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https://www.readbyqxmd.com/read/28941355/a-novel-method-to-detect-bias-in-short-read-ngs-data
#1
Jamie Alnasir, Hugh P Shanahan
Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. We outline a novel method to detect sequence specific bias in short read Next Generation Sequencing data. This is based on determining intra-exon correlations between specific motifs. This requires a mild assumption that short reads sampled from specific regions from the same exon will be correlated with each other. This has been implemented on Apache Spark and used to analyse two D. melanogaster eye-antennal disc data sets generated at the same laboratory...
September 23, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28938172/artificial-intelligence-for-breast-cancer-screening-opportunity-or-hype
#2
Nehmat Houssami, Christoph I Lee, Diana S M Buist, Dacheng Tao
Interpretation of mammography for breast cancer (BC) screening can confer a mortality benefit through early BC detection, can miss a cancer that is present or fast growing, or can result in false-positives. Efforts to improve screening outcomes have mostly focused on intensifying imaging practices (double instead of single-reading, more frequent screens, or supplemental imaging) that may add substantial resource expenditures and harms associated with population screening. Less attention has been given to making mammography screening practice 'smarter' or more efficient...
September 19, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/28937972/a-risk-factor-analysis-of-cognitive-impairment-in-elderly-patients-with-chronic-diseases-in-a-chinese-population
#3
Ye Li, Xiang Fang, Wei-Gang Zhao, Yan Chen, Shi-Lian Hu
BACKGROUND This study analyzed the risk factors of cognitive impairment (CI) in elderly patients with chronic diseases. MATERIAL AND METHODS In total of 385 elderly patients with chronic diseases were selected and assigned into CI and normal groups. The activities of daily living (ADL), global deterioration scale (GDS), Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment Scale (MoCA), patient-generated subjective global assessment (PG-SGA), and mini nutritional assessment (MNA) were performed to analyze the differences between the 2 groups...
September 22, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28936949/-clinical-practice-guidelines-of-hap-vap-in-2016-the-updates
#4
Meizhu Lu, Yan Kang
Hospital acquired pneumonia (HAP) and ventilatorassociated pneumonia (VAP) are common hospital-acquired infections with higher mortality, longer hospital stay and more hospitalization expenses. With the latest research results and evidence-based guideline methodology, Infectious Diseases Society of America (IDSA) and American Thoracic Society (ATS) have collaborated to create updated guidelines for the diagnosis and treatment of HAP and VAP in 2016. It is worth critically reading and thinking that most recommendations are supported by low-quality or very-low quality evidence and some strong recommendations is different from the actual clinical work in China...
September 2017: Zhonghua Wei Zhong Bing Ji Jiu Yi Xue
https://www.readbyqxmd.com/read/28936361/relationships-between-eye-movements-during-sentence-reading-comprehension-word-spelling-and-reading-and-dti-and-fmri-connectivity-in-students-with-and-without-dysgraphia-or-dyslexia
#5
Kevin Yagle, Todd Richards, Katie Askren, Zoe Mestre, Scott Beers, Robert Abbott, William Nagy, Peter Boord, Virginia Berninger
While eye movements were recorded and brains scanned, 29 children with and without specific learning disabilities (SLDs) decided if sentences they read (half with only correctly spelled words and half with homonym foils) were meaningful. Significant main effects were found for diagnostic groups (non-SLD control, dysgraphia control, and dyslexia) in total fixation (dwell) time, total number of fixations, and total regressions in during saccades; the dyslexia group had longer and more fixations and made more regressions in during saccades than either control group...
January 2017: Journal of Systems and Integrative Neuroscience
https://www.readbyqxmd.com/read/28936042/comparison-of-photographic-and-conventional-methods-for-tooth-shade-selection-a-clinical-evaluation
#6
Juzer S Miyajiwala, Mohit G Kheur, Anuya H Patankar, Tabrez A Lakha
AIM: This study aimed to compare three different methods used for shade selection, i.e., visual method, spectrophotometer, and digital photography method. MATERIALS AND METHODS: Fifty participants were selected from the Out Patient Department of Prosthodontics. Presence of the maxillary right central incisor with no history of any restorative or endodontic procedures was the primary inclusion criterion. The shade of the right maxillary central incisor was determined using all the three shade selection procedures, namely, visual, spectrophotometric, and digital photography method for all the selected participants...
July 2017: Journal of Indian Prosthodontic Society
https://www.readbyqxmd.com/read/28935631/cultural-crossings-of-care-an-appeal-to-the-medical-humanities
#7
Julia Kristeva, Marie Rose Moro, John Ødemark, Eivind Engebretsen
Modern medicine is confronted with cultural crossings in various forms. In facing these challenges, it is not enough to simply increase our insight into the cultural dimensions of health and well-being. We must, more radically, question the conventional distinction between the 'objectivity of science' and the 'subjectivity of culture'. This obligation creates an urgent call for the medical humanities but also for a fundamental rethinking of their grounding assumptions.Julia Kristeva (JK) has problematised the biomedical concept of health through her reading of the anthropogony of Cura (Care), who according to the Roman myth created man out of a piece of clay...
September 21, 2017: Medical Humanities
https://www.readbyqxmd.com/read/28935227/physiotherapy-education-and-training-prior-to-upper-abdominal-surgery-is-memorable-and-has-high-treatment-fidelity-a-nested-mixed-methods-randomised-controlled-study
#8
Ianthe Boden, Doa El-Ansary, Nadia Zalucki, Iain K Robertson, Laura Browning, Elizabeth H Skinner, Linda Denehy
OBJECTIVES: To (1) assess memorability and treatment fidelity of pre-operative physiotherapy education prior to elective upper abdominal surgery and, (2) to explore patient opinions on pre-operative education. DESIGN: Mixed-methods analysis of a convenience sample within a larger parallel-group, double-blinded, randomised controlled trial with concealed allocation and intention-to-treat analysis. SETTING: Tertiary Australian hospital. PARTICIPANTS: Twenty-nine patients having upper abdominal surgery attending pre-admission clinic within six-weeks of surgery...
September 1, 2017: Physiotherapy
https://www.readbyqxmd.com/read/28934929/single-molecule-counting-and-assessment-of-random-molecular-tagging-errors-with-transposable-giga-scale-error-correcting-barcodes
#9
Billy T Lau, Hanlee P Ji
BACKGROUND: RNA-Seq measures gene expression by counting sequence reads belonging to unique cDNA fragments. Molecular barcodes commonly in the form of random nucleotides were recently introduced to improve gene expression measures by detecting amplification duplicates, but are susceptible to errors generated during PCR and sequencing. This results in false positive counts, leading to inaccurate transcriptome quantification especially at low input and single-cell RNA amounts where the total number of molecules present is minuscule...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934711/alterations-of-larval-photo-dependent-swimming-responses-pdr-new-endpoints-for-rapid-and-diagnostic-screening-of-aquatic-contamination
#10
Luis Colón-Cruz, Lauren Kristofco, Jonathan Crooke-Rosado, Agnes Acevedo, Aranza Torrado, Bryan W Brooks, María A Sosa, Martine Behra
Detection and toxicity assessment of waterborne contaminants are crucial for protecting human health and the environment. Development of easy-to-implement, rapid and cost-effective tools to measure anthropogenic effects on watersheds are critical for responsible management, particularly in times of increasing development and urbanization. Traditionally, environmental toxicology has focused on limited endpoints, such as lethality and fertility, which are directly affecting population levels. However, more sensitive readings are needed to assess sub-lethal effects...
September 18, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28934479/targeted-reconstruction-of-t-cell-receptor-sequence-from-single-cell-rna-seq-links-cdr3-length-to-t-cell-differentiation-state
#11
Shaked Afik, Kathleen B Yates, Kevin Bi, Samuel Darko, Jernej Godec, Ulrike Gerdemann, Leo Swadling, Daniel C Douek, Paul Klenerman, Eleanor J Barnes, Arlene H Sharpe, W Nicholas Haining, Nir Yosef
The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934437/group-b-streptococcus-and-the-vaginal-microbiota
#12
Geoffrey H Rosen, Tara M Randis, Purnahamsi V Desai, Katherine J Sapra, Bing Ma, Pawel Gajer, Michael S Humphrys, Jacques Ravel, Shari E Gelber, Adam J Ratner
Background: Streptococcus agalactiae (group B Streptococcus [GBS]) is an important neonatal pathogen and emerging cause of disease in adults. The major risk factor for neonatal disease is maternal vaginal colonization. However, little is known about the relationship between GBS and vaginal microbiota. Methods: Vaginal lavage samples from nonpregnant women were tested for GBS, and amplicon-based sequencing targeting the 16S ribosomal RNA V3-V4 region was performed...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934382/complete-genome-analysis-of-lactobacillus-fermentum-sk152-from-kimchi-reveals-genes-associated-with-its-antimicrobial-activity
#13
DongAhn Yoo, Bernadette B Bagon, Valerie Diane V Valeriano, Ju Kyoung Oh, Heebal Kim, Seoae Cho, Dae-Kyung Kang
Research findings on probiotics highlight their importance in repressing harmful bacteria, leading to more extensive research on their potential applications. We analysed the genome of Lactobacillus fermentum SK152, which was isolated from the Korean traditional fermented vegetable dish kimchi, to determine the genetic makeup and genetic factors responsible for the antimicrobial activity of L. fermentum SK152 and performed a comparative genome analysis with other L. fermentum strains. The genome of L. fermentum SK152 was found to comprise a complete circular chromosome of 2092 273 bp, with an estimated GC content of 51...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28934310/sanger-and-next-generation-sequencing-data-for-characterization-of-ctl-epitopes-in-archived-hiv-1-proviral-dna
#14
Camille Tumiotto, Lionel Riviere, Pantxika Bellecave, Patricia Recordon-Pinson, Alice Vilain-Parce, Gwenda-Line Guidicelli, Hervé Fleury
One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes...
2017: PloS One
https://www.readbyqxmd.com/read/28933898/embodied-cognition-is-activation-of-the-motor-cortex-essential-for-understanding-action-verbs
#15
Jeff Miller, Kate Brookie, Sid Wales, Simon Wallace, Barbara Kaup
In 8 experiments using language processing tasks ranging from lexical decision to sensibility judgment, participants made hand or foot responses after reading hand- or foot-associated words such as action verbs. In general, response time (RT) tended to be faster when the hand- versus foot-associated word was compatible with the limb that was required to respond (e.g., hand response to a hand-associated word) than when it was incompatible (e.g., foot response to a hand-associated word). To see whether this compatibility effect reflects differential hand- versus foot-specific motor activation produced by the words, as suggested by some embodied theories of language understanding, we monitored 2 event-related potential (ERP) measures previously found to be sensitive to the activation of these limbs...
September 21, 2017: Journal of Experimental Psychology. Learning, Memory, and Cognition
https://www.readbyqxmd.com/read/28933873/is-testing-a-more-effective-learning-strategy-than-note-taking
#16
Ralf Rummer, Judith Schweppe, Kathleen Gerst, Simon Wagner
The testing effect is both robust and generalizable. However, most of the underlying studies compare testing to a rather ineffective control condition: massed repeated reading. This article therefore compares testing with note-taking, which has been shown to be more effective than repeated reading. Experiment 1 is based on a 3 × 3 between-participants design with the factors learning condition (repeated reading vs. repeated testing vs. repeated note-taking) and final test delay (5 min vs. 1 week vs. 2 weeks)...
September 2017: Journal of Experimental Psychology. Applied
https://www.readbyqxmd.com/read/28933570/developing-pictorial-asthma-action-plans-to-promote-self-management-and-health-in-rural-youth-with-asthma-a-qualitative-study
#17
Christina L Duncan, Heather A Walker, Laurel Brabson, Desireé N Williford, Lisa Hynes, Mary Beth Hogan
OBJECTIVE: Asthma action plans (AAPs) provide asthma management instructions to families; however, AAPs typically are written at a 7(th)-9(th) grade reading level, making them less useful in lower literacy families. There is a need to develop simpler AAP formats and content to optimize their utility across all families, including those who are rural and may be at risk for literacy concerns. Because using pictures can simplify and enhance health education, our study aim was to develop a pictorial AAP through a series of focus groups with key stakeholders - youth with asthma, caregivers, and physicians...
September 21, 2017: Journal of Asthma: Official Journal of the Association for the Care of Asthma
https://www.readbyqxmd.com/read/28932018/measuring-orthographic-transparency-and-morphological-syllabic-complexity-in-alphabetic-orthographies-a-narrative-review
#18
REVIEW
Elisabeth Borleffs, Ben A M Maassen, Heikki Lyytinen, Frans Zwarts
This narrative review discusses quantitative indices measuring differences between alphabetic languages that are related to the process of word recognition. The specific orthography that a child is acquiring has been identified as a central element influencing reading acquisition and dyslexia. However, the development of reliable metrics to measure differences between language scripts hasn't received much attention so far. This paper therefore reviews metrics proposed in the literature for quantifying orthographic transparency, syllabic complexity, and morphological complexity of alphabetic languages...
2017: Reading and Writing
https://www.readbyqxmd.com/read/28931860/towards-an-ultra-rapid-smartphone-connected-test-for-infectious-diseases
#19
Valérian Turbé, Eleanor R Gray, Victoria E Lawson, Eleni Nastouli, Jennifer C Brookes, Robin A Weiss, Deenan Pillay, Vincent C Emery, C Theo Verrips, Hiromi Yatsuda, Dale Athey, Rachel A McKendry
The development is reported of an ultra-rapid, point-of-care diagnostic device which harnesses surface acoustic wave (SAW) biochips, to detect HIV in a finger prick of blood within 10 seconds (sample-in-result-out). The disposable quartz biochip, based on microelectronic components found in every consumer smartphone, is extremely fast because no complex labelling, amplification or wash steps are needed. A pocket-sized control box reads out the SAW signal and displays results electronically. High analytical sensitivity and specificity are found with model and real patient blood samples...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931699/adoption-of-telehealth-remote-biometric-monitoring-among-peritoneal-dialysis-patients-in-the-united-states
#20
Susie Q Lew, Neal Sikka, Clinton Thompson, Teena Cherian, Manya Magnus
We examined participant uptake and utilization of remote monitoring devices, and the relationship between remote biometric monitoring (RBM) of weight (Wt) and blood pressure (BP) with self-monitoring requirements. Participants on peritoneal dialysis (PD) (n = 269) participated in a Telehealth pilot study of which 253 used remote monitoring of BP and 255 for Wt. Blood pressure and Wt readings were transmitted in real time to a Telehealth call center, which were then forwarded to the PD nurses for real-time review...
September 2017: Peritoneal Dialysis International: Journal of the International Society for Peritoneal Dialysis
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