17 results match your criteria removed adapters

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Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients.

Genomics Inform 2021 Sep 30;19(3):e31. Epub 2021 Sep 30.

Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. Read More

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September 2021

Characterizing dementia caregiver style in managing care challenges: Cognitive and behavioral components.

Dementia (London) 2021 Aug 31;20(6):2188-2204. Epub 2021 Jan 31.

Department of Psychiatry and Behavioral Sciences, 8789University of California Davis, USA; Department of Psychiatry, 1259University of Michigan, USA.

Background: Caring for a person living with dementia can take a physical and emotional toll, but understudied is the process by which family caregivers actually provide care. Caregiver management styles may vary and affect care decision-making, experiences, receptivity to and participation in interventions, and outcomes for the caregiver and person living with dementia.

Methods: Participants included 100 primary family caregivers for persons with dementia who were on average 64 years old and had been providing care for 55 months, 74% women, and 18% nonwhite. Read More

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Endovascular Rescue of Sheath Perforation During Inferior Vena Cava Filter Retrieval.

EJVES Vasc Forum 2020 13;49:40-44. Epub 2020 Nov 13.

Division of Vascular and Endovascular Surgery, University of Louisville, Louisville, KY, USA.

Introduction: Inferior vena cava (IVC) filter retrieval is generally a straightforward procedure but can be challenging with unique complications. A technique used for endovascular rescue of a patient where sheath perforation by the IVC filter occurred during IVC filter retrieval is described.

Report: A 75 year old man underwent retrieval of an IVC filter that had been in place for 10 months. Read More

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November 2020

Automated download and clean-up of family-specific databases for kmer-based virus identification.

Bioinformatics 2021 05;37(5):705-710

Department of Viroscience, Erasmus University Medical Centre, 3000 CA Rotterdam, The Netherlands.

Summary: Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants. Read More

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Shallow whole genome sequencing of adenoid cystic carcinomas of the salivary glands identifies specific chromosomal aberrations related to tumor progression.

Oral Oncol 2020 04 28;103:104615. Epub 2020 Feb 28.

Institute of Pathology, University Medical Center Goettingen, Germany. Electronic address:

Background And Purpose: Adenoid cystic carcinomas (ACC) are characterized by high rate of local recurrence and late distant metastasis. Chromosomal changes in the evolution from primary tumors to metastatic disease of ACC have not been appointed. Here we investigated the chromosomal alterations of 53 primary tumors from ACC patients with different progressive states by shallow whole genome sequencing to identify potential new markers for metastatic spread. Read More

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RNA-Sequencing of Snake Venom Glands.

Methods Mol Biol 2020 ;2068:87-96

Faculty of Medicine, Department of Medicine, Chulalongkorn University, Bangkok, Thailand.

Next-generation sequencing (NGS), particularly RNA-sequencing (RNA-Seq) technique, allows detection and quantification of different RNA transcripts in a tissue sample, and in our case toxin transcripts from snake venom glands. Using this approach, novel toxin transcripts can be detected and abundancies of different isoforms of each toxin measured. The analytical pipeline can be briefly outlined as follows. Read More

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December 2020

DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data.

PLoS One 2016 13;11(10):e0164228. Epub 2016 Oct 13.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

With the rapid accumulation of publicly available small RNA sequencing datasets, third-party meta-analysis across many datasets is becoming increasingly powerful. Although removing the 3´ adapter is an essential step for small RNA sequencing analysis, the adapter sequence information is not always available in the metadata. The information can be also erroneous even when it is available. Read More

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DUI offenders' experience with an ignition interlock program: comparing those who have and have not adapted from their primary drinking location.

Traffic Inj Prev 2015 23;16(4):329-35. Epub 2014 Dec 23.

a Department of Behavioral and Community Health , University of Maryland School of Public Health , College Park , Maryland.

Objective: The purpose of this study was to compare driving under the influence (DUI) offenders on an alcohol ignition interlock program who had or had not changed their primary drinking context from a bar/restaurant where they might be required to drive after drinking before the interlock was installed to drinking at home where driving would not be likely to be required following interlock installation.

Methods: A total of 171 DUI offenders who were on an ignition interlock program completed a web-based survey. All of these offenders reported that they drank primarily in a bar/restaurant before the interlock was installed. Read More

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Removing PCR for the elimination of undesired DNA fragments cycle by cycle.

Sci Rep 2013 ;3:2303

Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China.

A novel removing polymerase chain reaction (R-PCR) technique was developed, which can eliminate undesired genes, cycle by cycle, with efficiencies of 60.9% (cDNAs), 73.6% (genomic DNAs), and ~ 100% (four DNA fragments were tested). Read More

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February 2014

Transcriptome analysis of neoplastic hemocytes in soft-shell clams Mya arenaria: Focus on cell cycle molecular mechanism.

Results Immunol 2013 1;3:95-103. Epub 2013 Nov 1.

Laboratory of Ecotoxicology, University of Le Havre, 25 rue Philippe Lebon, BP540, 76058 Le Havre, France.

In North America, a high mortality of soft-shell clams Mya arenaria was found to be related to the disease known as disseminated neoplasia (DN). Disseminated neoplasia is commonly recognized as a tetraploid disorder related to a disruption of the cell cycle. However, the molecular mechanisms by which hemocytes of clams are transformed in the course of DN remain by far unknown. Read More

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AdapterRemoval: easy cleaning of next-generation sequencing reads.

Authors:
Stinus Lindgreen

BMC Res Notes 2012 Jul 2;5:337. Epub 2012 Jul 2.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen K, Denmark.

Background: With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. Read More

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Tunable fractionation of nucleic acids.

Biotechniques 2009 Dec;47(6):1041-3

Functional Genomics Technology Team, Omics Science Center (OSC), RIKEN Yokohama Institute, Kanagawa, Japan.

We developed a method for selective purification of DNA using the cationic detergent, cetyltrimethylammonium bromide (CTAB), accompanied with urea and controlled high-salt (NaCl) concentration. This method is effective for rapid separation of DNA fragments from artifacts such as PCR primer dimers or ligation adapters. The CTAB-associated purification completely removed the short PCR artifacts and primers, as well as enzymes and buffer, while recovering a sufficient quantity of amplicons for subsequent experiments such as preparation of libraries. Read More

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December 2009

[Construction and identification of cDNA library for colorectal carcinoma antigens].

Authors:
Hang Chen Jin Fang

Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2009 Jan;25(1):6-8

Department of Cell Biology, China Medical University, Shenyang, China.

Aim: To construct a cDNA phage expression library of colorectal carcinoma antigens for screening colorectal carcinoma specific-antigens.

Methods: The total RNA was extracted from two colorectal carcinoma cell lines CCL-187 and CX-1 . The mRNA from total RNA was isolated to synthesize the first and second strand cDNA. Read More

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January 2009

Construction and significance of directional expression cDNA library from human NB4 cells.

J Huazhong Univ Sci Technolog Med Sci 2004 ;24(1):52-4, 58

Department Of Hematology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004.

Human acute premyeloid leukemia cell cDNA expression library was constructed to screen acute premyeloid leukemia tumor antigen. Total RNA and purified mRNA were extracted from human premyeloid cell line NB4. First and second strands of cDNA were synthesized by reverse transcription. Read More

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December 2004

[Construction and significance of directional expression cDNA library from myeloid leukemia cell line U937].

Zhongguo Shi Yan Xue Ye Xue Za Zhi 2003 Aug;11(4):355-8

Department of Hematology, The Second Hospital, Xi'an Jiaotong University, Xi'an 710004, China.

To construct the cDNA expression library from human U937 cell, total RNA and purified mRNA in myeloid leukemia cell line U937 were extracted. The first and second strand of cDNA were synthesized through reverse transcription. After blunting the cDNA termini, the cDNA fragments were connected with EcoR I adapters, and the end of EcoR I adapters was phosphorylated. Read More

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Metered dose inhaler aerosol characteristics are affected by the endotracheal tube actuator/adapter used.

Anesthesiology 1990 Dec;73(6):1263-5

Department of Anesthesiology, University of Washington, Seattle, Washington.

The authors studied the particle size of aerosols of metaproterenol produced by three different actuators designed for use in patients with endotracheal tubes in place. These were compared with the metaproterenol aerosol produced by the actuator (provided by Boehringer-Ingelheim [BI]) that was supplied by the manufacturer for use in patients whose tracheas are not intubated. The volume of particles in the respiratory size range (1. Read More

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December 1990

Feeding gastrostomy button: experience and recommendations.

J Pediatr Surg 1988 Jan;23(1 Pt 2):24-8

Department of Surgery, Rainbow Babies and Children's Hospital, Cleveland, OH.

To circumvent the common problems and complications of long-term gastrostomy management, a skin-level nonrefluxing nonreactive gastrostomy "button" (GB) was designed. This silicon device is self-retaining, employing a one-way (in) valve. For feeding purposes, an adapter is inserted. Read More

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January 1988
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