1,469 results match your criteria resource repository


Thoracic Point-of-Care Ultrasound: A SARS-CoV-2 Data Repository for Future Artificial Intelligence and Machine Learning.

Surg Innov 2021 May 7:15533506211018671. Epub 2021 May 7.

Department of Surgery, 1267Anne Arundel Medical Center, Annapolis, MD, USA.

Current experience suggests that artificial intelligence (AI) and machine learning (ML) may be useful in the management of hospitalized patients, including those with COVID-19. In light of the challenges faced with diagnostic and prognostic indicators in SARS-CoV-2 infection, our center has developed an international clinical protocol to collect standardized thoracic point of care ultrasound data in these patients for later AI/ML modeling. We surmise that in the future AI/ML may assist in the management of SARS-CoV-2 patients potentially leading to improved outcomes, and to that end, a corpus of curated ultrasound images and linked patient clinical metadata is an invaluable research resource. Read More

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From integrative structural biology to cell biology.

Authors:
Andrej Sali

J Biol Chem 2021 May 3:100743. Epub 2021 May 3.

Research Collaboratory for Structural Bioinformatics Protein Data Bank, the Department of Bioengineering and Therapeutic Sciences, the Quantitative Biosciences Institute (QBI), and the Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA. Electronic address:

Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ∼52 MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving integrative modeling include expanding model representations, increasing the variety of input data and prior information, quantifying a match between input information and a model in a Bayesian fashion, inventing more efficient structural sampling, as well as developing better model validation, analysis, and visualization. Read More

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Cross-Sectional Exploration of Plasma Biomarkers of Alzheimer's Disease in Down Syndrome: Early Data from the Longitudinal Investigation for Enhancing Down Syndrome Research (LIFE-DSR) Study.

J Clin Med 2021 Apr 28;10(9). Epub 2021 Apr 28.

Department of Psychiatry, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114, USA.

With improved healthcare, the Down syndrome (DS) population is both growing and aging rapidly. However, with longevity comes a very high risk of Alzheimer's disease (AD). The LIFE-DSR study (NCT04149197) is a longitudinal natural history study recruiting 270 adults with DS over the age of 25. Read More

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Deep Learning Classifier with Patient's Metadata of Dermoscopic Images in Malignant Melanoma Detection.

J Multidiscip Healthc 2021 21;14:877-885. Epub 2021 Apr 21.

Graduate Institute of Injury Prevention and Control, College of Public Health, Taipei Medical University, Taipei, Taiwan.

Background: Incidence of skin cancer is one of the global burdens of malignancies that increase each year, with melanoma being the deadliest one. Imaging-based automated skin cancer detection still remains challenging owing to variability in the skin lesions and limited standard dataset availability. Recent research indicates the potential of deep convolutional neural networks (CNN) in predicting outcomes from simple as well as highly complicated images. Read More

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SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly.

Comput Biol Med 2021 Apr 10;133:104391. Epub 2021 Apr 10.

Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi-110020, India. Electronic address: http://webs.iiitd.edu.in/raghava/.

Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of this rapidly expanding field, there is no dedicated resource to study peptide nanostructures. This study endeavours to create a repository of short peptides, which may prove to be the best models to study ordered nanostructures formed by peptide self-assembly. Read More

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Factors Associated With Perceived Trust of False Abortion Websites: Cross-sectional Online Survey.

J Med Internet Res 2021 Apr 19;23(4):e25323. Epub 2021 Apr 19.

Oregon Health & Science University, Portland, OR, United States.

Background: Most patients use the internet to search for health information. While there is a vast repository of searchable information online, much of the content is unregulated and therefore potentially incorrect, conflicting, or confusing. Abortion information online is particularly prone to being inaccurate as antichoice websites publish purposefully misleading information in formats that appear as neutral resources. Read More

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A simplified approach for derivation of induced pluripotent stem cells from Epstein-Barr virus immortalized B-lymphoblastoid cell lines.

Heliyon 2021 Apr 3;7(4):e06617. Epub 2021 Apr 3.

Department of Rehabilitation Medicine and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.

Given the limited availability of tissue, especially brain tissue, for neurological diseases and disorders research, the development of alternative biological tools for investigations of underlying molecular and genetic mechanisms is imperative. One important resource for this task is the large repositories that bank immortalized blood cells (i.e. Read More

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Multi-schema computational prediction of the comprehensive SARS-CoV-2 vs. human interactome.

PeerJ 2021 5;9:e11117. Epub 2021 Apr 5.

Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada.

Background: Understanding the disease pathogenesis of the novel coronavirus, denoted SARS-CoV-2, is critical to the development of anti-SARS-CoV-2 therapeutics. The global propagation of the viral disease, denoted COVID-19 ("coronavirus disease 2019"), has unified the scientific community in searching for possible inhibitory small molecules or polypeptides. A holistic understanding of the SARS-CoV-2 vs. Read More

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Application of machine-learning techniques in classification of HIV medical care status for people living with HIV in South Carolina.

AIDS 2021 May;35(Suppl 1):S19-S28

Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, Columbia, South Carolina, USA.

Objectives: Ending the HIV epidemic requires innovative use of data for intelligent decision-making from surveillance through treatment. This study sought to examine the usefulness of using linked integrated PLWH health data to predict PLWH's future HIV care status and compare the performance of machine-learning methods for predicting future HIV care status for SC PLWH.

Design: We employed supervised machine learning for its ability to predict PLWH's future care status by synthesizing and learning from PLWH's existing health data. Read More

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One-Size-Fits All: A Scalable Solution to Formal Telemedicine Provider Training to Support the COVID-19 Pandemic Response.

Front Pediatr 2021 30;9:647458. Epub 2021 Mar 30.

Telehealth Programs, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.

Formalized training in telemedicine addresses barriers to provider adoption and engagement and assures a level of competence for independent practice. We previously developed a blended-model training program, customizable according to role and specialty; this method of training was not feasible in the pandemic response. We describe the development and implementation of a multi- and interdisciplinary telemedicine provider training program enabling the rapid scaling of telemedicine at our institution. Read More

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Understanding the barriers and facilitators to trauma registry development in resource-constrained settings: A survey of trauma registry stewards and researchers.

Injury 2021 Mar 30. Epub 2021 Mar 30.

Division of General Surgery, Vancouver General Hospital, Vancouver, Canada; Department of Surgery, University of British Columbia, Vancouver, Canada.

Background: The implementation of trauma registries has proven a highly effective means of injury control. However, many low and middle-income countries lack trauma registries. Those that have trauma registries vary widely in terms of both implementation and structure. Read More

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Developing Clinical Practice Guidelines for Dental Caries Management for the Malaysian Population through the ADAPTE Trans-Contextual Adaptation Process.

Oral Health Prev Dent 2021 Jan;19(1):217-227

Purpose: To develop an evidence-based Clinical Practice Guideline (CPG) on caries management for the Malaysian population using the ADAPTE trans-contextual adaptation framework.

Materials And Methods: A systematic search was conducted to identify all CPGs related to caries management on guideline repository websites and other platforms. The search findings were screened and the quality of the identified guidelines was evaluated using the AGREE II tool. Read More

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January 2021

Immortalization of shrimp lymphoid cells by hybridizing with the continuous cell line Sf9 leading to the development of 'PmLyO-Sf9 '.

Fish Shellfish Immunol 2021 Jun 4;113:196-207. Epub 2021 Apr 4.

National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India. Electronic address:

Shrimp progressively gets more attention among marine invertebrates from researchers all over the world due to it being a healthy food as well as having economic importance. There were a lot of attempts to develop a continuous cell line from shrimp but none successful. In this context a novel hybrid cell line named 'PmLyO-Sf9' could be developed by fusing shrimp lymphoid organ cells with Sf9 cells after to metabolic blocking of Sf9 cells using puromycin and actinomycin D and effecting the fusion by way of PEG application. Read More

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COVID-19 vs influenza viruses: A cockroach optimized deep neural network classification approach.

Int J Imaging Syst Technol 2021 Feb 24. Epub 2021 Feb 24.

Faculty of Computer and Artificial intelligence Cairo University Cairo Egypt.

Among Coronavirus, as with many other viruses, receptor interactions are an essential determinant of species specificity, virulence, and pathogenesis. The pathogenesis of the COVID-19 depends on the virus's ability to attach to and enter into a suitable human host cell. This paper presents a cockroach optimized deep neural network to detect COVID-19 and differentiate between COVID-19 and influenza types A, B, and C. Read More

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February 2021

RcdMathLib: An Open Source Software Library for Computing on Resource-Limited Devices.

Sensors (Basel) 2021 Mar 1;21(5). Epub 2021 Mar 1.

Technische Universität Darmstadt, Institut für Baubetrieb, El-Lissitzky-Straße 1, 64287 Darmstadt, Germany.

We developped an open source library called RcdMathLib for solving multivariate linear and nonlinear systems. RcdMathLib supports on-the-fly computing on low-cost and resource-constrained devices, e.g. Read More

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SNAPSHOT USA 2019: a coordinated national camera trap survey of the United States.

Ecology 2021 Apr 1:e03353. Epub 2021 Apr 1.

Department of Biology, Francis Marion University, Florence, SC, 29502, USA.

With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August - 24 November of 2019). Read More

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Racial Disparities in the Epidemiology of COVID-19 in Georgia: Trends Since State-Wide Reopening.

Health Equity 2021 2;5(1):91-99. Epub 2021 Mar 2.

Institute of Preventive and Public Health, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.

To examine county-level factors associated with coronavirus disease 2019 (COVID-19) incidence and mortality in Georgia, focusing on changes after relaxation of "shelter-in-place" orders on April 24, 2020. County-level data on confirmed COVID-19 cases and deaths were obtained from the Johns Hopkins 2019 Novel Coronavirus Data Repository and linked with county-level data from the 2020 County Health Rankings. We examined associations of county-level factors with mortality and incidence rates (quantiles) using a logistic regression model. Read More

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Economic and Clinical Burden of Virus-Associated Hemorrhagic Cystitis in Patients Following Allogeneic Hematopoietic Stem Cell Transplantation in the United States.

Transplant Cell Ther 2021 Feb 26. Epub 2021 Feb 26.

Memorial Sloan Kettering Cancer Center, New York, New York.

Hemorrhagic cystitis (HC) caused by viral infections such as BK virus, cytomegalovirus, and/or adenovirus after allogeneic hematopoietic stem cell transplantation (allo-HCT) causes morbidity and mortality, affects quality of life, and poses a substantial burden to the health care system. At present, HC management is purely supportive, as there are no approved or recommended antivirals for virus-associated HC. The objective of this retrospective observational study was to compare the economic burden, health resource utilization (HRU), and clinical outcomes among allo-HCT recipients with virus-associated HC to those without virus-associated HC using a large US claims database. Read More

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February 2021

A proposal to leverage high-quality veterinary diagnostic laboratory large data streams for animal health, public health, and One Health.

J Vet Diagn Invest 2021 May 26;33(3):399-409. Epub 2021 Mar 26.

Veterinary Diagnostic Laboratory, Department of Veterinary Science, College of Agriculture, Food & the Environment, University of Kentucky, Lexington, KY.

Test data generated by ~60 accredited member laboratories of the American Association of Veterinary Laboratory Diagnosticians (AAVLD) is of exceptional quality. These data are captured by 1 of 13 laboratory information management systems (LIMSs) developed specifically for veterinary diagnostic laboratories (VDLs). Beginning ~2000, the National Animal Health Laboratory Network (NAHLN) developed an electronic messaging system for LIMS to automatically send standardized data streams for 14 select agents to a national repository. Read More

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Viral Etiologies of Meningitis in Patients with Presumed Pyogenic Meningitis at University Hospitals in Ethiopia.

Infect Drug Resist 2021 17;14:1083-1088. Epub 2021 Mar 17.

Armauer Hansen Research Institute, Addis Ababa, Ethiopia.

Introduction: Viral meningitis is common in most resource-limited settings, posing a challenge for the management and prognosis of suspected patients. No study has been done on the detection of either viral or viral-bacterial co-infection among presumed pyogenic meningitis cases in Ethiopia. We, therefore, aimed to determine the distribution of cytomegalovirus (CMV) and human enteroviruses (HEVs) among patients with presumptive pyogenic meningitis at University hospitals in Ethiopia. Read More

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Automated Production of Research Data Marts from a Canonical Fast Healthcare Interoperability Resource (FHIR) Data Repository: Applications to COVID-19 Research.

medRxiv 2021 Mar 12. Epub 2021 Mar 12.

Objective: Objective: The COVID-19 pandemic has enhanced the need for timely real-world data (RWD) for research. To meet this need, several large clinical consortia have developed networks for access to RWD from electronic health records (EHR), each with its own common data model (CDM) and custom pipeline for extraction, transformation, and load operations for production and incremental updating. However, the demands of COVID-19 research for timely RWD (e. Read More

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Radiologist observations of computed tomography (CT) images predict treatment outcome in TB Portals, a real-world database of tuberculosis (TB) cases.

PLoS One 2021 17;16(3):e0247906. Epub 2021 Mar 17.

Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, United States of America.

The TB Portals program provides a publicly accessible repository of TB case data containing multi-modal information such as case clinical characteristics, pathogen genomics, and radiomics. The real-world resource contains over 3400 TB cases, primarily drug resistant cases, and CT images with radiologist annotations are available for many of these cases. The breadth of data collected offers a patient-centric view into the etiology of the disease including the temporal context of the available imaging information. Read More

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Metagenomic sequencing revealed the potential of banknotes as a repository of microbial genes.

BMC Genomics 2021 Mar 11;22(1):173. Epub 2021 Mar 11.

Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.

Background: Genetic resources are important natural assets. Discovery of new enzyme gene sequences has been an ongoing effort in biotechnology industry. In the genomic age, genomes of microorganisms from various environments have been deciphered. Read More

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riboCIRC: a comprehensive database of translatable circRNAs.

Genome Biol 2021 Mar 8;22(1):79. Epub 2021 Mar 8.

State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.

riboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www. Read More

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lncRNADetector: a bioinformatics pipeline for long non-coding RNA identification and MAPslnc: a repository of medicinal and aromatic plant lncRNAs.

RNA Biol 2021 Mar 18:1-6. Epub 2021 Mar 18.

Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.

Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs and potent regulatory elements in the living cells. High throughput RNA sequencing analyses have generated a tremendous amount of transcript sequence data. A large proportion of these transcript sequences does not code for proteins and are known as non-coding RNAs. Read More

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Characteristics Of The Macs-Wihs Combined Cohort Study: Opportunities For Research On Aging With Hiv In The Longest Us Observational Study Of HIV.

Am J Epidemiol 2021 Mar 2. Epub 2021 Mar 2.

Department of Medicine, University of California San Francisco, San Francisco, California.

In 2019, NIH combined the Multicenter AIDS Cohort Study and the Women's Interagency HIV Study into the MACS/WIHS Combined Cohort Study (MWCCS). Participants completing a visit October 2018-September 2019 (targeted for MWCCS enrollment) are described by HIV serostatus and compared to people living with HIV (PLWH) in the U.S. Read More

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Inflect: Optimizing Computational Workflows for Thermal Proteome Profiling Data Analysis.

J Proteome Res 2021 Apr 4;20(4):1874-1888. Epub 2021 Mar 4.

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.

The CETSA and Thermal Proteome Profiling (TPP) analytical methods are invaluable for the study of protein-ligand interactions and protein stability in a cellular context. These tools have increasingly been leveraged in work ranging from understanding signaling paradigms to drug discovery. Consequently, there is an important need to optimize the data analysis pipeline that is used to calculate protein melt temperatures () and relative melt shifts from proteomics abundance data. Read More

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Testing repository safety assessment models for deep geological disposal using legacy contaminated sites.

Sci Total Environ 2021 Jul 18;776:145949. Epub 2021 Feb 18.

McKinley Consulting, Badstrasse 20B, 5408 Ennetbaden, Switzerland.

An important property of locations selected to host deep geological repositories for higher level radioactive wastes is their capacity to retard the movement of any radionuclides released from engineered barriers. Site characterization cannot measure this characteristic directly and hence models form the essential link between field observations and supporting laboratory rock/water/radionuclide interaction studies. However, residual uncertainties always remain, associated with the complexity of radionuclide interactions in natural environments and the extrapolations in time and space that are included in safety assessments. Read More

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sRNAanno-a database repository of uniformly annotated small RNAs in plants.

Hortic Res 2021 Mar 1;8(1):45. Epub 2021 Mar 1.

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.

Small RNAs (sRNAs) are essential regulatory molecules, and there are three major sRNA classes in plants: microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Excluding miRNAs, the other two classes are not well annotated or available in public databases for most sequenced plant genomes. We performed a comprehensive sRNA annotation of 143 plant species that have fully sequenced genomes and next-generation sequencing sRNA data publicly available. Read More

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Experience of outreach in a resource-constrained environment: 10 years of outcomes in burn care.

Burns 2021 Feb 9. Epub 2021 Feb 9.

Medicover Group, Lviv, Ukraine.

Objective: The objective of this work was to describe an efficient and sustainable outreach model in a resource-constrained environment, with a multifaceted approach focusing on national policy change, telemedicine, injury prevention, education and treatment of burns.

Summary Background Data: Burn injury constitutes a significant portion of morbidity and mortality worldwide, particularly in children, and in low- and middle-income countries.

Methods: We reviewed the impact of ten-years of a burn outreach program. Read More

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February 2021