11,701 results match your criteria repository primary


IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.

Extremophiles 2021 May 7. Epub 2021 May 7.

Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Room no. 508, SRM Nagar, Kattankulathur, 603203, Kanchipuram, TN, India.

Biocatalysts provide many advantages over the traditional chemically assisted processes prevalent in industries. Consequently, the search for novel enzymes has increased over the years with a renewed interest in thermophilic and psychrophilic bacterial species. Enzymes or extremozymes extracted from such species have exhibited an affinity to extreme temperatures which is a prerequisite for many industrial applications. Read More

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VisuaLife: Library for interactive visualization in rich web applications.

Bioinformatics 2021 May 7. Epub 2021 May 7.

Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.

Motivation: Visualization is a powerful tool to analyze, understand and present big data. Computational biology, bioinformatics, and molecular modeling require dedicated tools, tailored to very complex, highly multidimensional data. Over the recent years, numerous tools have been developed for online presentation, but new challenges like the COVID-19 pandemic require new libraries which will guarantee fast development of online tools for a better understanding of biomedical data/results. Read More

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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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ESCCABase project: A repository in progress.

Cytometry A 2021 May 7. Epub 2021 May 7.

Dipartimento di Scienze Biomolecolari, Università di Urbino, Urbino, Italy.

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Core-Symptom-Defined Cortical Gyrification Differences in Autism Spectrum Disorder.

Front Psychiatry 2021 20;12:619367. Epub 2021 Apr 20.

Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China.

Autism spectrum disorder (ASD) is a heterogeneous disease that is characterized by abnormalities in social communication and interaction as well as repetitive behaviors and restricted interests. Structural brain imaging has identified significant cortical folding alterations in ASD; however, relatively less known is whether the core symptoms are related to neuroanatomical differences. In this study, we aimed to explore core-symptom-anchored gyrification alterations and their developmental trajectories in ASD. Read More

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Current Challenges and Future Possibilities for Immunization Information Systems.

Acad Pediatr 2021 May-Jun;21(4S):S57-S64

American Immunization Registry Association (R Coyle, MB Kurilo, and E Abbott), Washington, DC.

Immunizations have proven to be an important tool for public health and for reducing the impact of vaccine preventable diseases. To realize the maximum benefits of immunizations, a coordinated effort between public policy, health care providers and health systems is required to increase vaccination coverage and to ensure high-quality data are available to inform clinical and public health interventions. Immunization information systems (IIS) are confidential, population-based, computerized databases that record all immunization doses administered by participating providers to persons residing within a given geopolitical area. Read More

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Feasibility and preliminary data for a State-wide South Carolina Lupus Registry.

Lupus 2021 May 6:9612033211014591. Epub 2021 May 6.

Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.

Background: Systemic lupus erythematosus (SLE) or lupus is an autoimmune disorder whose cause and reason for disproportionate impact on minorities remains enigmatic. Furthermore, statistics describing lupus incidence and prevalence are outdated and often based on small samples. To begin to address this disparity this report describes preliminary data to be utilized in the development of a state-wide lupus registry in South Carolina. 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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Structural Genomics and the Protein Data Bank.

J Biol Chem 2021 May 3:100747. Epub 2021 May 3.

Center for Structural Genomics of Infectious Diseases, University of Chicago, USA; Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, USA; Department of Biochemistry and Molecular Biology, University of Chicago, USA. Electronic address:

The field of Structural Genomics arose over the last three decades to address a large and rapidly growing divergence between microbial genomic, functional, and structural data. Several international programs took advantage of the vast genomic sequence information and evaluated the feasibility of structure determination for expanded and newly discovered protein families. As a consequence, structural genomics has developed structure-determination pipelines and applied them to a wide range of novel, uncharacterized proteins, often from "microbial dark matter", and later to proteins from human pathogens. Read More

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TCGA-TCIA-Based CT Radiomics Study for Noninvasively Predicting Epstein-Barr Virus Status in Gastric Cancer.

AJR Am J Roentgenol 2021 May 6:1-11. Epub 2021 May 6.

Department of Radiology, The First Affiliated Hospital of Zhengzhou University, No. 1, E Jianshe Rd, Zhengzhou 450052, China.

The purpose of this study was to investigate the value of TCGA-TCIA (The Cancer Genome Atlas and The Cancer Imaging Archive)-based CT radiomics for noninvasive prediction of Epstein-Barr virus (EBV) status in gastric cancer (GC). A total of 133 patients with pathologically confirmed GC (94 in the training cohort and 39 in the validation cohort) who were identified from the TCGA-TCIA public data repository and two hospitals were retrospectively enrolled in the study. Two-dimensional and 3D radiomics features were extracted to construct corresponding radiomics signatures. Read More

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Current and future deep learning algorithms for MS/MS-based small molecule structure elucidation.

Rapid Commun Mass Spectrom 2021 May 6:e9120. Epub 2021 May 6.

Janssen Research & Development, Beerse, Belgium.

Rationale: Structure elucidation of small molecules has been one of the cornerstone applications of mass spectrometry for decades. Despite the increasing availability of software tools, structure elucidation from MS/MS data remains a challenging task, leaving many spectra unidentified. However, as an increasing number of reference MS/MS spectra are being curated at a repository scale and shared on public servers, there is an exciting opportunity to develop powerful new deep learning (DL) models for automated structure elucidation. Read More

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The protective role of PHB and its degradation products against stress situations in bacteria.

FEMS Microbiol Rev 2021 May;45(3)

Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, P.O. Box 3000, FI-90014 Oulu, Finland.

Many bacteria produce storage biopolymers that are mobilized under conditions of metabolic adaptation, for example, low nutrient availability and cellular stress. Polyhydroxyalkanoates are often found as carbon storage in Bacteria or Archaea, and of these polyhydroxybutyrate (PHB) is the most frequently occurring PHA type. Bacteria usually produce PHB upon availability of a carbon source and limitation of another essential nutrient. Read More

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Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant.

Sci Rep 2021 May 5;11(1):9586. Epub 2021 May 5.

Matís, Reykjavík, Iceland.

Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. Read More

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Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy.

J Am Soc Nephrol 2021 May 5. Epub 2021 May 5.

Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts

Background: Identification of target antigens PLA2R, THSD7A, NELL1, or Semaphorin-3B can explain the majority of cases of primary membranous nephropathy (MN). However, target antigens remain unidentified in 15%-20% of patients.

Methods: A multipronged approach, using traditional and modern technologies, converged on a novel target antigen, and capitalized on the temporal variation in autoantibody titer for biomarker discovery. Read More

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-A psychoanalytic interpretation including some remarks on the psychosocial function of modern TV series.

Int J Psychoanal 2018 Aug 6;99(4):1004-1016. Epub 2018 Jul 6.

Institute of Psychosocial Intervention, Faculty of Educational Sciences, University of Innsbruck, Innsbruck, Austria.

Cultural products such as films or TV series can be understood as articulations of socio-political fantasies that contain conscious and unconscious elements. At first glance, , a fierce medieval show full of violence and sex, appears to offer hardly any topical references. Psychoanalytic examination, which unveils the series from its unmistakable vesture, reveals essential elements and their relations that bear remarkable parallels to prevailing socio-political fantasies. Read More

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Preliminary report on SARS-CoV-2 Spike mutation T478K.

J Med Virol 2021 May 5. Epub 2021 May 5.

Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40138, Bologna, Italy.

Several SARS-CoV-2 variants have emerged, posing a renewed threat to COVID-19 containment and to vaccine and drug efficacy. In this study, we analyzed more than 1,000,000 SARS-CoV-2 genomic sequences deposited up to April 27, 2021 on the GISAID public repository, and identified a novel T478K mutation located on the SARS-CoV-2 Spike protein. The mutation is structurally located in the region of interaction with human receptor ACE2 and was detected in 11,435 distinct cases. Read More

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Personalized analytics and wearable biosensor platform for early detection of COVID-19 decompensation (DeCODe: Detection of COVID-19 Decompensation): protocol for development of COVID-19 Decompensation Index.

JMIR Res Protoc 2021 May 4. Epub 2021 May 4.

University of Illinois Health, Chicago, US.

Background: During the COVID-19 pandemic, novel digital health technologies have the potential to improve our understanding of SARS Co-V2/ COVID-19, improve care delivery and produce better health outcomes. The National Institutes of Health called on digital health leaders to contribute to a high-quality data repository that will support the work of researchers to make discoveries not possible through small, limited data sets.

Objective: To this end, we seek to develop a COVID-19 digital biomarker that could provide early detection of a patient's physiologic worsening or decompensation. Read More

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Antivirals virtual screening to SARS-CoV-2 non-structural proteins.

J Biomol Struct Dyn 2021 May 5:1-15. Epub 2021 May 5.

NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brasil.

In March 2020, the World Health Organization (WHO) declared coronavirus disease-19 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a pandemic. Since then, the search for a vaccine or drug for COVID-19 treatment has started worldwide. In this regard, a fast approach is the repurposing of drugs, primarily antiviral drugs. Read More

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A database of global storm surge reconstructions.

Sci Data 2021 05 4;8(1):125. Epub 2021 May 4.

Civil, Environmental, and Construction Engineering & National Center for Integrated Coastal Research, University of Central Florida, Orlando, USA.

Storm surges are among the deadliest coastal hazards and understanding how they have been affected by climate change and variability in the past is crucial to prepare for the future. However, tide gauge records are often too short to assess trends and perform robust statistical analyses. Here we use a data-driven modeling framework to simulate daily maximum surge values at 882 tide gauge locations across the globe. Read More

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Natural History of Afferent Baroreflex Failure in Adults.

Neurology 2021 May 4. Epub 2021 May 4.

Department of Neurology, Mayo Clinic, Rochester, MN

Objective: To describe the natural history of afferent baroreflex failure (ABF) based on systematic review of clinical and laboratory data in patients with a diagnosis of ABF at Mayo Clinic Rochester.

Methods: We performed a retrospective chart review of all patients who underwent standardized autonomic reflex testing between 2000 and 2020 and had confirmation of the diagnosis of ABF by an autonomic disorders specialist. Patients were identified using a data repository of medical records. Read More

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SERUM GLP-2 is Increased in Association with Excess Gestational Weight Gain.

Am J Perinatol 2021 May 3. Epub 2021 May 3.

Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas.

Objective:  Obesity in pregnancy bears unique maternal and fetal risks. Obesity has also been associated with chronic inflammation, including elevated serum levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). Higher serum lipopolysaccharide (LPS) levels have been implicated in driving this inflammation, a phenomenon called metabolic endotoxemia (ME). Read More

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Proteomic Profiling of Leukocytes Reveals Dysregulation of Adhesion and Integrin Proteins in Chronic Kidney Disease-Related Atherosclerosis.

J Proteome Res 2021 May 3. Epub 2021 May 3.

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

A progressive loss of functional nephrons defines chronic kidney disease (CKD). Complications related to cardiovascular disease (CVD) are the principal causes of mortality in CKD; however, the acceleration of CVD in CKD remains unresolved. Our study used a complementary proteomic approach to assess mild and advanced CKD patients with different atherosclerosis stages and two groups of patients with different classical CVD progression but without renal dysfunction. Read More

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Patients with Autoimmune Hepatitis Report Lower Lifetime Coffee Consumption.

Dig Dis Sci 2021 Apr 30. Epub 2021 Apr 30.

Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, MN, USA.

Background: Coffee drinking has been associated with decreased risk of some autoimmune diseases as well liver disease and outcomes. Environmental factors, such as coffee consumption, are yet to be assessed among patients with autoimmune hepatitis (AIH).

Aim: We sought to investigate the relationship between coffee consumption and risk of AIH utilizing the Genetic Repository of Autoimmune Liver Disease and Contributing Exposures (GRACE) database. Read More

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Association Between Income Inequality and County-Level COVID-19 Cases and Deaths in the US.

JAMA Netw Open 2021 05 3;4(5):e218799. Epub 2021 May 3.

Department of Epidemiology and Population Health, Stanford University, Stanford, California.

Importance: Socioeconomically marginalized communities have been disproportionately affected by the COVID-19 pandemic. Income inequality may be a risk factor for SARS-CoV-2 infection and death from COVID-19.

Objective: To evaluate the association between county-level income inequality and COVID-19 cases and deaths from March 2020 through February 2021 in bimonthly time epochs. Read More

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Compilation of data on model cheeses composition, rheological and sensory properties, from six research projects exported from the BaGaTel database.

Data Brief 2021 Jun 31;36:106971. Epub 2021 Mar 31.

Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000 Dijon, France.

This paper presents data on model cheeses extracted from the BaGaTel database. The data are issued from 6 different research projects in which data on composition, rheological and sensory properties were collected. The manufacturing of the 68 different samples is described. Read More

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Human Cytomegalovirus Genome Diversity in Longitudinally Collected Breast Milk Samples.

Front Cell Infect Microbiol 2021 16;11:664247. Epub 2021 Apr 16.

Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany.

Reactivation and shedding of human cytomegalovirus (HCMV) in breast milk during lactation is highly frequent in HCMV-seropositive mothers. This represents a key transmission route for postnatal HCMV infection and can lead to severe disease in preterm neonates. Little is known about HCMV strain composition or longitudinal intrahost viral population dynamics in breast milk from immunocompetent women. Read More

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Genome wide identification, phylogeny, and synteny analysis of family in common carp ().

Biotechnol Rep (Amst) 2021 Jun 16;30:e00607. Epub 2021 Mar 16.

Division of Fish Genetics and Biotechnology, Fauclty of Fisheries Rangil, Ganderbal, SKUAST-Kashmir, India.

Common carp () is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. Read More

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Privacy-Preserving Methods for Vertically Partitioned Incomplete Data.

AMIA Annu Symp Proc 2020 25;2020:348-357. Epub 2021 Jan 25.

University of Pennsylvania, Philadelphia, PA, USA.

Distributed health data networks that use information from multiple sources have drawn substantial interest in recent years. However, missing data are prevalent in such networks and present significant analytical challenges. The current state-of-the-art methods for handling missing data require pooling data into a central repository before analysis, which may not be possible in a distributed health data network. Read More

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January 2021

Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique.

Biodivers Data J 2021 21;9:e64461. Epub 2021 Apr 21.

Natural History Museum of Maputo, Maputo, Mozambique Natural History Museum of Maputo Maputo Mozambique.

Background: The collections of the Natural History Museum of Maputo have a crucial role in the safeguarding of Mozambique's biodiversity, representing an important repository of data and materials regarding the natural heritage of the country. In this paper, a dataset is described, based on the Museum's Entomological Collection recording 409 species belonging to seven orders and 48 families. Each specimen's available data, such as geographical coordinates and taxonomic information, have been digitised to build the dataset. Read More

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The sharing of research data facing the COVID-19 pandemic.

Scientometrics 2021 Apr 26:1-16. Epub 2021 Apr 26.

UISYS, Joint Research Unit CSIC-University of Valencia, Pza. Cisneros 4, 46003 Valencia, Spain.

During the previous Ebola and Zika outbreaks, researchers shared their data, allowing many published epidemiological studies to be produced only from open research data, to speed up investigations and control of these infections. This study aims to evaluate the dissemination of the COVID-19 research data underlying scientific publications. Analysis of COVID-19 publications from December 1, 2019, to April 30, 2020, was conducted through the PubMed Central repository to evaluate the research data available through its publication as supplementary material or deposited in repositories. Read More

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