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JOURNAL ARTICLE
Rie Sadohara, David Jacobs, Mark A Pereira, Abigail J Johnson
BACKGROUND: There are few resources available for researchers aiming to conduct 24-h dietary record and recall analysis using R. OBJECTIVES: We aimed to develop DietDiveR, which is a toolkit of functions written in R for the analysis of recall or record data collected with the Automated Self-Administered 24-h Dietary Assessment Tool or 2-d 24-h dietary recall data from the National Health and Nutrition Examination Survey (NHANES). The R functions are intended for food and nutrition researchers who are not computational experts...
May 2024: American Journal of Clinical Nutrition
#22
JOURNAL ARTICLE
Sharon Jiang, Barbara D Lam, Monica Agrawal, Shannon Shen, Nicholas Kurtzman, Steven Horng, David R Karger, David Sontag
OBJECTIVE: Leverage electronic health record (EHR) audit logs to develop a machine learning (ML) model that predicts which notes a clinician wants to review when seeing oncology patients. MATERIALS AND METHODS: We trained logistic regression models using note metadata and a Term Frequency Inverse Document Frequency (TF-IDF) text representation. We evaluated performance with precision, recall, F1, AUC, and a clinical qualitative assessment. RESULTS: The metadata only model achieved an AUC 0...
May 3, 2024: Journal of the American Medical Informatics Association: JAMIA
#23
Joseph D Berleant, James L Banal, Dhriti K Rao, Mark Bathe
The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages...
April 15, 2024: medRxiv
#24
JOURNAL ARTICLE
Enrique G Villarreal, Emilia Ramos-Barrera, Ricardo J Estrada-Mendizabal, Pablo D Treviño-Valdez, Oscar Tamez-Rivera
BACKGROUND: Analyzing the epidemiology and clinical manifestations of pediatric tuberculosis in endemic regions is crucial to meet the goal of ending tuberculosis. The objective was to assess the various clinical scenarios of tuberculosis in a large pediatric cohort in Mexico. METHODS: This retrospective study from a pediatric referral center in Mexico included patients diagnosed with tuberculosis from 2012 to 2021. We analyzed clinical data and diagnostic study results, including demographic characteristics, underlying medical conditions, BCG vaccination, clinical presentation, imaging findings, microbiologic data, treatment, and clinical outcomes...
August 2024: Journal of Clinical Tuberculosis and Other Mycobacterial Diseases
#25
JOURNAL ARTICLE
Sema Tural Bozoğlu, Hatice Sonay Yalçın Cömert, Gül Şalcı, Ahmet Alver, İsmail Saygın, Neslihan Sağlam, Şeniz Erdem, Mustafa İmamoğlu, Haluk Sarıhan
PURPOSE: We aimed to examine the effectiveness of mother milk exosomes in treating corrosive esophageal burns. MATERIALS AND METHODS: 32 rats were separated into four equal groups and weighed individually before the procedure. A corrosive esophageal burn model was created with 12.5% sodium hydroxide by a 3F Fogarty catheter. Group 1 did not apply any process or treatment, Group 2 was burned, and no treatment was performed. Group 3 was burned, and then 0.5 cc/day of mother milk exosome extract was given...
May 2, 2024: Pediatric Surgery International
#26
JOURNAL ARTICLE
Adham M Alkhadrawi, Lisa Y Lin, Saul A Langarica, Kyungsu Kim, Sierra K Ha, Nahyoung G Lee, Synho Do
PURPOSE: Thyroid eye disease (TED) is characterized by proliferation of orbital tissues and complicated by compressive optic neuropathy (CON). This study aims to utilize a deep-learning (DL)-based automated segmentation model to segment orbital muscle and fat volumes on computed tomography (CT) images and provide quantitative volumetric data and a machine learning (ML)-based classifier to distinguish between TED and TED with CON. METHODS: Subjects with TED who underwent clinical evaluation and orbital CT imaging were included...
May 1, 2024: Investigative Ophthalmology & Visual Science
#27
JOURNAL ARTICLE
Hila Shamon, Roi Maor, Michael V Cove, Roland Kays, Jessie Adley, Peter D Alexander, David N Allen, Maximilian L Allen, Cara L Appel, Evan Barr, Erika L Barthelmess, Carolina Baruzzi, Kelli Bashaw, Guillaume Bastille-Rousseau, Madison E Baugh, Jerrold Belant, John F Benson, Bethany A Bespoyasny, Tori Bird, Daniel A Bogan, LaRoy S E Brandt, Claire E Bresnan, Jarred M Brooke, Frances E Buderman, Suzannah G Buzzell, Amanda E Cheeseman, M Colter Chitwood, Petros Chrysafis, Merri K Collins, D Parks Collins, Justin A Compton, L Mike Conner, Olivia G Cosby, Stephanie S Coster, Benjamin Crawford, Anthony P Crupi, Andrea K Darracq, Miranda L Davis, Brett A DeGregorio, Kimberly L Denningmann, Kyle D Dougherty, Ace Driver, Andrew J Edelman, E Hance Ellington, Susan N Ellis-Felege, Caroline N Ellison, Jean E Fantle-Lepczyk, Zach J Farris, Jorie Favreau, Pilar Fernandez, M Caitlin Fisher-Reid, Matthew C Fitzpatrick, Elizabeth A Flaherty, Tavis D Forrester, Sarah R Fritts, Travis Gallo, Brian D Gerber, Sean T Giery, Jessica L Glasscock, Alex D Gonatas, Anna C Grady, Austin M Green, Tremaine Gregory, Noel Griffin, Robert H Hagen, Christopher P Hansen, Lonnie P Hansen, Steven C Hasstedt, Haydée Hernández-Yáñez, Daniel J Herrera, Robert V Horan, Victoria L Jackson, Luanne Johnson, Mark J Jordan, Willaine Kahano, Joseph Kiser, Travis W Knowles, Molly M Koeck, Caroline Koroly, Kellie M Kuhn, Erin K Kuprewicz, Diana J R Lafferty, Scott D LaPoint, Marcus Lashley, Richard G Lathrop, Thomas E Lee, Christopher A Lepczyk, Damon B Lesmeister, Jason V Lombardi, Robert A Long, Robert C Lonsinger, Paula MacKay, Sean P Maher, David S Mason, Joshua J Millspaugh, Remington J Moll, Jessica B Moon, Alessio Mortelliti, Alexis M Mychajliw, Christopher M Nagy, Sean A Neiswenter, Dana L Nelson, Claire E Nemes, Clayton K Nielsen, Elizabeth Olson, M Teague O'Mara, Brian J O'Neill, Blake R Page, Elizabeth Parsons, Brent S Pease, Mary E Pendergast, Mike Proctor, Heather Quick, Christine C Rega-Brodsky, Michael S Rentz, Kylie Rezendes, Daric Rich, Derek R Risch, Andrea Romero, Brigit R Rooney, Christopher T Rota, Corey A Samples, Christopher M Schalk, Çağan H Sekercioğlu, Maksim Sergeyev, Austin B Smith, Daniel S Smith, Jinelle H Sperry, Jennifer L Stenglein, Michael K Stokes, Johnathon S Stutzman, Kimberly R Todd, John P Vanek, Wren Varga, Zachary M Wardle, Stephen L Webb, Nathaniel H Wehr, Laura S Whipple, Christopher A Whittier, Jane S Widness, Jacque Williamson, Andrew M Wilson, Alexander J Wolf, Marketa Zimova, Adam S Zorn, William J McShea
SNAPSHOT USA is a multicontributor, long-term camera trap survey designed to survey mammals across the United States. Participants are recruited through community networks and directly through a website application (https://www.snapshot-usa.org/). The growing Snapshot dataset is useful, for example, for tracking wildlife population responses to land use, land cover, and climate changes across spatial and temporal scales. Here we present the SNAPSHOT USA 2021 dataset, the third national camera trap survey across the US...
May 1, 2024: Ecology
#28
JOURNAL ARTICLE
Ying Zhang, Matthew Kim, Michael Prerau, Daniel Mobley, Michael Rueschman, Kathryn Sparks, Meg Tully, Shaun Purcell, Susan Redline
This paper presents a comprehensive overview of the National Sleep Research Resource (NSRR), a National Heart Lung and Blood Institute-supported repository developed to share data from clinical studies focused on the evaluation of sleep disorders. The NSRR addresses challenges presented by the heterogeneity of sleep-related data, leveraging innovative strategies to optimize the quality and accessibility of available datasets. It provides authorized users with secure centralized access to a large quantity of sleep-related data including polysomnography, actigraphy, demographics, patient-reported outcomes, and other data...
April 30, 2024: Sleep
#29
JOURNAL ARTICLE
Rahel Paloots, Michael Baudis
Cancer cell lines are an important component in biological and medical research, enabling studies of cellular mechanisms as well as the development and testing of pharmaceuticals. Genomic alterations in cancer cell lines are widely studied as models for oncogenetic events and are represented in a wide range of primary resources. We have created a comprehensive, curated knowledge resource-cancercelllines.org-with the aim to enable easy access to genomic profiling data in cancer cell lines, curated from a variety of resources and integrating both copy number and single nucleotide variants data...
April 30, 2024: Database: the Journal of Biological Databases and Curation
#30
JOURNAL ARTICLE
Shuai Ming, Jie Han, Xi Yao, Xiaohong Guo, Qingge Guo, Bo Lei
BACKGROUND: TikTok is emerging as a vital platform for health information dissemination. Despite myopia being a global public health issue, the high-quality myopia information shared by health educators often fails to go viral. It is imperative to analyze the factors influencing video quality and popularity, especially from diverse perspectives of researchers, health educators, and audiences. METHODS: TikTok myopia-related videos were retrieved using TikTok's default comprehensive search (DCS) and most liked search (MLS) strategies...
April 29, 2024: BMC Public Health
#31
COMPARATIVE STUDY
Samuel P Forry, Stephanie L Servetas, Jason G Kralj, Keng Soh, Michalis Hadjithomas, Raul Cano, Martha Carlin, Maria G de Amorim, Benjamin Auch, Matthew G Bakker, Thais F Bartelli, Juan P Bustamante, Ignacio Cassol, Mauricio Chalita, Emmanuel Dias-Neto, Aaron Del Duca, Daryl M Gohl, Jekaterina Kazantseva, Muyideen T Haruna, Peter Menzel, Bruno S Moda, Lorieza Neuberger-Castillo, Diana N Nunes, Isha R Patel, Rodrigo D Peralta, Adrien Saliou, Rolf Schwarzer, Samantha Sevilla, Isabella K T M Takenaka, Jeremy R Wang, Rob Knight, Dirk Gevers, Scott A Jackson
Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods...
April 29, 2024: Scientific Reports
#32
JOURNAL ARTICLE
Jason Williams, Bruce Nash, Cornel Ghiban, Mohammed Khalfan, Uwe Hilgert, Susan Lauter, Chun-Hua Yang, David Andrew Micklos
DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees...
2024: Methods in Molecular Biology
#33
JOURNAL ARTICLE
Todd D O'Brien, Leocadio Blanco-Bercial, Jennifer M Questel, Paola G Batta-Lona, Ann Bucklin
The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/ ) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles)...
2024: Methods in Molecular Biology
#34
JOURNAL ARTICLE
Miguel Vences, Stefanos Patmanidis, Alexander Fedosov, Aurélien Miralles, Nicolas Puillandre
The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy...
2024: Methods in Molecular Biology
#35
JOURNAL ARTICLE
Sreymom Pol, Teemu Kallonen, Tommi Mäklin, Poda Sar, Jill Hopkins, Sona Soeng, Thyl Miliya, Clare L Ling, Stephen D Bentley, Jukka Corander, Paul Turner
UNLABELLED: The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks...
April 29, 2024: MBio
#36
JOURNAL ARTICLE
Andreas Walker, Werner O Hackl, Bernhard Pfeifer
Secondary use of clinical health data implies a prior integration of mostly heterogenous and multidimensional data sets. A clinical data warehouse addresses the technological and organizational framework conditions required for this, by making any data available for analysis. However, users of a data warehouse often do not have a comprehensive overview of all available data and only know about their own data in their own systems - a situation which is also referred to as 'data siloed state'. This problem can be addressed and ultimately solved by implementation of a data catalog...
April 26, 2024: Studies in Health Technology and Informatics
#37
JOURNAL ARTICLE
Hein S Zelisse, Sander de Ridder, Mignon D J M van Gent, Constantijne H Mom, G Bea A Wisman, Eva-Maria Roes, Anna K L Reyners, Jurgen M Piek, Gatske M Nieuwenhuyzen-de Boer, Christianne A R Lok, Cornelis D de Kroon, Loes F S Kooreman, Marc-Jan Janssen, Maurice Phm Jansen, Hugo M Horlings, Margriet Collée, Annegien Broeks, Ingrid A Boere, Joost Bart, Anne M van Altena, Marlou Heeling, I Matthijs Stoter, Quirinus J Voorham, Marc J van de Vijver, Frederike Dijk, Jeroen A M Belien
Objective: Biobanks play a crucial role in fundamental and translational research by storing valuable biomaterials and data for future analyses. However, the design of their information technology (IT) infrastructures is often customized to specific requirements, thereby lacking the ability to be used for biobanks comprising other (types of) diseases. This results in substantial costs, time, and efforts for each new biobank project. The Dutch multicenter Archipelago of Ovarian Cancer Research (AOCR) biobank has developed an innovative, reusable IT infrastructure capable of adaptation to various biobanks, thereby enabling cost-effective and efficient implementation and management of biobank IT systems...
April 29, 2024: Biopreservation and Biobanking
#38
JOURNAL ARTICLE
Daniel Alvitez-Temoche, Elca Del Aguila, Diego Galarza-Valencia, Iván Calderón, Fran Espinoza-Carhuancho, Josmel Pacheco-Mendoza, Frank Mayta-Tovalino
BACKGROUND AND AIM: Understanding dental care in dogs has made remarkable progress in veterinary medicine. Therefore, this study aimed to analyze the academic literature published in veterinary dentistry from 1990 to 2023. MATERIALS AND METHODS: A descriptive study was conducted using a scientometric approach and metadata from the Web of Science database. A search strategy adapted for this database was developed using MeSH and Emtree terms and the Boolean operators AND and OR...
March 2024: Veterinary World
#39
JOURNAL ARTICLE
Liu Pei, Wen Weiye, Yu Ka Fung, Tong Raymond Wai Man, Gao Xiaoli, Lo Edward Chin Man, Wong May Chun Mei
OBJECTIVES: This study aimed to identify the oral microbiota factors contributing to low birth weight (LBW) in Chinese pregnant women and develop a prediction model using machine learning. METHODS: A nested case-control study was conducted in a prospective cohort of 580 Chinese pregnant women, with 23 LBW cases and 23 healthy delivery controls matched for age and smoking habit. Saliva samples were collected at early and late pregnancy, and microbiome profiles were analyzed through 16S rRNA gene sequencing...
April 26, 2024: Journal of Dentistry
#40
JOURNAL ARTICLE
Ashley L Cooper, Alex Wong, Sandeep Tamber, Burton W Blais, Catherine D Carrillo
Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans...
March 30, 2024: Microorganisms
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