241 results match your criteria 6000 platform

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China.

Gut Pathog 2021 Oct 13;13(1):59. Epub 2021 Oct 13.

Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.

Background: To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.

Methods: Four Citrobacter spp. Read More

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October 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail.

Genomics Inform 2021 Sep 30;19(3):e32. Epub 2021 Sep 30.

Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Read More

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September 2021

May Measurement Month 2019: an analysis of blood pressure screening results from Australia.

Eur Heart J Suppl 2021 May 20;23(Suppl B):B18-B20. Epub 2021 May 20.

Dobney Hypertension Centre, Department of Medicine, Royal Perth Hospital/University of Western Australia, Level 3, MRF Building, Rear 50 Murray St, Perth, Western Australia 6000, Australia.

May Measurement Month (MMM) is an annual global blood pressure (BP) screening campaign aimed at obtaining standardized BP measurements and other relevant health information from members of the community to increase awareness of elevated BP and the associated risks. Adults (≥18 years) were recruited through opportunistic sampling across the various Australian states during May 2019. Three BP readings were recorded in a standardized manner for each participant, and data on lifestyle factors and comorbidities were collected. Read More

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Classifying the degree of exposure of customers to COVID-19 in the restaurant industry: A novel intuitionistic fuzzy set extension of the TOPSIS-Sort.

Appl Soft Comput 2021 Dec 21;113:107906. Epub 2021 Sep 21.

Center for Applied Mathematics and Operations Research, Cebu Technological University, Corner M.J. Cuenco Ave. & R. Palma St., Cebu City, 6000, Philippines.

Despite the rigid public safety protocols of the restaurant sector amid the COVID-19 pandemic in an effort to restart economic activities, customers do not feel secure eating at a sit-in restaurant, which is associated with prolonged restrictions on movement. As a mitigating initiative, holistically evaluating customers' perceived degree of exposure to COVID-19 in restaurants is deemed relevant in the design of mitigation measures. Such an agenda is associated with multiple attributes under decision-making uncertainty within the framework of multiple criteria sorting (MCS). Read More

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December 2021

The effect of framing and communicating COVID-19 vaccine side-effect risks on vaccine intentions for adults in the UK and the USA: A structured summary of a study protocol for a randomized controlled trial.

Trials 2021 Sep 6;22(1):592. Epub 2021 Sep 6.

Heidelberg Institute of Global Health, Heidelberg University, Heidelberg, Germany.

Objectives: Vaccine hesitancy is a major hurdle for stopping the COVID-19 pandemic. Recently, fear of vaccine side effects created widespread concern and paused global vaccination efforts. Many studies find that how medical risks are framed and communicated can influence individuals' perceptions and behavior, yet there is little evidence on how the communication of COVID-19 vaccine side-effect risks influences vaccine intentions. Read More

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September 2021

Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages.

BMC Genomics 2021 Sep 3;22(1):637. Epub 2021 Sep 3.

Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO, USA.

Background: The pond snail, Lymnaea stagnalis (L. stagnalis), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. Read More

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September 2021

A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism.

PeerJ 2021 18;9:e12034. Epub 2021 Aug 18.

Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, United States of America.

The Copepoda is a clade of pancrustaceans containing 14,485 species that are extremely varied in their morphology and lifestyle. Not only do copepods dominate marine plankton and sediment communities and make up a sizeable component of the freshwater plankton, but over 6,000 species are symbiotically associated with every major phylum of marine metazoans, mostly as parasites. Unfortunately, our understanding of copepod evolutionary relationships is relatively limited in part because of their extremely divergent morphology, sparse taxon sampling in molecular phylogenetic analyses, a reliance on only a handful of molecular markers, and little taxonomic overlap between phylogenetic studies. Read More

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First Report of Turnip Mosaic Virus in Peanut (Arachis hypogaea L.) in China.

Plant Dis 2021 Aug 29. Epub 2021 Aug 29.

Ningbo University, 47862, State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Fenghua Road 818, Ningbo, China, 315211;

Peanut (Arachis hypogaea L.) is an important source of edible oil in China but its yield and quality in agricultural production are affected by a number of diseases including those caused by viruses. The four viruses most commonly reported to affect the production of peanut worldwide are peanut stripe virus, cucumber mosaic virus, peanut stunt virus and peanut bud necrosis virus (Srinivasan et al. Read More

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Porous Ion Gel: A Versatile Ionotronic Sensory Platform for High-Performance, Wearable Ionoskins with Electrical and Optical Dual Output.

ACS Nano 2021 09 24;15(9):15132-15141. Epub 2021 Aug 24.

Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea.

The development of elastic ionic conductors offers opportunities to fabricate key wearable ionic components such as ionoskins that can perceive mechanical deformation. However, there is still plenty of room to overcome the trade-off between sensitivity and detectable range of previous systems and impart additional functionality. Here, we propose porous ion gels for high-performance, functional ionic sensory platforms. Read More

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September 2021

CRISPR-PN2: a flexible and genome-aware platform for diverse CRISPR experiments in parasitic nematodes.

Biotechniques 2021 Sep 23;71(3):495-498. Epub 2021 Aug 23.

Department of Biological Sciences, The George Washington University, Science & Engineering Hall, Suite 6000, 800 22nd St. NW, Washington, DC 20052, USA.

Parasitic nematodes represent a significant threat to human health, causing diseases of major socioeconomic importance worldwide. Central to controlling infections of parasitic nematodes is a more detailed molecular picture of host specificity, parasite activation and immune suppression. CRISPR technology holds huge potential for researchers in the field of parasitic nematology, as it provides a powerful genetic tool to dissect questions in parasite biology. Read More

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September 2021

Evaluation of drought resistance and transcriptome analysis for the identification of drought-responsive genes in Iris germanica.

Sci Rep 2021 08 11;11(1):16308. Epub 2021 Aug 11.

State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China.

Iris germanica, a species with very high ornamental value, exhibits the strongest drought resistance among the species in the genus Iris, but the molecular mechanism underlying its drought resistance has not been evaluated. To investigate the gene expression profile changes exhibited by high-drought-resistant I. germanica under drought stress, 10 cultivars with excellent characteristics were included in pot experiments under drought stress conditions, and the changes in the chlorophyll (Chl) content, plasma membrane relative permeability (RP), and superoxide dismutase (SOD), malondialdehyde (MDA), free proline (Pro), and soluble protein (SP) levels in leaves were compared among these cultivars. Read More

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Comprehensive Library Generation for Identification and Quantification of Endometrial Cancer Protein Biomarkers in Cervico-Vaginal Fluid.

Cancers (Basel) 2021 Jul 28;13(15). Epub 2021 Jul 28.

Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK.

Endometrial cancer is the most common gynaecological malignancy in high-income countries and its incidence is rising. Early detection, aided by highly sensitive and specific biomarkers, has the potential to improve outcomes as treatment can be provided when it is most likely to effect a cure. Sequential window acquisition of all theoretical mass spectra (SWATH-MS), an accurate and reproducible platform for analysing biological samples, offers a technological advance for biomarker discovery due to its reproducibility, sensitivity and potential for data re-interrogation. Read More

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A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.

PLoS Comput Biol 2021 Jul 2;17(7):e1009180. Epub 2021 Jul 2.

Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America.

Broad scale remote sensing promises to build forest inventories at unprecedented scales. A crucial step in this process is to associate sensor data into individual crowns. While dozens of crown detection algorithms have been proposed, their performance is typically not compared based on standard data or evaluation metrics. Read More

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Structural and Functional Impacts of Microbiota on and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea.

Microorganisms 2021 Jun 12;9(6). Epub 2021 Jun 12.

Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples ( = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Read More

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Characterization of the complete mitochondrial genome of , a wild saprobic mushroom in China.

Mitochondrial DNA B Resour 2021 Jun 14;6(7):1979-1981. Epub 2021 Jun 14.

College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China.

The Glistening Inkcap () is a wild saprobic mushroom in China. In this study, we assembled and annotated its complete mitochondrial genome using raw data sequenced through Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). The length of the . Read More

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First-Principles-Based Machine-Learning Molecular Dynamics for Crystalline Polymers with van der Waals Interactions.

J Phys Chem Lett 2021 Jul 24;12(25):6000-6006. Epub 2021 Jun 24.

Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea.

Machine-learning (ML) techniques have drawn an ever-increasing focus as they enable high-throughput screening and multiscale prediction of material properties. Especially, ML force fields (FFs) of quantum mechanical accuracy are expected to play a central role for the purpose. The construction of ML-FFs for polymers is, however, still in its infancy due to the formidable configurational space of its composing atoms. Read More

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e-CoVig: A Novel mHealth System for Remote Monitoring of Symptoms in COVID-19.

Sensors (Basel) 2021 May 13;21(10). Epub 2021 May 13.

Instituto Superior Técnico (IST), Av. Rovisco Pais n. 1, 1049-001 Lisboa, Portugal.

In 2019, a new virus, SARS-CoV-2, responsible for the COVID-19 disease, was discovered. Asymptomatic and mildly symptomatic patients were forced to quarantine and closely monitor their symptoms and vital signs, most of the time at home. This paper describes e-CoVig, a novel mHealth application, developed as an alternative to the current monitoring paradigm, where the patients are followed up by direct phone contact. Read More

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Biotin Interference in Assays for Thyroid Hormones, Thyrotropin and Thyroglobulin.

Thyroid 2021 08 26;31(8):1160-1170. Epub 2021 May 26.

MedStar Health Research Institute, MedStar Washington Hospital Center, Washington, District of Columbia, USA.

Biotin has been reported to interfere with several commonly used laboratory assays resulting in misleading values and possible erroneous diagnosis and treatment. This report describes a prospective study of possible biotin interference in thyroid-related laboratory assays, with a comparison of different commonly used assay platforms. Thirteen adult subjects (mean age 45 ± 13 years old) were administered biotin 10 mg/day for eight days. Read More

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Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus.

Sci Rep 2021 05 11;11(1):9987. Epub 2021 May 11.

National Center for Biotechnology,, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia.

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Read More

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The Illumina Sequencing Protocol and the NovaSeq 6000 System.

Methods Mol Biol 2021 ;2242:15-42

Department of Biology, University of Firenze, Firenze, Italy.

The NovaSeq 6000 is a sequencing platform from Illumina that enables the sequencing of short reads with an output up to 6 Tb. The NovaSeq 6000 uses the typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Read More

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Gynura japonica: A new host of Apple stem grooving virus and Chrysanthemum virus B in China.

Plant Dis 2021 Apr 28. Epub 2021 Apr 28.

Ningbo University, 47862, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo, Zhejiang, China;

Gynura japonica (Thunb.) Juel [Asteraceae; syn: G. segetum (Lour. Read More

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Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook.

Phytochemistry 2021 Jul 16;187:112772. Epub 2021 Apr 16.

Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India. Electronic address:

Fritillaria roylei Hook. is a critically endangered high altitude Himalayan medicinal plant species with rich source of pharmaceutically active structurally diverse steroidal alkaloids. Nevertheless, except few marker compounds, the chemistry of the plant remains unexplored. Read More

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Comparison between MGI and Illumina sequencing platforms for whole genome sequencing.

Genes Genomics 2021 Jul 17;43(7):713-724. Epub 2021 Apr 17.

Personalized Genomic Medicine Research Center, KRIBB, 34141, Daejeon, South Korea.

Background: Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencing instruments.

Objective: In this study, we compared the performance of the two platform's major sequencing instruments-Illumina's NovaSeq 6000 and MGI's MGISEQ-2000 and DNBSEQ-T7-to test whether the MGISEQ-2000 and DNBSEQ-T7 sequencing instruments are also suitable for whole genome sequencing. Read More

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Sequencing error profiles of Illumina sequencing instruments.

NAR Genom Bioinform 2021 Mar 27;3(1):lqab019. Epub 2021 Mar 27.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets. Read More

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From Turkey: First Report of KPC-3- and CTX-M-27-Producing Multidrug-Resistant ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations.

Microb Drug Resist 2021 Sep 31;27(9):1265-1270. Epub 2021 Mar 31.

Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gumushane University, Gümüşhane, Turkey.

The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant strain. Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Read More

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September 2021

Genomic and phylogenetic analysis of multidrug-resistant Achromobacter xylosoxidans ST273 strain MTYH1 co-carrying bla and bla recovered from a wound infection in China.

J Glob Antimicrob Resist 2021 06 22;25:110-113. Epub 2021 Mar 22.

Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, China. Electronic address:

Objectives: Achromobacter xylosoxidans is widely distributed in the environment and is increasingly recognised as a significant nosocomial pathogen in healthcare settings. However, the genomic and phylogenetic characteristics of this pathogen are not fully understood. Here we report the first genome sequence of a multidrug-resistant A. Read More

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Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases.

Clin Epigenetics 2021 03 22;13(1):60. Epub 2021 Mar 22.

The Framingham Heart Study, 73 Mt. Wayte Avenue, Framingham, MA, 01702, USA.

Background: DNA methylation is a key epigenetic modification that can directly affect gene regulation. DNA methylation is highly influenced by environmental factors such as cigarette smoking, which is causally related to chronic obstructive pulmonary disease (COPD) and lung cancer. To date, there have been few large-scale, combined analyses of DNA methylation and gene expression and their interrelations with lung diseases. Read More

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The complete chloroplast genome of a medical herb, Fisch. (Rosaceae), from Qinghai-Tibet Plateau in China.

Mitochondrial DNA B Resour 2021 Feb 8;6(2):349-350. Epub 2021 Feb 8.

The College of Biological Science, Qinghai Normal University, Xining, China.

Fisch. (Rosaceae) is one of the genuine medicinal materials in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of using Illumina NovaSeq 6000 platform. Read More

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February 2021

Inter-Patient Classification With Encoded Peripheral Pulse Series and Multi-Task Fusion CNN: Application in Type 2 Diabetes.

IEEE J Biomed Health Inform 2021 08 5;25(8):3130-3140. Epub 2021 Aug 5.

Diabetes mellitus, a chronic disease associated with elevated accumulation of glucose in the blood, is generally diagnosed through an invasive blood test such as oral glucose tolerance test (OGTT). An effective method is proposed to test type 2 diabetes using peripheral pulse waves, which can be measured fast, simply and inexpensively by a force sensor on the wrist over the radial artery. A self-designed pulse waves collection platform includes a wristband, force sensor, cuff, air tubes, and processing module. Read More

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