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https://www.readbyqxmd.com/read/28936969/systematic-integration-of-biomedical-knowledge-prioritizes-drugs-for-repurposing
#1
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms...
September 22, 2017: ELife
https://www.readbyqxmd.com/read/28936638/examining-reproducibility-in-psychology-a-hybrid-method-for-combining-a-statistically-significant-original-study-and-a-replication
#2
Robbie C M van Aert, Marcel A L M van Assen
The unrealistically high rate of positive results within psychology has increased the attention to replication research. However, researchers who conduct a replication and want to statistically combine the results of their replication with a statistically significant original study encounter problems when using traditional meta-analysis techniques. The original study's effect size is most probably overestimated because it is statistically significant, and this bias is not taken into consideration in traditional meta-analysis...
September 21, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28933800/prevalence-and-morphometric-analysis-of-idiopathic-osteosclerosis-in-a-chilean-population
#3
Ramón Fuentes, Alain Arias, Nicolás Astete, Constanza Farfán, Ivonne Garay, Fernando Dias
The aim of this study was to analyse the prevalence and morphometric parameters of idiopathic osteosclerosis (IO) in a Chilean population. IO is an intraosseous growth of compact, benign, unilocular, non-expandable bone that is referred to as an anatomical variation. A cross-sectional study was performed using 1000 digital panoramic radiographs of adults in which data on the location (maxillary/mandibular, right/left hemiarcades), shape, position to the dental apex, and the prevalence of IOs were observed in relation to gender and age...
September 21, 2017: Folia Morphologica (Warsz)
https://www.readbyqxmd.com/read/28932610/pneumocystis-pneumonia-in-non-hiv-pregnant-women-receiving-chemotherapy-for-malignant-lymphoma-two-case-reports
#4
Yuki Fukutani, Yoshitsugu Chigusa, Eiji Kondoh, Kaoru Kawasaki, Shingo Io, Noriomi Matsumura
Pneumocystis pneumonia (PCP) is a life-threatening opportunistic infection that sometimes occurs in immunocompromised patients with human immunodeficiency virus (HIV). Here, we report two extremely rare cases of PCP in non-HIV pregnant women who underwent chemotherapy for malignant lymphoma. Case  1 is a 34-year-old primigravida who was diagnosed with Hodgkin's lymphoma. She received ABVD chemotherapy and developed PCP at 37 weeks of gestation. After the onset of PCP, emergent cesarean section was performed due to a nonreassuring fetal status...
2017: Case Reports in Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28929970/bayesian-unidimensional-scaling-for-visualizing-uncertainty-in-high-dimensional-datasets-with-latent-ordering-of-observations
#5
Lan Huong Nguyen, Susan Holmes
BACKGROUND: Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as microbial community composition or gene expression data, observations can be generated from a continuous process, often unknown. Estimating data points' 'natural ordering' and their corresponding uncertainties can help researchers draw insights about the mechanisms involved...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28922049/magnitudes-of-muscle-activation-of-spine-stabilizers-in-healthy-adults-during-prone-on-elbow-planking-exercises-with-and-without-a-fitness-ball
#6
James W Youdas, Kendra C Coleman, Erin E Holstad, Stephanie D Long, Nicole L Veldkamp, John H Hollman
Prone planking exercises have been used by rehabilitation professionals to activate torso muscles in healthy persons and those with low back pain. The aim of this study was to compare the magnitude of electromyographic (EMG) muscle activation from 10 right-sided muscles as demonstrated by the percentage of maximum voluntary isometric contraction (%MVIC) during four planking procedures. Surface EMG activity was acquired from the following muscles: (1) iliocostalis lumborum (IL), (2) longissimus thoracis (LT), (3) lumbar multifidus (LM), (4) rectus abdominis (RA), (5) external oblique (EO), (6) internal oblique (IO), (7) serratus anterior (SA), (8) latissimus dorsi (LD), (9) hamstrings (HS), and (10) gluteus maximus (GM)...
September 18, 2017: Physiotherapy Theory and Practice
https://www.readbyqxmd.com/read/28919965/the-cerrado-brazil-plant-cytogenetics-database
#7
Fernando Roa, Mariana Pires de Campos Telles
Cerrado is a biodiversity hotspot that has lost ca. 50% of its original vegetation cover and hosts ca. 11,000 species belonging to 1,423 genera of phanerogams. For a fraction of those species some cytogenetic characteristics like chromosome numbers and C-value were available in databases, while other valuable information such as karyotype formula and banding patterns are missing. In order to integrate and share all cytogenetic information published for Cerrado species, including frequency of cytogenetic attributes and scientometrics aspects, Cerrado plant species were searched in bibliographic sources, including the 50 richest genera (with more than 45 taxa) and 273 genera with only one species in Cerrado...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/28918062/detection-of-no-model-input-output-pairs-in-closed-loop-systems
#8
Alain Segundo Potts, Christiam Segundo Morales Alvarado, Claudio Garcia
The detection of no-model input-output (IO) pairs is important because it can speed up the multivariable system identification process, since all the pairs with null transfer functions are previously discarded and it can also improve the identified model quality, thus improving the performance of model based controllers. In the available literature, the methods focus just on the open-loop case, since in this case there is not the effect of the controller forcing the main diagonal in the transfer matrix to one and all the other terms to zero...
September 13, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28916823/digging-into-the-low-molecular-weight-peptidome-with-the-oligonet-web-server
#9
Youzhong Liu, Sara Forcisi, Marianna Lucio, Mourad Harir, Florian Bahut, Magali Deleris-Bou, Sibylle Krieger-Weber, Régis D Gougeon, Hervé Alexandre, Philippe Schmitt-Kopplin
Bioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as "hidden treasure" of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28912520/intraoperative-intorsional-traction-test-of-the-inferior-oblique
#10
A J Connor, S P Kraft
PurposeWe present a novel variation of the traction test of the inferior oblique (IO) muscle. We demonstrate the correlation between the traction test and clinically graded IO overaction and describe the utility of this test to confirm IO weakening.MethodsWe performed a retrospective chart review on all patients who underwent IO surgery and intraoperative intorsion traction tests by a single surgeon over a 10-year period. We compared the traction test results, in 'clock hours' of freedom, before and after IO surgery...
September 15, 2017: Eye
https://www.readbyqxmd.com/read/28910187/sternal-route-more-effective-than-tibial-route-for-intraosseous-amiodarone-administration-in-a-swine-model-of-ventricular-fibrillation
#11
James M Burgert, Andre Martinez, Mara O'Sullivan, Dawn Blouin, Audrey Long, Arthur D Johnson
OBJECTIVE: The pharmacokinetics of IO administered lipid soluble amiodarone during ventricular fibrillation (VF) with ongoing CPR are unknown. This study measured mean plasma concentration over 5 minutes, maximum plasma concentration (Cmax), and time to maximum concentration (Tmax) of amiodarone administered by the sternal IO (SIO), tibial IO (TIO), and IV routes in a swine model of VF with ongoing CPR. METHODS: Twenty-one Yorkshire-cross swine were randomly assigned to three groups: SIO, TIO, and IV...
September 14, 2017: Prehospital Emergency Care
https://www.readbyqxmd.com/read/28895031/utility-of-endoanal-ultrasonography-in-assessment-of-primary-and-recurrent-anal-fistulas-and-for-detection-of-associated-anal-sphincter-defects
#12
Sameh Hany Emile, Alaa Magdy, Mohamed Youssef, Waleed Thabet, Mahmoud Abdelnaby, Waleed Omar, Wael Khafagy
BACKGROUND: Tridimensional endoanal ultrasonography (3D-EAUS) has been used for the assessment of various anorectal lesions. Previous studies have reported good accuracy of 3D-EAUS in preoperative assessment of fistula-in-ano (FIA). This study aimed to assess the diagnostic utility of 3D-EAUS in preoperative evaluation of primary and recurrent FIA and its role in detection of associated anal sphincter (AS) defects. PATIENTS AND METHODS: Prospectively collected data of patients with FIA who were investigated with 3D-EAUS were reviewed...
September 11, 2017: Journal of Gastrointestinal Surgery: Official Journal of the Society for Surgery of the Alimentary Tract
https://www.readbyqxmd.com/read/28893316/intraosseous-blood-samples-for-point-of-care-analysis-agreement-between-intraosseous-and-arterial-analyses
#13
Milla Jousi, Simo Saikko, Jouni Nurmi
BACKGROUND: Point-of-care (POC) testing is highly useful when treating critically ill patients. In case of difficult vascular access, the intraosseous (IO) route is commonly used, and blood is aspirated to confirm the correct position of the IO-needle. Thus, IO blood samples could be easily accessed for POC analyses in emergency situations. The aim of this study was to determine whether IO values agree sufficiently with arterial values to be used for clinical decision making. METHODS: Two samples of IO blood were drawn from 31 healthy volunteers and compared with arterial samples...
September 11, 2017: Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine
https://www.readbyqxmd.com/read/28891005/evaluation-of-the-internal-oblique-external-oblique-and-transversus-abdominalis-muscles-in-patients-with-ankylosing-spondylitis-an-ultrasonographic-study
#14
Ahmet Üşen, Banu Kuran, Figen Yılmaz, Neşe Aksu, Cem Erçalık
The objectives of the study are to compare abdominal muscle thickness in ankylosing spondylitis (AS) patients with healthy subjects and determine the factors affecting these muscle thickness. Thirty-five male patients with a previous diagnosis of AS according to the Modified New York criteria and a control group consisting of 35 healthy male individuals were included in this cross-sectional and case-control study. Thicknesses of the internal oblique (IO), external oblique (EO), and transversus abdominalis (TrA) muscles were measured with ultrasound (US)...
September 10, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28881972/abundance-estimation-and-differential-testing-on-strain-level-in-metagenomics-data
#15
Martina Fischer, Benjamin Strauch, Bernhard Y Renard
Motivation: Current metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number of tools approach taxa abundance estimation beyond species level and there is a strong need for dedicated tools for strain resolution and differential abundance testing...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881963/deep-learning-with-word-embeddings-improves-biomedical-named-entity-recognition
#16
Maryam Habibi, Leon Weber, Mariana Neves, David Luis Wiegandt, Ulf Leser
Motivation: Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878825/rna-sequence-data-normalization-through-in-silico-prediction-of-reference-genes-the-bacterial-response-to-dna-damage-as-case-study
#17
Bork A Berghoff, Torgny Karlsson, Thomas Källman, E Gerhart H Wagner, Manfred G Grabherr
BACKGROUND: Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes...
2017: BioData Mining
https://www.readbyqxmd.com/read/28877583/leaf-lims-a-flexible-laboratory-information-management-system-with-a-synthetic-biology-focus
#18
Thomas Craig, Richard Holland, Rosalinda D'Amore, James Johnson, Hannah V McCue, Anthony West, Valentin Zulkower, Hille Tekotte, Yizhi Cai, Daniel Swan, Robert P Davey, Christiane Hertz-Fowler, Anthony Hall, Mark Caddick
This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most LIMS systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture...
September 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28876160/abdominal-draw-in-maneuver-combined-with-simulated-weight-bearing-increases-transversus-abdominis-and-internal-oblique-thickness
#19
Jeong-Soo Kim, Cynn-Heon Seok, Hye-Seon Jeon
The abdominal draw-in maneuver (ADIM) is a method commonly used to reestablish neuromuscular control of the deep spine muscles among individuals with musculoskeletal problems. The purpose of this study was to evaluate the effect of ADIM combined with simulated weight-bearing (SWB) activities in the facilitation of the deep spine muscles. The subjects were 30 young healthy individuals. Ultrasound images were used to measure the relative changes in transverse abdominal (TrA), internal oblique (IO) and external oblique (EO) muscle thickness during a simulated weight-bearing ADIM (SWB-ADIM)...
September 6, 2017: Physiotherapy Theory and Practice
https://www.readbyqxmd.com/read/28874585/active-molecular-iodine-photochemistry-in-the-arctic
#20
Angela R W Raso, Kyle D Custard, Nathaniel W May, David Tanner, Matt K Newburn, Lawrence Walker, Ronald J Moore, L G Huey, Liz Alexander, Paul B Shepson, Kerri A Pratt
During springtime, the Arctic atmospheric boundary layer undergoes frequent rapid depletions in ozone and gaseous elemental mercury due to reactions with halogen atoms, influencing atmospheric composition and pollutant fate. Although bromine chemistry has been shown to initiate ozone depletion events, and it has long been hypothesized that iodine chemistry may contribute, no previous measurements of molecular iodine (I2) have been reported in the Arctic. Iodine chemistry also contributes to atmospheric new particle formation and therefore cloud properties and radiative forcing...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
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