2,120 results match your criteria recovered sampled


Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence.

bioRxiv 2021 Apr 29. Epub 2021 Apr 29.

CD8+ T cells are important antiviral effectors that can potentiate long-lived immunity against COVID-19, but a detailed characterization of these cells has been hampered by technical challenges. We screened 21 well-characterized, longitudinally-sampled convalescent donors that recovered from mild COVID-19 against a collection of SARS-CoV-2 tetramers, and identified one participant with an immunodominant response against Nuc , a peptide that is conserved in all the SARS-CoV-2 variants-of-concern reported to date. We conducted 38- parameter CyTOF phenotyping on tetramer-identified Nuc -specific CD8+ T cells, and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins from SARS- CoV-2, and took 32 serological measurements on longitudinal specimens from this participant. Read More

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Compositional and functional responses of bacterial community to titanium dioxide nanoparticles varied with soil heterogeneity and exposure duration.

Sci Total Environ 2021 Jun 4;773:144895. Epub 2021 Feb 4.

Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA Leiden, the Netherlands.

Titanium dioxide nanoparticles (TiO NPs) are widely used as nano-agrochemicals. In this study we investigated the influence of soil heterogeneity on bacterial communities exposed to TiO NPs over time. Clay and sandy soils with low- and high-organic matter contents were exposed to environmentally relevant concentration of TiO NPs (1 mg/kg) and soil bacterial communities were sampled after short-term (15 days) and long-term exposure (60 days). Read More

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The first report of Meloidogyne enterolobii on Thai basil in Florida, United States.

Plant Dis 2021 Apr 29. Epub 2021 Apr 29.

University of Florida, Entomology and Nematology, Gulf Coast Research and Education Center, 14625 CR672, Wimauma, Florida, United States, 33598;

Thai basil (Ocimum basilicum var. thyrsiflora) is an important ethnic aromatic herb native to Southeast Asia. According to the Vegetable Production Handbook of Florida 2020-2021, Asian vegetables are currently grown on more than 4,000 ha in Florida, and Thai basil is one of the most commonly grown among these. Read More

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New World Cactaceae Plants Harbor Diverse Geminiviruses.

Viruses 2021 04 16;13(4). Epub 2021 Apr 16.

The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA.

The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Read More

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The effect of vegetation barriers at reducing the transmission of Salmonella and Escherichia coli from animal operations to fresh produce.

Int J Food Microbiol 2021 Apr 14;347:109196. Epub 2021 Apr 14.

Department of Population Health & Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA. Electronic address:

Due to the recent outbreaks of Salmonella and Escherichia coli in fresh produce in the United States, the transfer of foodborne pathogens between animal feeding operations and fresh produce continues to be a considerable risk. The purpose of this study was to determine if the establishment of a vegetation barrier (VB) on small-scale sustainable farms could prevent the transmission of Salmonella and E. coli to nearby fresh produce fields. Read More

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A rapid change in microbial communities of the shale gas drilling fluid from 3548 m depth to the above-ground storage tank.

Sci Total Environ 2021 Apr 10;784:147009. Epub 2021 Apr 10.

State Key Laboratory of Petroleum Resources and Prospecting, Beijing Key Laboratory of Petroleum Pollution and Control, Research Centre for Geomicrobial Resources and Application, Institute of Unconventional Oil and Gas Science and Technology, College of Geosciences, China University of Petroleum, Beijing 102249, China; China Petroleum & Chemical Corporation, Beijing 100728, China. Electronic address:

Despite the growing body of studies on the various fracturing phrases, the research on the differences between subterranean and surface microorganisms at shale gas drilling sites is still limited. Generally, shale gas development and the production process are divided into drilling and fracturing. The distribution of microbial communities in the latter has been paid some attention, but a deficit remains in terms of our understanding of the microbial community in the former, especially for the phase of drilling flowback and drilling flowback surface. Read More

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Suitability of specific soft tissue swabs for the forensic identification of highly decomposed bodies.

Int J Legal Med 2021 Apr 20. Epub 2021 Apr 20.

Department of Forensic Medicine and Forensic Neuropsychiatry, University of Salzburg, Salzburg, Austria.

When decomposition of a recovered body is fairly advanced, identification based on common morphologic features is often impossible. In these cases, short tandem repeat (STR) marker genotyping has established itself as a convenient and reliable alternative. However, at very progressed stages of decomposition, postmortem tissue putrefaction processes can decrease DNA yields considerably. Read More

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eDNA as a tool for non-invasive monitoring of the fauna of a turbid, well-mixed system, the Elbe estuary in Germany.

PLoS One 2021 16;16(4):e0250452. Epub 2021 Apr 16.

Center of Natural History, Universität Hamburg, Hamburg, Germany.

The Elbe is one of the longest European rivers and features a large, turbid and well-mixed estuary, which runs through the inner city of Hamburg. The Elbe has been closely monitored using classical catch techniques in the past. Here we tested a COI-based eDNA approach for assessing the biodiversity within the Elbe. Read More

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Characterization of staphylococci sampled from diabetic foot ulcer of Jordanian patients.

J Appl Microbiol 2021 Apr 4. Epub 2021 Apr 4.

Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.

Aims: The aim of this study was to isolate and characterize staphylococcal isolates from diabetic foot ulcers (DFU) in Jordanian patients.

Methods And Results: Selected aerobic pathogens recovered from DFU specimens and patients' nares with a focus on staphylococci were investigated. Antimicrobial susceptibilities and the prevalence of methicillin-resistant staphylococci (MRS) were determined. Read More

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Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan.

Viruses 2021 03 31;13(4). Epub 2021 Mar 31.

Virus Ecology Section, Laboratory of Virology, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA.

Middle East respiratory syndrome-related coronavirus (MERS-CoV) is a persistent zoonotic pathogen with frequent spillover from dromedary camels to humans in the Arabian Peninsula, resulting in limited outbreaks of MERS with a high case-fatality rate. Full genome sequence data from camel-derived MERS-CoV variants show diverse lineages circulating in domestic camels with frequent recombination. More than 90% of the available full MERS-CoV genome sequences derived from camels are from just two countries, the Kingdom of Saudi Arabia (KSA) and United Arab Emirates (UAE). Read More

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T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity.

medRxiv 2021 Mar 22. Epub 2021 Mar 22.

Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Read More

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Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China.

Food Res Int 2021 Apr 5;142:110198. Epub 2021 Feb 5.

Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China; Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Sanya, China. Electronic address:

Salmonella is a major foodborne pathogen worldwide, causing serious cases of morbidity and mortality due to the consumption of contaminated foods. Animal-borne foods were considered the main source of transferring Salmonella to humans; however, route surveillance by genomic platforms along the food-chain is limited in China. Here, we proceeded to the application of whole genome sequencing in the epidemiological analysis of Salmonella isolated along the food-chain in Xinjiang, China. Read More

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Prevalence and Host Specificity of Bat Flies (Streblidae) from Selected Caves in Unisan, Quezon, Philippines.

Acta Parasitol 2021 Mar 26. Epub 2021 Mar 26.

Mathematics and Natural Sciences Department, College of Arts and Sciences, Southern Luzon State University, 4328, Lucban, Quezon, Philippines.

Purpose: Bats belong to different guilds and thus differ in the environmental resources that they exploit. They also evolved to have a very rich diversity of roosting and feeding habits. Therefore, it enables them to harbor different species of parasites that could be zoonotic and may pose public health importance. Read More

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution.

Sci Rep 2021 Mar 25;11(1):6858. Epub 2021 Mar 25.

Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia.

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Read More

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Characterizing the COVID-19 illness experience to inform the study of post-acute sequalae and recovery: a qualitative study.

medRxiv 2021 Mar 12. Epub 2021 Mar 12.

We aimed to characterize the variability in the illness experience and recovery process from COVID-19. We conducted in-depth individual interviews with participants enrolled in the Long-term Immunological Impact of Novel Coronavirus (LIINC) cohort study in San Francisco, California from June through October of 2020. Participants were adults who had a previously confirmed positive SARV-CoV-2 nucleic acid amplification test result, had recovered or were recovering from acute infection, and underwent serial evaluations at our clinical research center. Read More

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Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids.

Virol J 2021 Mar 22;18(1):61. Epub 2021 Mar 22.

Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.

Background: High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount.

Methods: Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Read More

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Passive Sampling and Dosing of Aquatic Organic Contaminant Mixtures for Ecotoxicological Analyses.

Environ Sci Technol 2021 Mar 22. Epub 2021 Mar 22.

Environmental Safety Group, KIST Europe, Korea Institute of Science and Technology, Campus E 7.1, Saarbrücken, Germany.

Toxicity results from exposure to mixtures of organic contaminants. Assessing this using ecotoxicity bioassays involves sampling of the environmental mixture and then introducing this into the test. The first step is accounting for the bioavailable levels of all mixture constituents. Read More

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Plasma cholesterol levels and short-term adaptations of metabolism and milk production during feed restriction in early lactating dairy cows on pasture.

J Anim Physiol Anim Nutr (Berl) 2021 Mar 16. Epub 2021 Mar 16.

Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

Low plasma total cholesterol (TC) concentrations are characteristic during the negative energy balance in early lactating dairy cows. The objective was to investigate short-term effects of different TC concentrations during an aggravated energy deficiency through a 1-week concentrate withdrawal on adaptations of metabolism and milk production. Multiparous Holstein cows (n = 15) were investigated during 3 week beginning at 24 ± 7 DIM (mean ± SD). Read More

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Influence of Schirmer strip wetness on volume absorbed, volume recovered, and total protein content in canine tears.

Vet Ophthalmol 2021 Mar 15. Epub 2021 Mar 15.

Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.

Objective: Determine the protein content and volume of tears sampled by Schirmer strips wetness ranging from 20 to 35 mm.

Animals Studied: Ten healthy beagle dogs.

Procedures: Each dog underwent 20 tear collections per day (10 sessions in each eye, spaced by ≥1 h) for 4 separate days, providing 200 tear samples for each length of wetness evaluated: 20, 25, 30, and 35 mm. Read More

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Annelids of the eastern Australian abyss collected by the 2017 RV 'Investigator' voyage.

Zookeys 2021 24;1020:1-198. Epub 2021 Feb 24.

South China Sea Environmental Monitoring Centre, State Oceanic Administration, Guangzhou, China.

In Australia, the deep-water (bathyal and abyssal) benthic invertebrate fauna is poorly known in comparison with that of shallow (subtidal and shelf) habitats. Benthic fauna from the deep eastern Australian margin was sampled systematically for the first time during 2017 RV 'Investigator' voyage 'Sampling the Abyss'. Box core, Brenke sledge, and beam trawl samples were collected at one-degree intervals from Tasmania, 42°S, to southern Queensland, 24°S, from 900 to 4800 m depth. Read More

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February 2021

The Perceptions and Views of Rural Residents Towards COVID-19 Recovered Patients in China: A Descriptive Qualitative Study.

Int J Gen Med 2021 2;14:709-720. Epub 2021 Mar 2.

Zhejiang University School of Medicine, Affiliated Sir Run Run Shaw Hospital, Hangzhou, Zhejiang, People's Republic of China.

Introduction: With the effective treatments of novel coronavirus disease 2019 (COVID-19), thousands of patients have recovered from COVID-19 globally. The public perceptions and views are vital to facilitate recovered COVID-19 patients reintegrate into society. In China, the rural population accounts for nearly 70% of the total population. Read More

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Disease Surveillance during the Reintroduction of the Iberian Lynx () in Southwestern Spain.

Animals (Basel) 2021 Feb 19;11(2). Epub 2021 Feb 19.

Instituto de Investigación en Recursos Cinegéticos-(CSIC-UCLM-JCCM), 13071 Ciudad Real, Spain.

The restoration of Iberian lynx () populations in Extremadura (Southwestern Spain) have been carried out since 2014. One of the measures to ensure the success of this program is to examine the effects that diseases may have on reintroduction. Since diseases may be greatly located at certain sites because of the specific ecological requirements of the pathogens and/or vectors, reintroduced individuals may present a risk of infection once released. Read More

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February 2021

Thyroid nocardiosis: Case report and review of the literature.

Transpl Infect Dis 2021 Mar 1:e13594. Epub 2021 Mar 1.

AP-HP, Service de maladies infectieuses et tropicales, CHU Bicêtre, Le Kremlin-Bicêtre, France.

Disseminated nocardiosis is a rare but growing concern in immunocompromised patients. Typical localizations include the lung, brain and/or soft tissues, but laboratory confirmation of nocardiosis usually requires sampling of infected organs by invasive procedures such as bronchoalveolar lavage or brain biopsy. We report a case of disseminated nocardiosis occurring in a hematopoietic stem-cell transplant recipient, with clinical lung and brain localizations. Read More

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Genetic diversity analysis of Dermacentor nuttalli within Inner Mongolia, China.

Parasit Vectors 2021 Mar 1;14(1):131. Epub 2021 Mar 1.

Inner Mongolia Center for Disease Control and Prevention, Hohhot, 010000, Inner Mongolia, China.

Background: Ticks (Arthropoda, Ixodida), after mosquitoes, are the second most prevalent vector of infectious diseases. They are responsible for spreading a multitude of pathogens and threatening the health and welfare of animals and human beings. However, given the history of tick-borne pathogen infections in the Inner Mongolia Autonomous Region of China, surprisingly, neither the genetic diversity nor the spatial distribution of haplotypes within ticks has been studied. Read More

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Chromosome Classification and Straightening Based on an Interleaved and Multi-task Network.

IEEE J Biomed Health Inform 2021 Feb 25;PP. Epub 2021 Feb 25.

Karyotyping is the gold standard in the detection of chromosomal abnormalities. To facilitate the diagnostic process, in this paper, a method for chromosome classification and straightening based on an interleaved and multi-task network is proposed. This method consists of three stages. Read More

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February 2021

Limited window for donation of convalescent plasma with high live-virus neutralizing antibody titers for COVID-19 immunotherapy.

Commun Biol 2021 02 24;4(1):267. Epub 2021 Feb 24.

Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.

Millions of individuals who have recovered from SARS-CoV-2 infection may be eligible to participate in convalescent plasma donor programs, yet the optimal window for donating high neutralizing titer convalescent plasma for COVID-19 immunotherapy remains unknown. Here we studied the response trajectories of antibodies directed to the SARS-CoV-2 surface spike glycoprotein and in vitro SARS-CoV-2 live virus neutralizing titers (VN) in 175 convalescent donors longitudinally sampled for up to 142 days post onset of symptoms (DPO). We observed robust IgM, IgG, and viral neutralization responses to SARS-CoV-2 that persist, in the aggregate, for at least 100 DPO. Read More

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February 2021

Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones.

Int J Legal Med 2021 Feb 24. Epub 2021 Feb 24.

Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.

DNA analysis of Second World War skeletal remains is challenging because of the limited yield of DNA that is usually recovered. Recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA, and little focus has been placed on measuring intra-bone variability. Metatarsals and metacarpals outperformed all the other bones in DNA yield when analyzing all representative skeletal elements of three Second World War victims, and intra-bone variability was not studied. Read More

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February 2021

Plasmid-Borne and Chromosomal ESBL/AmpC Genes in and in Global Food Products.

Front Microbiol 2021 3;12:592291. Epub 2021 Feb 3.

Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.

Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular and , with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Read More

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February 2021

Positive no-touch surfaces and undetectable SARS-CoV-2 aerosols in long-term care facilities: An attempt to understand the contributing factors and the importance of timing in air sampling campaigns.

Am J Infect Control 2021 Feb 12. Epub 2021 Feb 12.

Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC, Canada; Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada; Canada Research Chair on Bioaerosols, Quebec city, QC, Canada. Electronic address:

Background: Long-term care facilities (LTCF) are environments particularly favorable to coronavirus disease (SARS-CoV-2) pandemic outbreaks, due to the at-risk population they welcome and the close proximity of residents. Yet, the transmission dynamics of the disease in these establishments remain unclear.

Methods: Air and no-touch surfaces of 31 rooms from 7 LTCFs were sampled and SARS-CoV-2 was quantified by real-time reverse transcription polymerase chain reaction (RT-qPCR). Read More

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February 2021

Tissue Harvesting Site Effect on the Canine Adipose Stromal Vascular Fraction Quantity and Quality.

Animals (Basel) 2021 Feb 9;11(2). Epub 2021 Feb 9.

Laboratory of Veterinary Surgery, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.

Mesenchymal stem cells (MSCs) constitute a great promise for regenerative therapy, but these cells are difficultly recovered in large amounts. A potent alternative is the stromal vascular fraction (SVF), non-cultured MSCs, separated from adipose tissue (AT). We aim to evaluate AT harvesting site effect on the SVF cells' quantity and quality in dogs. Read More

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February 2021