872 results match your criteria 977 sequence

Bacterial characteristics of carbapenem-resistant Enterobacteriaceae (CRE) colonized strains and their correlation with subsequent infection.

BMC Infect Dis 2021 Jul 2;21(1):638. Epub 2021 Jul 2.

Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Background: Searching the risk factors for carbapenem-resistant Enterobacteriaceae (CRE) infection is important in clinical practice. In the present study, we aim to investigate bacterial characteristics of colonizing strains and their correlation with subsequent CRE infection.

Methods: Between May 2018 and January 2019, patients hospitalized in the department of haematology and intensive care unit (ICU) were screened for CRE by rectal swabs and monitored for the outcome of infection. Read More

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Sensory Reactivity Phenotype in Phelan-McDermid Syndrome Is Distinct from Idiopathic ASD.

Genes (Basel) 2021 Jun 26;12(7). Epub 2021 Jun 26.

Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Phelan-McDermid syndrome (PMS) is one of the most common genetic forms of autism spectrum disorder (ASD). While sensory reactivity symptoms are widely reported in idiopathic ASD (iASD), few studies have examined sensory symptoms in PMS. The current study delineates the sensory reactivity phenotype and examines genotype-phenotype interactions in a large sample of children with PMS. Read More

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Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019.

Viruses 2021 May 25;13(6). Epub 2021 May 25.

Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand.

Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Read More

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Individualized Prediction of Early Alzheimer's Disease Based on Magnetic Resonance Imaging Radiomics, Clinical, and Laboratory Examinations: A 60-Month Follow-Up Study.

J Magn Reson Imaging 2021 May 13. Epub 2021 May 13.

Department of Radiology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.

Background: Accurately predicting whether and when mild cognitive impairment (MCI) will progress to Alzheimer's disease (AD) is of vital importance to help developing individualized treatment plans to defer the occurrence of irreversible dementia.

Purpose: To develop and validate radiomics models and multipredictor nomogram for predicting the time to progression (TTP) from MCI to AD.

Study Type: Retrospective. Read More

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Hemodynamic study of unenhanced magnetic resonance angiography using spatial labeling with multiple inversion pulses sequence: a phantom study.

Quant Imaging Med Surg 2021 May;11(5):1828-1835

Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Background: This study sought to explore the functional relationship between displayed vascular length and blood suppression inversion time (BSP TI) and flow velocity in a phantom, and to provide a theoretical basis for quantitatively assessing vascular hemodynamic responses using unenhanced magnetic resonance angiography (MRA) and spatial labeling with multiple inversion pulses sequence (SLEEK).

Methods: A polyethylene catheter was laid in a long rectangular container filled with pork fat. The entrance of the catheter into the container was connected to a high-pressure syringe filled with normal saline. Read More

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Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition.

Database (Oxford) 2021 Apr;2021

Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA.

High-quality metadata annotations for data hosted in large public repositories are essential for research reproducibility and for conducting fast, powerful and scalable meta-analyses. Currently, a majority of sequencing samples in the National Center for Biotechnology Information's Sequence Read Archive (SRA) are missing metadata across several categories. In an effort to improve the metadata coverage of these samples, we leveraged almost 44 million attribute-value pairs from SRA BioSample to train a scalable, recurrent neural network that predicts missing metadata via named entity recognition (NER). Read More

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Radiomics-based differentiation between glioblastoma and primary central nervous system lymphoma: a comparison of diagnostic performance across different MRI sequences and machine learning techniques.

Eur Radiol 2021 Apr 23. Epub 2021 Apr 23.

College of Engineering, University of Iowa, Iowa City, IA, USA.

Objectives: Despite the robust diagnostic performance of MRI-based radiomic features for differentiating between glioblastoma (GBM) and primary central nervous system lymphoma (PCNSL) reported on prior studies, the best sequence or a combination of sequences and model performance across various machine learning pipelines remain undefined. Herein, we compare the diagnostic performance of multiple radiomics-based models to differentiate GBM from PCNSL.

Methods: Our retrospective study included 94 patients (34 with PCNSL and 60 with GBM). Read More

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MSIFinder: a python package for detecting MSI status using random forest classifier.

BMC Bioinformatics 2021 Apr 12;22(1):185. Epub 2021 Apr 12.

Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, No. 88 Jiefang Road, Shangcheng District, Hangzhou, 310009, Zhejiang, China.

Background: Microsatellite instability (MSI) is a common genomic alteration in colorectal cancer, endometrial carcinoma, and other solid tumors. MSI is characterized by a high degree of polymorphism in microsatellite lengths owing to the deficiency in the mismatch repair system. Based on the degree, MSI can be classified as microsatellite instability-high (MSI-H) and microsatellite stable (MSS). Read More

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Voxel-level Classification of Prostate Cancer on Magnetic Resonance Imaging: Improving Accuracy Using Four-Compartment Restriction Spectrum Imaging.

J Magn Reson Imaging 2021 Mar 31. Epub 2021 Mar 31.

Department of Radiation Medicine and Applied Sciences, UC San Diego School of Medicine, La Jolla, California, USA.

Background: Diffusion magnetic resonance imaging (MRI) is integral to detection of prostate cancer (PCa), but conventional apparent diffusion coefficient (ADC) cannot capture the complexity of prostate tissues and tends to yield noisy images that do not distinctly highlight cancer. A four-compartment restriction spectrum imaging (RSI ) model was recently found to optimally characterize pelvic diffusion signals, and the model coefficient for the slowest diffusion compartment, RSI -C , yielded greatest tumor conspicuity.

Purpose: To evaluate the slowest diffusion compartment of a four-compartment spectrum imaging model (RSI -C ) as a quantitative voxel-level classifier of PCa. Read More

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Severity of Airway Obstruction May Not Correlate With Weight Gain or Failure to Thrive in Infants With Robin Sequence: A Pilot Study.

J Craniofac Surg 2021 Mar 22. Epub 2021 Mar 22.

Division of Plastic and Reconstructive Surgery, Children's National Hospital Joseph E. Robert, Jr., Center for Surgical Care, Children's National Hospital, Washington, DC.

Objective: Patients with Robin sequence (RS) can present with varying degrees of upper airway obstruction, difficulty maintaining adequate weight gain, and failure to thrive (FTT). Although inductive reasoning would suggest that these issues should be interrelated, the relationships between these factors have not been formally studied. This investigation explores the correlation between polysomnographic (PSG) findings, weight gain, and FTT in patients with RS. Read More

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Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil.

Sci Rep 2021 Mar 23;11(1):6695. Epub 2021 Mar 23.

Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea.

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1 was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1 formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. Read More

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Homozygous variant in MADD, encoding a Rab guanine nucleotide exchange factor, results in pleiotropic effects and a multisystemic disorder.

Eur J Hum Genet 2021 Jun 15;29(6):977-987. Epub 2021 Mar 15.

Department of Genetics, Hadassah Medical Center, Jerusalem, Israel.

Rab proteins coordinate inter-organellar vesicle-mediated transport, facilitating intracellular communication, protein recycling, and signaling processes. Dysfunction of Rab proteins or their direct interactors leads to a wide range of diseases with diverse manifestations. We describe seven individuals from four consanguineous Arab Muslim families with an infantile-lethal syndrome, including failure to thrive (FTT), chronic diarrhea, neonatal respiratory distress, variable pituitary dysfunction, and distal arthrogryposis. Read More

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tRFTars: predicting the targets of tRNA-derived fragments.

J Transl Med 2021 02 25;19(1):88. Epub 2021 Feb 25.

Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Affiliated Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang, 110001, China.

Background: tRNA-derived fragments (tRFs) are 14-40-nucleotide-long, small non-coding RNAs derived from specific tRNA cleavage events with key regulatory functions in many biological processes. Many studies have shown that tRFs are associated with Argonaute (AGO) complexes and inhibit gene expression in the same manner as miRNAs. However, there are currently no tools for accurately predicting tRF target genes. Read More

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February 2021

Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data.

NAR Genom Bioinform 2020 Jun 20;2(2):lqaa019. Epub 2020 Mar 20.

CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.

Recent RNA knockdown experiments revealed that a dozen divergent long noncoding RNAs (lncRNAs) positively regulate the transcription of genes in cis. Here, to understand the regulatory mechanism of divergent lncRNAs, we proposed a computational model IRDL (dentify the egulatory ivergent ncRNAs) to associate divergent lncRNAs with target genes. IRDL took advantage of the cross-tissue paired expression and chromatin accessibility data in ENCODE and a dozen experimentally validated divergent lncRNA target genes. Read More

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[Identification and differential expression of miRNA related to seed dormancy of Paris polyphylla var. chinensis].

Zhongguo Zhong Yao Za Zhi 2020 Dec;45(24):5958-5966

College of Horticulture, Nanjing Agricultural University Nanjing 210095, China.

The purpose of this study was to explore the expression pattern of miRNA in the process of embryo dormancy and provide a reference for the mechanism of regulating seed dormancy and germination by miRNA. We used high-throughput sequencing technology, bioinformatics analysis and real-time fluorescent quantitative PCR(qPCR) technology to sequence, screen and identify miRNAs of dormant and dormant embryos. The results showed that there were 23 811 977, 24 276 695, 20 611 876 and 20 601 811 unique sequences in the four sample libraries during the period of dormancy and dormancy release. Read More

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December 2020

Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.

Environ Monit Assess 2021 Jan 11;193(2):56. Epub 2021 Jan 11.

Department of Biotechnology, Mizoram University, Aizawl, Mizoram, 796 004, India.

In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Read More

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January 2021

A novel gammapartitivirus from the entomopathogenic fungus Metarhizium brunneum.

Arch Virol 2021 Mar 11;166(3):977-981. Epub 2021 Jan 11.

Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230036, China.

Here, we report a novel partitivirus infecting Metarhizium brunneum, which was designated "Metarhizium brunneum partitivirus 2" (MbPV2). The complete genome of MbPV2 consists of two segments, dsRNA1 and dsRNA2, with each dsRNA possessing a single open reading frame (ORF). dsRNA1 (1,775 bp) encodes a conserved RNA-dependent RNA polymerase (RdRp) with the highest sequence similarity to Plasmopara viticola associated partitivirus 1 (PvAPV1), while dsRNA2 (1,568 bp) encodes a coat protein (CP) with the highest sequence similarity to Colletotrichum partitivirus 1 (CtParV1). Read More

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Comprehensive identification of lysine 2-hydroxyisobutyrylated proteins in Ustilaginoidea virens reveals the involvement of lysine 2-hydroxyisobutyrylation in fungal virulence.

J Integr Plant Biol 2021 Feb;63(2):409-425

Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China.

Lysine 2-hydroxyisobutyrylation (K ) is a newly identified post-translational modification (PTM) that plays important roles in transcription and cell proliferation in eukaryotes. However, its function remains unknown in phytopathogenic fungi. Here, we performed a comprehensive assessment of K in the rice false smut fungus Ustilaginoidea virens, using Tandem Mass Tag (TMT)-based quantitative proteomics approach. Read More

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February 2021

The Genome Sequence of the Citrus Melanose Pathogen and Two Citrus-Related Species.

Phytopathology 2021 Mar 24:PHYTO08200376SC. Epub 2021 Mar 24.

Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.

Melanose disease is one the most widely distributed and economically important fungal diseases of citrus worldwide. The causative agent is the filamentous fungus (syn. ). Read More

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Large genome-wide association study identifies three novel risk variants for restless legs syndrome.

Commun Biol 2020 11 25;3(1):703. Epub 2020 Nov 25.

The National Institute for Health Research Blood and Transplant Unit in Donor Health and Genomics, University of Cambridge, Cambridge, CB1 8RN, UK.

Restless legs syndrome (RLS) is a common neurological sensorimotor disorder often described as an unpleasant sensation associated with an urge to move the legs. Here we report findings from a meta-analysis of genome-wide association studies of RLS including 480,982 Caucasians (cases = 10,257) and a follow up sample of 24,977 (cases = 6,651). We confirm 19 of the 20 previously reported RLS sequence variants at 19 loci and report three novel RLS associations; rs112716420-G (OR = 1. Read More

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November 2020

Isolation and Characterization of Three Sodium-Phosphate Cotransporter Genes and Their Transcriptional Regulation in the Grass Carp .

Int J Mol Sci 2020 Nov 3;21(21). Epub 2020 Nov 3.

Laboratory of Molecular Nutrition for Aquatic Economic Animals, Fishery College, Huazhong Agricultural University, Wuhan 430070, China.

It is important to explore the regulatory mechanism of phosphorus homeostasis in fish, which help avoid the risk of P toxicity and prevent P pollution in aquatic environment. The present study obtained the full-length cDNA sequences and the promoters of three SLC20 members (, and ) from grass carp , and explored their responses to inorganic phosphorus (Pi). Grass carp SLC20s proteins possessed conservative domains and amino acid sites relevant with phosphorus transport. Read More

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November 2020

Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome.

Am J Hum Genet 2020 11 14;107(5):977-988. Epub 2020 Oct 14.

Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, 12622, Egypt.

PRKACA and PRKACB code for two catalytic subunits (Cα and Cβ) of cAMP-dependent protein kinase (PKA), a pleiotropic holoenzyme that regulates numerous fundamental biological processes such as metabolism, development, memory, and immune response. We report seven unrelated individuals presenting with a multiple congenital malformation syndrome in whom we identified heterozygous germline or mosaic missense variants in PRKACA or PRKACB. Three affected individuals were found with the same PRKACA variant, and the other four had different PRKACB mutations. Read More

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November 2020

The comparative gene expression concern to the seed pigmentation in maize (Zea mays L.).

Genomics Inform 2020 Sep 9;18(3):e29. Epub 2020 Sep 9.

Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, Korea.

Maize seed pigmentation is one of the important issue to develop maize seed breeding. The differently gene expression was characterized and compared for three inbred lines, such as the pigment accumulated seed (CM22) and non-pigmented seed (CM5 and CM19) at 10 days after pollination. We obtained a total of 63,870, 82,496, and 54,555 contigs by de novo assembly to identify gene expression in the CM22, CM5, and CM19, respectably. Read More

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September 2020

Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle.

Genet Sel Evol 2020 Oct 1;52(1):55. Epub 2020 Oct 1.

Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.

Background: Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. Read More

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October 2020

Fat-Water Swaps in Iterative Decomposition of Water and Fat With Echo Asymmetry and Least-Squares Estimation Magnetic Resonance Imaging for Postinstrumentation Spine.

J Comput Assist Tomogr 2020 Nov/Dec;44(6):977-983

Objective: To determine the frequencies of fat-water swaps in iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) water-only images of the postinstrumentation spine and discuss the efficiency of in-phase imaging in improving visibility of the thecal sac.

Materials And Methods: A total of 276 patients (167 women; mean age, 62.3 years; range, 23-89 years) with metallic devices on the lumbar spine who received complete routine 1. Read More

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December 2020

A sporadic case of congenital aniridia caused by pericentric inversion inv(11)(p13q14) associated with a 977 kb deletion in the 11p13 region.

BMC Med Genomics 2020 09 18;13(Suppl 8):130. Epub 2020 Sep 18.

Research Centre for Medical Genetics, Moscow, Russian Federation.

Background: Because of the significant occurrence of "WAGR-region" deletions among de novo mutations detected in congenital aniridia, DNA diagnosis is critical for all sporadic cases of aniridia due to its help in making an early diagnosis of WAGR syndrome. Standard cytogenetic karyotype study is a necessary step of molecular diagnostics in patients with deletions and in the patients' parents as it reveals complex chromosomal rearrangements and the risk of having another affected child, as well as to provide prenatal and/or preimplantation diagnostics.

Case Presentation: DNA samples were obtained from the proband (a 2-year-old boy) and his two healthy parents. Read More

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September 2020

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma.

PLoS One 2020 15;15(9):e0238420. Epub 2020 Sep 15.

General Department, Guangzhou University of Traditional Chinese Medicine First Affiliated Hospital, Guangzhou, Guangdong, China.

Background: Patients diagnosed with Oral Floor Squamous Cell Carcinoma (OFSCC) face considerable challenges in physiology and psychology. This study explored prognostic signatures to predict prognosis in OFSCC through a detailed transcriptomic analysis.

Method: We built an interactive competing endogenous RNA (ceRNA) network that included lncRNAs, miRNAs and mRNAs. Read More

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October 2020

Genetic diversity of mitochondrial cytochrome b gene in swamp buffalo.

Anim Genet 2020 Dec 10;51(6):977-981. Epub 2020 Sep 10.

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.

The swamp buffalo (Bubalus carabanensis) is mainly bred for meat, transport and rice cultivation in China and Southeast Asian countries. In the current study, we investigated the genetic diversity, maternal origin and phylogenetic relationship of swamp buffalo by analyzing 1,786 mitochondrial cytochrome b (cytb) sequences from China, Vietnam, Laos, Thailand, India and Bangladesh. Our results indicated that the swamp buffalo can be divided into two major lineages (SA and SB with the sublineages) and three rare lineages (SC, SD and SE), which showed strong geographic differentiation. Read More

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December 2020

Inter-scanner reproducibility of brain volumetry: influence of automated brain segmentation software.

BMC Neurosci 2020 09 4;21(1):35. Epub 2020 Sep 4.

Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.

Background: The inter-scanner reproducibility of brain volumetry is important in multi-site neuroimaging studies, where the reliability of automated brain segmentation (ABS) tools plays an important role. This study aimed to evaluate the influence of ABS tools on the consistency and reproducibility of the quantified brain volumetry from different scanners.

Methods: We included fifteen healthy volunteers who were scanned with 3D isotropic brain T1-weighted sequence on three different 3. Read More

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September 2020

Single-Molecule Real-Time Transcript Sequencing of Turnips Unveiling the Complexity of the Turnip Transcriptome.

G3 (Bethesda) 2020 10 5;10(10):3505-3514. Epub 2020 Oct 5.

Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, China

To generate the full-length transcriptome of Xinjiang green and purple turnips, , using single-molecule real-time (SMRT) sequencing. The samples of two varieties of at five developmental stages were collected and combined to perform SMRT sequencing. Meanwhile, next generation sequencing was performed to correct SMRT sequencing data. Read More

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October 2020