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https://www.readbyqxmd.com/read/28401899/improved-imputation-accuracy-of-rare-and-low-frequency-variants-using-population-specific-high-coverage-wgs-based-imputation-reference-panel
#1
Mario Mitt, Mart Kals, Kalle Pärn, Stacey B Gabriel, Eric S Lander, Aarno Palotie, Samuli Ripatti, Andrew P Morris, Andres Metspalu, Tõnu Esko, Reedik Mägi, Priit Palta
Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 × ) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28386328/kallistatin-protects-against-bleomycin-induced-idiopathic-pulmonary-fibrosis-by-inhibiting-angiogenesis-and-inflammation
#2
Xiaoping Huang, Xiao Wang, Xiaolan Xie, Shulan Zeng, Zhaofa Li, Xianxiang Xu, Huiyong Yang, Fei Qiu, Junsheng Lin, Yong Diao
Aberrant angiogenesis and vascular remodeling are the main features of idiopathic pulmonary fibrosis. Kallistatin is an anti-angiogenic peptide with known effects on endothelial cells. This study aimed to demonstrate that kallistatin has beneficial effects on bleomycin (BLM)-induced pulmonary fibrosis in a rat model by inhibiting angiogenesis. Twenty-five rats were randomly divided into five experimental groups: (A) Saline only (SA)-as the negative control, (B) BLM only (BLM)-as the model group, (C) BLM and 0...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28352926/the-effect-of-requesting-a-reason-for-non-adherence-to-a-guideline-in-a-long-running-automated-reminder-system-for-ponv-prophylaxis
#3
Fabian O Kooij, Toni Klok, Benedikt Preckel, Markus W Hollmann, Jasper E Kal
BACKGROUND: Automated reminders are employed frequently to improve guideline adherence, but limitations of automated reminders are becoming more apparent. We studied the reasons for non-adherence in the setting of automated reminders to test the hypothesis that a separate request for a reason in itself may further improve guideline adherence. METHODS: In a previously implemented automated reminder system on prophylaxis for postoperative nausea and vomiting (PONV), we included additional automated reminders requesting a reason for non-adherence...
March 29, 2017: Applied Clinical Informatics
https://www.readbyqxmd.com/read/28295652/long-term-survival-following-kidney-transplantation-in-previous-lung-transplant-recipients-an-analysis-of-the-unos-registry
#4
Asishana A Osho, Sameer A Hirji, Anthony W Castleberry, Michael S Mulvihill, Asvin M Ganapathi, Paul J Speicher, Babatunde Yerokun, Laurie D Snyder, Robert D Davis, Mathew G Hartwig
BACKGROUND: Kidney transplantation has been advocated as a therapeutic option in lung recipients who develop end-stage renal disease (ESRD). This analysis outlines patterns of allograft survival following kidney transplantation in previous lung recipients (KAL). METHODS: Data from the UNOS lung and kidney transplantation registries (1987-2013) were cross-linked to identify lung recipients who were subsequently listed for and/or underwent kidney transplantation. Time-dependent Cox models compared the survival rates in KAL patients with those waitlisted for renal transplantation who never received kidneys...
March 10, 2017: Clinical Transplantation
https://www.readbyqxmd.com/read/28263850/laser-capture-micro-dissection-combined-with-next-generation-sequencing-analysis-of-cell-type-specific-deafness-gene-expression-in-the-mouse-cochlea
#5
Shin-Ya Nishio, Yutaka Takumi, Shin-Ichi Usami
Cochlear implantation (CI), which directly stimulates the cochlear nerves, is the most effective and widely used medical intervention for patients with severe to profound sensorineural hearing loss. The etiology of the hearing loss is speculated to have a major influence of CI outcomes, particularly in cases resulting from mutations in genes preferentially expressed in the spiral ganglion region. To elucidate precise gene expression levels in each part of the cochlea, we performed laser-capture micro dissection in combination with next-generation sequencing analysis and determined the expression levels of all known deafness-associated genes in the organ of Corti, spiral ganglion, lateral wall, and spiral limbs...
May 2017: Hearing Research
https://www.readbyqxmd.com/read/28261890/ozone-prevents-cochlear-damage-from-ischemia-reperfusion-injury-in-guinea-pigs
#6
Merih Onal, Cagdas Elsurer, Nebil Selimoglu, Mustafa Yilmaz, Ender Erdogan, Jale Bengi Celik, Oznur Kal, Ozkan Onal
The cochlea is an end organ, which is metabolically dependent on a nutrient and oxygen supply to maintain its normal physiological function. Cochlear ischemia and reperfusion (IR) injury is considered one of the most important causes of human idiopathic sudden sensorineural hearing loss. The aim of the present study was to study the efficacy of ozone therapy against cochlear damage caused by IR injury and to investigate the potential clinical use of this treatment for sudden deafness. Twenty-eight guinea pigs were randomized into four groups...
March 5, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28210972/evidence-against-vs-in-favour-of-a%C3%A2-null-hypothesis
#7
Jimmie Leppink, Patricia O'Sullivan, Kal Winston
No abstract text is available yet for this article.
April 2017: Perspectives on Medical Education
https://www.readbyqxmd.com/read/28127547/characterization-and-expression-analysis-of-common-bean-histone-deacetylase-6-during-development-and-cold-stress-response
#8
Rita Kusi-Appiah Hayford, Ayalew Ligaba-Osena, Mayavan Subramani, Adrianne Brown, Kalpalatha Melmaiee, Khwaja Hossain, Venu Kal Kalavacharla
Histone deacetylases (HDACs) are important regulators of gene transcription thus controlling multiple cellular processes. Despite its essential role in plants, HDA6 is yet to be validated in common bean. In this study, we show that HDA6 is involved in plant development and stress response. Differential expression of HDA6 was determined in various tissues and the expression was seen to be upregulated with plant age (seedling < flowering < maturity). Higher expression was observed in flowers and pods than in stem, leaf, and root...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#9
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28074320/algorithmic-three-dimensional-analysis-of-tumor-shape-in-mri-improves-prognosis-of-survival-in-glioblastoma-a-multi-institutional-study
#10
Nicholas Czarnek, Kal Clark, Katherine B Peters, Maciej A Mazurowski
In this retrospective, IRB-exempt study, we analyzed data from 68 patients diagnosed with glioblastoma (GBM) in two institutions and investigated the relationship between tumor shape, quantified using algorithmic analysis of magnetic resonance images, and survival. Each patient's Fluid Attenuated Inversion Recovery (FLAIR) abnormality and enhancing tumor were manually delineated, and tumor shape was analyzed by automatic computer algorithms. Five features were automatically extracted from the images to quantify the extent of irregularity in tumor shape in two and three dimensions...
January 10, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28074299/dioxygen-activation-by-nonheme-iron-enzymes-with-the-2-his-1-carboxylate-facial-triad-that-generate-high-valent-oxoiron-oxidants
#11
REVIEW
Subhasree Kal, Lawrence Que
The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O2 and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions...
January 10, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28031487/comprehensive-population-based-genome-sequencing-provides-insight-into-hematopoietic-regulatory-mechanisms
#12
Michael H Guo, Satish K Nandakumar, Jacob C Ulirsch, Seyedeh M Zekavat, Jason D Buenrostro, Pradeep Natarajan, Rany M Salem, Roberto Chiarle, Mario Mitt, Mart Kals, Kalle Pärn, Krista Fischer, Lili Milani, Reedik Mägi, Priit Palta, Stacey B Gabriel, Andres Metspalu, Eric S Lander, Sekar Kathiresan, Joel N Hirschhorn, Tõnu Esko, Vijay G Sankaran
Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27992442/is-implicit-motor-learning-preserved-after-stroke-a-systematic-review-with-meta-analysis
#13
E Kal, M Winters, J van der Kamp, H Houdijk, E Groet, C van Bennekom, E Scherder
Many stroke patients experience difficulty with performing dual-tasks. A promising intervention to target this issue is implicit motor learning, as it should enhance patients' automaticity of movement. Yet, although it is often thought that implicit motor learning is preserved post-stroke, evidence for this claim has not been systematically analysed yet. Therefore, we systematically reviewed whether implicit motor learning is preserved post-stroke, and whether patients benefit more from implicit than from explicit motor learning...
2016: PloS One
https://www.readbyqxmd.com/read/27915583/the-six-minute-walk-test-predicts-cardiorespiratory-fitness-in-individuals-with-aneurysmal-subarachnoid-hemorrhage
#14
Wouter J Harmsen, Gerard M Ribbers, Jorrit Slaman, Majanka H Heijenbrok-Kal, Ladbon Khajeh, Fop van Kooten, Sebastiaan J C M M Neggers, Rita J van den Berg-Emons
BACKGROUND: Peak oxygen uptake (VO2peak) established during progressive cardiopulmonary exercise testing (CPET) is the "gold-standard" for cardiorespiratory fitness. However, CPET measurements may be limited in patients with aneurysmal subarachnoid hemorrhage (a-SAH) by disease-related complaints, such as cardiovascular health-risks or anxiety. Furthermore, CPET with gas-exchange analyses require specialized knowledge and infrastructure with limited availability in most rehabilitation facilities...
December 5, 2016: Topics in Stroke Rehabilitation
https://www.readbyqxmd.com/read/27886941/management-of-musculoskeletal-pain-in-a-compensable-environment-implementation-of-helpful-and-unhelpful-models-of-care-in-supporting-recovery-and-return-to-work
#15
REVIEW
Darren Beales, Kal Fried, Michael Nicholas, Fiona Blyth, Damien Finniss, G Lorimer Moseley
Models of Care (MoCs) for injured workers in the compensation environment recommend adoption of biopsychosocial management approaches. Still, widespread dominance of biomedical constructs at the system, organisational and individual levels of the compensation system prevails, contributing to suboptimal management practices and outcomes for injured workers. Efforts to implement contemporary MoCs in the compensation environment show some promise in improving outcomes. Areas of promise at the organisational level, particularly in the workplace, and at the system level are discussed...
June 2016: Best Practice & Research. Clinical Rheumatology
https://www.readbyqxmd.com/read/27862601/in-silico-synthesis-of-synthetic-receptors-a-polymerization-algorithm
#16
Todd Cowen, Mirko Busato, Kal Karim, Sergey A Piletsky
Molecularly imprinted polymer (MIP) synthetic receptors have proposed and applied applications in chemical extraction, sensors, assays, catalysis, targeted drug delivery, and direct inhibition of harmful chemicals and pathogens. However, they rely heavily on effective design for success. An algorithm has been written which mimics radical polymerization atomistically, accounting for chemical and spatial discrimination, hybridization, and geometric optimization. Synthetic ephedrine receptors were synthesized in silico to demonstrate the accuracy of the algorithm in reproducing polymers structures at the atomic level...
December 2016: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/27821718/arterio-venous-anastomoses-in-isolated-perfused-rat-lungs
#17
Robert L Conhaim, Gilad S Segal, Kal E Watson
Several studies have suggested that large-diameter (>25 μm) arterio-venous shunt pathways exist in the lungs of rats, dogs, and humans. We investigated the nature of these pathways by infusing specific-diameter fluorescent latex particles (4, 7, 15, 30, or 50 μm) into isolated, ventilated rat lungs perfused at constant pressure. All lungs received the same mass of latex (5 mg), which resulted in infused particle numbers that ranged from 1.7 × 10(7) 4 μm particles to 7.5 × 10(4) 50 μm particles...
November 2016: Physiological Reports
https://www.readbyqxmd.com/read/27816849/a-collaborative-ednap-exercise-on-snapshot%C3%A2-based-mtdna-control-region-typing
#18
N E C Weiler, K Baca, D Ballard, F Balsa, M Bogus, C Børsting, F Brisighelli, J Červenáková, L Chaitanya, M Coble, V Decroyer, S Desmyter, K J van der Gaag, K Gettings, C Haas, J Heinrich, M João Porto, A J Kal, M Kayser, A Kúdelová, N Morling, A Mosquera-Miguel, F Noel, W Parson, V Pereira, C Phillips, P M Schneider, D Syndercombe Court, M Turanska, A Vidaki, P Woliński, L Zatkalíková, T Sijen
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment...
January 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27812750/comparative-transcriptome-profiling-of-upland-vs16-and-lowland-ap13-ecotypes-of-switchgrass
#19
COMPARATIVE STUDY
Vasudevan Ayyappan, Malay C Saha, Jyothi Thimmapuram, Venkateswara R Sripathi, Ketaki P Bhide, Elizabeth Fiedler, Rita K Hayford, Venu Kal Kalavacharla
Transcriptomes of two switchgrass genotypes representing the upland and lowland ecotypes will be key tools in switchgrass genome annotation and biotic and abiotic stress functional genomics. Switchgrass (Panicum virgatum L.) is an important bioenergy feedstock for cellulosic ethanol production. We report genome-wide transcriptome profiling of two contrasting tetraploid switchgrass genotypes, VS16 and AP13, representing the upland and lowland ecotypes, respectively. A total of 268 million Illumina short reads (50 nt) were generated, of which, 133 million were obtained in AP13 and the rest 135 million in VS16...
January 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/27805514/relation-between-pulmonary-hypertension-and-health-related-quality-of-life-in-patients-undergoing-hemodialysis
#20
Tülay Kıvanç, Öznur Kal, Öznur Çiftçi, Şule Akçay
OBJECTIVES: Pulmonary hypertension has been reported to occur in a considerable proportion of patients with end-stage renal disease. End-stage renal disease affects the health-related quality of life of patients. There is a lack of specific information on the relation between pulmonary hypertension and health-related quality of life in patients with end-stage renal disease in the literature. We aimed to evaluate this relation in patients undergoing hemodialysis. MATERIALS AND METHODS: This prospective case-control study included 68 patients treated with hemodialysis and 30 healthy participants as controls...
2016: Experimental and Clinical Transplantation
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