages

Reference Gene Validation for RT–qPCR in PBMCs from Asthmatic Patients with or without Obesity

  • Marina Bantulà,
  • Ebymar Arismendi,
  • César Picado,
  • Joaquim Mullol,
  • Jordi Roca-Ferrer and
  • Valeria Tubita

Obesity is known to impair the efficacy of glucocorticoid medications for asthma control. Glucocorticoid-induced gene expression studies may be useful to discriminate those obese asthmatic patients who present a poor response to glucocorticoids. The...

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Methods Protoc. - ISSN 2409-9279