keyword
MENU ▼
Read by QxMD icon Read
search

software

keyword
https://www.readbyqxmd.com/read/28240008/role-of-plasticity-region-genes-and-cage-gene-of-cagpai-of-helicobacter-pylori-in-development-of-gastrointestinal-gi-diseases
#1
Shokufe GholizadeTobnagh, Seyedeh Zahra Bakhti, Saeid Latifi Navid, Saber Zahri, Fatemeh Sadat Bakhti
Background: Helicobacter pylori is a Gram-negative, micro aerophilic bacterium in the human stomach that is associated with the development of gastrointestinal ailments such as peptic ulcer (PU) and gastric cancer (GC). In the present study, plasticity region genes (jhp0940, jhp0945 and jhp0947) and and cagE gene of cagPAI were assessed independently and in combination for their ability to predict clinical consequences. Materials and Methods: A total of 211 strains which were isolated from patients with different gastrointestinal diseases (114 with non-atrophic gastritis, 59 with PU, and 38 with GC) were genotyped by PCR and sequencing...
1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28239843/liver-transection-using-indocyanine-green-fluorescence-imaging-and-hepatic-vein-clamping
#2
Y Kawaguchi, Y Nomura, M Nagai, D Koike, Y Sakuraoka, T Ishida, T Ishizawa, N Kokudo, N Tanaka
BACKGROUND: Three-dimensional (3D) imaging has facilitated liver resection with excision of hepatic veins by estimating the liver volume of portal and hepatic venous territories. However, 3D imaging cannot be used for real-time navigation to determine the liver transection line. This study assessed the value of indocyanine green (ICG) fluorescence imaging with hepatic vein clamping for navigation during liver transection. METHODS: Consecutive patients who underwent liver resection with excision of major hepatic veins between 2012 and 2013 were evaluated using ICG fluorescence imaging after clamping veins and injecting ICG...
February 27, 2017: British Journal of Surgery
https://www.readbyqxmd.com/read/28239799/the-consistency-of-myocardial-strain-derived-from-heart-deformation-analysis
#3
Eric J Keller, Shanna Fang, Kai Lin, Benjamin H Freed, Peter M Smith, Bruce S Spottiswoode, Rachel Davids, Maria Carr, Marie-Pierre Jolly, Michael Markl, James C Carr, Jeremy D Collins
The purpose of this study was to assess the consistency of semi-automated myocardial strain analysis by prototype software across field strengths, temporal resolutions, and examinations. 35 volunteers (48 ± 13 years; 20% women) and 25 patients (54 ± 12 years; 44% women) without significant cardiac dysfunction underwent cine cardiac magnetic resonance imaging (CMR) at 1.5 T with a temporal resolution of 39.2 msec. 34 subjects also underwent imaging at 3.0 T; 16 had repeat examinations within 14 days; and 9 underwent CMR with temporal resolutions of 12...
February 26, 2017: International Journal of Cardiovascular Imaging
https://www.readbyqxmd.com/read/28239666/making-the-most-of-rna-seq-pre-processing-sequencing-data-with-opossum-for-reliable-snp-variant-detection
#4
Laura Oikkonen, Stefano Lise
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller...
January 17, 2017: Wellcome Open Res
https://www.readbyqxmd.com/read/28239610/preparing-and-analyzing-expressed-sequence-tags-ests-library-for-the-mammary-tissue-of-local-turkish-kivircik-sheep
#5
Nehir Ozdemir Ozgenturk, Zehra Omeroglu Ulu, Salih Ulu, Cemal Un, Kemal Ozdem Oztabak, Kemal Altunatmaz
Kivircik sheep is an important local Turkish sheep according to its meat quality and milk productivity. The aim of this study was to analyze gene expression profiles of both prenatal and postnatal stages for the Kivircik sheep. Therefore, two different cDNA libraries, which were taken from the same Kivircik sheep mammary gland tissue at prenatal and postnatal stages, were constructed. Total 3072 colonies which were randomly selected from the two libraries were sequenced for developing a sheep ESTs collection...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28239549/red-legged-partridge-alectoris-rufa-de-novo-transcriptome-assembly-and-identification-of-gene-related-markers
#6
Natalia Sevane, Javier Cañon, Paulina G Eusebi, Ignacio Gil, Susana Dunner
The red-legged partridge (Alectoris rufa) has a great socio-economic importance as a game species and is reared by millions in farms in several European countries. The ability to respond to a wide spectrum of pathogens and environmental changes is key for farm-reared animals that, as such, face even higher pathogen exposure and specifically for those submitted to restocking programs. In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues were performed. The raw FASTQ files were submitted to the NCBI SRA database with accession number PRJNA289204...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28239530/hippocampal-atrophy-and-memory-dysfunction-associated-with-physical-inactivity-in-community-dwelling-elderly-subjects-the-sefuri-study
#7
Manabu Hashimoto, Yuko Araki, Yuki Takashima, Kohjiro Nogami, Akira Uchino, Takefumi Yuzuriha, Hiroshi Yao
BACKGROUND: Physical inactivity is one of the modifiable risk factors for hippocampal atrophy and Alzheimer's disease. We investigated the relationship between physical activity, hippocampal atrophy, and memory using structural equation modeling (SEM). MATERIALS AND METHODS: We examined 213 community-dwelling elderly subjects (99 men and 114 women with a mean age of 68.9 years) without dementia or clinically apparent depression. All participants underwent Mini-Mental State Examination (MMSE) and Rivermead Behavioral Memory Test (RBMT)...
February 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28239411/reliable-measurement-of-e-coli-single-cell-fluorescence-distribution-using-a-standard-microscope-set-up
#8
Marilisa Cortesi, Lucia Bandiera, Alice Pasini, Alessandro Bevilacqua, Alessandro Gherardi, Simone Furini, Emanuele Giordano
BACKGROUND: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. METHODS: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28239248/efficient-computation-of-the-joint-sample-frequency-spectra-for-multiple-populations
#9
John A Kamm, Jonathan Terhorst, Yun S Song
A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on...
2017: Journal of Computational and Graphical Statistics
https://www.readbyqxmd.com/read/28239219/higher-quality-and-lower-cost-from-improving-hospital-discharge-decision-making
#10
James C Cox, Vjollca Sadiraj, Kurt E Schnier, John F Sweeney
This paper reports research on improving decisions about hospital discharges - decisions that are now made by physicians based on mainly subjective evaluations of patients' discharge status. We report an experiment on uptake of our clinical decision support software (CDSS) which presents physicians with evidence-based discharge criteria that can be effectively utilized at the point of care where the discharge decision is made. One experimental treatment we report prompts physician attentiveness to the CDSS by replacing the default option of universal "opt in" to patient discharge with the alternative default option of "opt out" from the CDSS recommendations to discharge or not to discharge the patient on each day of hospital stay...
November 2016: Journal of Economic Behavior & Organization
https://www.readbyqxmd.com/read/28238895/hispanic-mothers-views-of-the-fathers-role-in-promoting-healthy-behaviors-at-home-focus-group-findings
#11
Karina R Lora, Marshall Cheney, Paul Branscum
BACKGROUND: Overweight and obesity prevention interventions rarely take into account the unique role of fathers in promoting healthy home environments. OBJECTIVE: To use qualitative methodology to examine the views of Hispanic mothers of children aged 2 to 5 years regarding fathers' roles in promoting healthy behaviors at home. DESIGN: Nine focus groups were conducted in Spanish with Hispanic mothers of preschool-aged children (N=55) from October to December 2015...
February 23, 2017: Journal of the Academy of Nutrition and Dietetics
https://www.readbyqxmd.com/read/28238738/reference-standard-space-hippocampus-labels-according-to-the-eadc-adni-harmonized-protocol-utility-in-automated-volumetry
#12
Dominik Wolf, Martina Bocchetta, Gregory M Preboske, Marina Boccardi, Michel J Grothe
BACKGROUND: A harmonized protocol (HarP) for manual hippocampal segmentation on magnetic resonance imaging (MRI) has recently been developed by an international European Alzheimer's Disease Consortium-Alzheimer's Disease Neuroimaging Initiative project. We aimed at providing consensual certified HarP hippocampal labels in Montreal Neurological Institute (MNI) standard space to serve as reference in automated image analyses. METHODS: Manual HarP tracings on the high-resolution MNI152 standard space template of four expert certified HarP tracers were combined to obtain consensual bilateral hippocampus labels...
February 23, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28238561/magnetic-resonance-imaging-of-the-inferior-alveolar-nerve-with-special-regard-to-metal-artifact-reduction
#13
Monika Probst, Vivien Richter, Jochen Weitz, Jan Stefan Kirschke, Carl Ganter, Matthias Troeltzsch, Mathias Nittka, Carl-Peter Cornelius, Claus Zimmer, Florian Andreas Probst
PURPOSE: Magnetic resonance imaging (MRI) is an excellent imaging modality for displaying peripheral nerves. Since the knowledge about MRI of the inferior alveolar nerve (IAN) is limited, this pilot study aims to identify the prospects and limitations of MRI of the IAN, with special consideration of metal artifacts. MATERIALS AND METHODS: Initially, in vitro MRI of a dental implant was performed to establish an optimized protocol for metal artifact reduction using WARP sequences (a software package provided by Siemens Healthcare, Erlangen, Germany) including view angle tilting (VAT) and slice-encoding metal artifact correction (SEMAC) techniques...
January 25, 2017: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/28238558/a-novel-computer-system-for-the-evaluation-of-nasolabial-morphology-symmetry-and-aesthetics-after-cleft-lip-and-palate-treatment-part-1-general-concept-and-validation
#14
Piotr Pietruski, Marcin Majak, Tomasz Debski, Boguslaw Antoszewski
PURPOSE: The need for a widely accepted method suitable for a multicentre quantitative evaluation of facial aesthetics after surgical treatment of cleft lip and palate (CLP) has been emphasized for years. The aim of this study was to validate a novel computer system 'Analyse It Doc' (A.I.D.) as a tool for objective anthropometric analysis of the nasolabial region. MATERIALS AND METHODS: An indirect anthropometric analysis of facial photographs was conducted with the A...
February 1, 2017: Journal of Cranio-maxillo-facial Surgery
https://www.readbyqxmd.com/read/28238177/digital-volumetric-measurement-of-mammographic-density-and-the-risk-of-overlooking-cancer-in-japanese-women
#15
Terumasa Sawada, Sadako Akashi, Seigo Nakamura, Takashi Kuwayama, Katsutoshi Enokido, Miwa Yoshida, Rikako Hashimoto, Toshimi Ide, Hiroko Masuda, Kanae Taruno, Hiroto Oyama, Tomoko Takamaru, Yoko Kanada, Murasaki Ikeda, Natsuko Kosugi, Hiroki Sato, Sayuka Nakayama, Arisa Ata, Yumi Tonouchi, Haruna Sakai, Yuki Matsunaga, Akiko Matsutani
BACKGROUND: Breast density often affects cancer detection via mammography (MMG). Because of this, additional tests are recommended for women with dense breasts. This study aimed to reveal trends in breast density among Japanese women and determine whether differences in breast density differentially affected the detection of abnormalities via MMG. METHODS: We retrospectively analyzed 397 control women who underwent MMG screening as well as 269 patients who underwent surgery for breast cancer for whom preoperative MMG data were available...
February 25, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/28238148/long-term-cancer-control-outcomes-of-robot-assisted-radical-prostatectomy-for-prostate-cancer-treatment-a-meta-analysis
#16
Lei Wang, Baojun Wang, Qing Ai, Yu Zhang, Xiangjun Lv, Hongzhao Li, Xin Ma, Xu Zhang
PURPOSE: Robot-assisted radical prostatectomy (RARP) provides significant advantages in short-term oncological outcomes for prostate cancer patients. However, data regarding the long-term cancer control outcomes of RARP are limited and inconsistent. This study aimed to evaluate these long-term outcomes. METHODS: Medline, Scopus, and other databases were searched for studies published from January 2010 to July 2016. Case series and prospective cohort studies on the long-term cancer control outcomes of patients who underwent RARP were subjected to meta-analyses by using the R statistical software...
February 25, 2017: International Urology and Nephrology
https://www.readbyqxmd.com/read/28238145/high-accuracy-determination-of-cytotoxic-responses-from-graphene-oxide-exposure-using-imaging-flow-cytometry
#17
Sandra Vranic, Kostas Kostarelos
Graphene and other 2D materials have received increased attention in the biomedical field due to their unique properties and potential use as carriers for targeted drug delivery or in regenerative medicine. Before the exploitation of graphene-based materials in biomedicine becomes a reality, it is necessary to establish the full toxicological profile and better understand how the material interacts with cells and tissues. Because specific properties, such as flake size and surface chemistry, might determine whether graphene can achieve therapeutic efficacy without causing toxicity, it is important to develop highly accurate and reliable screening techniques to accurately assess the biocompatibility of different types of graphene-based materials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28238103/association-between-overweight-obesity-and-periodontal-disease-in-children-and-adolescents-a-systematic-review-and-meta-analysis
#18
REVIEW
L Martens, S De Smet, M Y P M Yusof, S Rajasekharan
AIM: To provide a systematic review and meta-analyses investigating the association between overweight/obesity as defined by Body Mass Index (BMI) and periodontal disease in terms of clinical periodontal outcomes. MATERIALS AND METHODS: A systematic search of the literature was conducted by two authors (SR and SD) independently in the Cochrane Library, PubMed, Web of Science (ISI), Scopus, Scielo, Lilacs and System for Information on Grey Literature in Europe (SIGLE) for full articles published until September 2015...
February 25, 2017: European Archives of Paediatric Dentistry: Official Journal of the European Academy of Paediatric Dentistry
https://www.readbyqxmd.com/read/28237870/the-treatment-of-premenstrual-syndrome-with-preparations-of-vitex-agnus-castus-a-systematic-review-and-meta-analysis
#19
REVIEW
Saskia Verkaik, Astrid M Kamperman, Roos van Westrhenen, Peter F J Schulte
OBJECTIVE: The objective is to determine the efficacy, tolerability and acceptability of Vitex agnus castus (VAC) preparations for treatment of premenstrual syndrome. DATA SOURCES: All journals in the OVID software from inception to January 2016 were searched, including the Cochrane Central Register of Controlled Trials, MEDLINE, Embase and PsycINFO. Gray literature was searched by Google Scholar and manufacturers of VAC preparations were contacted for information about unpublished trials...
February 22, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28237840/comparison-between-in-vitro-properties-of-washed-platelet-concentrates-suspended-in-m-sol-and-those-in-brs-a-both-of-which-were-prepared-with-an-automated-cell-processor
#20
Akira Iwama, Junichi Hirayama, Masayuki Nogawa, Masayuki Shiba, Masahiro Satake, Shigeru Takamoto, Kenji Tadokoro
BACKGROUND: Washed platelet concentrate (WPC) is prepared manually in general, but automated preparation is desirable to minimize variation in the WPC quality and enhance WPC production. Recently, the software was improved for an automated cell processor (ACP) to control all processes of WPC preparation. M-sol and BRS-A, which are mixtures of medical solutions, are widely used for WPC preparation with a manual method in Japan. In this study, we prepared WPC suspended in M-sol (WPC-M) or BRS-A (WPC-B) with the ACP, and compared their in vitro properties during 7-day storage...
February 9, 2017: Transfusion and Apheresis Science
keyword
keyword
20049
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"