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https://www.readbyqxmd.com/read/29342247/peath-single-individual-haplotyping-by-a-probabilistic-evolutionary-algorithm-with-toggling
#1
Joong Chae Na, Jong-Chan Lee, Je-Keun Rhee, Soo-Yong Shin
Motivation: Single individual haplotyping (SIH) is critical in genomic association studies and genetic diseases analysis. However, most genomic analysis studies do not perform haplotype-phasing analysis due to its complexity. Several computational methods have been developed to solve the SIH problem, but these approaches have not generated sufficiently reliable haplotypes. Results: Here, we propose a novel SIH algorithm, called PEATH (Probabilistic Evolutionary Algorithm with Toggling for Haplotyping), to achieve more accurate and reliable haplotyping...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340954/the-cultural-epigenesis-of-gender-based-violence-in-cambodia-local-and-buddhist-perspectives
#2
Maurice Eisenbruch
Almost one in four women in Cambodia is a victim of physical, emotional or sexual violence. The study aims to provide a comprehensive understanding of the ways in which Cambodians see its causes and effects and to identify and analyse the cultural forces that underpin and shape its landscape. An ethnographic study was carried out with 102 perpetrators and survivors of emotional, physical and sexual violence against women and 228 key informants from the Buddhist and healing sectors. Their views and experiences of it were recorded-the popular idioms expressed and the symptoms of distress experienced by survivors and perpetrators...
January 16, 2018: Culture, Medicine and Psychiatry
https://www.readbyqxmd.com/read/29338297/unusual-case-of-left-atrial-myxoma-with-gastroesophageal-junction-adenocarcinoma
#3
Narinder Pal Singh, Swapan Deep Singh Nagpal, Arun Kumar Goel, Bhupendra Kr Dhingra
Cardiac myxomas are rare tumors. Esophageal adenocarcinomas are common tumors of the gastrointestinal tract. Simultaneous occurrence of these tumors has not been reported. A 52-year-old gentleman presented to our hospital with dysphagia and was diagnosed with esophageal adenocarcinoma. Routine echocardiography discovered a cardiac tumor in the left atrium. The cardiac tumor was surgically removed and biopsy confirmed a myxoma. We removed the cardiac tumor as the first step and then initiated neoadjuvant chemotherapy...
January 1, 2018: Asian Cardiovascular & Thoracic Annals
https://www.readbyqxmd.com/read/29334505/the-association-of-chronic-air-pollutants-with-coronary-artery-spasm-vasospastic-angina-and-endothelial-dysfunction
#4
Byoung Geol Choi, Jiwon Lee, Suhng Wook Kim, Min Woo Lee, Man Jong Baek, Yang Gi Ryu, Se Yeon Choi, Jae Kyeong Byun, Ahmed Mashaly, Yoonjee Park, Won Young Jang, Woohyeun Kim, Jah Yeon Choi, Eun Jin Park, Jin Oh Na, Cheol Ung Choi, Hong Euy Lim, Eung Ju Kim, Chang Gyu Park, Hong Seog Seo, Dong Joo Oh, Seung-Woon Rha
BACKGROUND: We evaluated the effect of chronic exposure to air pollutants (APs) on coronary endothelial function and significant coronary artery spasm (CAS) as assessed by intracoronary acetylcholine (ACH) provocation test. PATIENTS AND METHODS: A total of 6430 patients with typical or atypical chest pain who underwent intracoronary ACH provocation test were enrolled. We obtained data on APs from the Korean National Institute of Environmental Research (http://www...
January 12, 2018: Coronary Artery Disease
https://www.readbyqxmd.com/read/29327002/charge-separation-properties-of-ta3n5-photoanodes-synthesized-via-a-simple-metal-organic-precursor-decomposition-process
#5
Sung Gyu Han, Sang Youn Chae, Si Young Lee, Byoung Koun Min, Yun Jeong Hwang
Here, we successfully synthesized a Ta3N5 thin film using a simple metal-organic-precursor decomposition process followed by its conversion to nitride and studied its photoelectrochemical (PEC) properties to understand charge separation on the surface. Newly synthesized Ta3N5 photoanodes showed a significant difference in the PEC activity in relation to the annealing temperature under ammonia flow, although similar light absorption properties or electronic states were obtained. Charge separation related PEC properties were analyzed using intensity modulated photocurrent density spectroscopy (IMPS) and photocurrent measurements in the absence/presence of scavengers...
January 12, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29326022/the-effects-of-repetitive-transcranial-magnetic-stimulation-on-eating-behaviors-and-body-weight-in-obesity-a-randomized-controlled-study
#6
Se-Hong Kim, Ju-Hye Chung, Tae-Hong Kim, Seong Hoon Lim, Youngkook Kim, Yun-Ah Lee, Sang-Wook Song
BACKGROUND: Although some studies have reported significant reductions in food cravings following repetitive transcranial magnetic stimulation (rTMS), none have examined changes in body weight. OBJECTIVE: We conducted 2-week randomized, sham-controlled, single-blind, parallel-group trial to examine the effect of rTMS on body weight in obese patients. METHODS: Sixty obese patients (body mass index [BMI] ≥25 kg/m2) aged between 18 and 65 years were recruited...
December 1, 2017: Brain Stimulation
https://www.readbyqxmd.com/read/29321549/probing-the-molecular-basis-of-herg-drug-block-with-unnatural-amino-acids
#7
Logan C Macdonald, Robin Y Kim, Harley T Kurata, David Fedida
Repolarization of the cardiac action potential is primarily mediated by two voltage-dependent potassium currents: I Kr and I Ks . The voltage-gated potassium channel that gives rise to I Kr, Kv11.1 (hERG), is uniquely susceptible to high-affinity block by a wide range of drug classes. Pore residues Tyr652 and Phe656 are critical to potent drug interaction with hERG. It is considered that the molecular basis of this broad-spectrum drug block phenomenon occurs through interactions specific to the aromatic nature of the side chains at Tyr652 and Phe656...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29314423/kr%C3%A3-ppel-homologue-1-acts-as-a-repressor-and-an-activator-in-the-transcriptional-response-to-juvenile-hormone-in-adult-mosquitoes
#8
R Ojani, X Fu, T Ahmed, P Liu, J Zhu
Krüppel homologue 1 (Kr-h1) is a zinc finger transcription factor that is upregulated in insects by juvenile hormone (JH) in metamorphosis and adult reproduction. The molecular function of Kr-h1 in reproduction remains largely unknown. Here we report that AaKr-h1 functions as an important transcription regulator in adult female Aedes aegypti mosquitoes. The amount of AaKr-h1 protein increases with rising JH levels after adult emergence, reaches its peak at 48 h after eclosion, then decreases gradually and disappears after blood feeding...
January 4, 2018: Insect Molecular Biology
https://www.readbyqxmd.com/read/29313576/pharmacological-reperfusion-therapy-with-tenecteplase-in-7-668-indian-patients-with-st-elevation-myocardial-infarction-a-real-world-indian-experience
#9
S S Iyengar, Tiny Nair, Jagdish Hiremath, Anjan Lal Dutta, Uday Jadhav, V K Katyal, Dayanand Kumbla, Immaneni Sathyamurthy, R K Jain, M Srinivasan, Prasant Kr Sahoo
Objective: This real-world, observational, prescription event monitoring study was conducted to evaluate safety and efficacy of indigenous tenecteplase (TNK-tPA) in Indian patients presenting with ST elevation myocardial infarction (STEMI). Methods: This is a multi-centric, observational, prescription event monitoring study. Data was collected for 7,668 patients from 1,307 investigator sites across India from January 2011 to February 2016. Results: Overall, 76...
September 2017: Journal of the Association of Physicians of India
https://www.readbyqxmd.com/read/29301084/photochemical-formation-of-diazenecarbaldehyde-hnncho-and-diazenecarbothialdehyde-hnnchs-in-low-temperature-matrices
#10
Tamás Vörös, Győző György Lajgút, Gábor Magyarfalvi, György Tarczay
The photochemical decomposition of 1,2,4-oxadiazole-3,5-diamine and 1,2,4-thiadiazole-3,5-diamine was investigated in low-temperature Ar and Kr matrices at different wavelengths. The analysis of matrix-isolation infrared (MI-IR) spectra aided by high-level quantum chemical computations showed that these photochemical reactions yield not only [NH2, C, N, X] (X=O, S) isomers, but the bands of a novel, formerly unobserved species were also observed. The comparison of computed IR spectra of potential products with the observed spectra suggests that these species are the diazenecarbaldehyde (HNNCHO) and diazenecarbothialdehyde (HNNCHS)...
January 4, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29300412/the-influence-of-chemical-degradation-during-dietary-exposures-to-fish-on-biomagnification-factors-and-bioaccumulation-factors
#11
Jon A Arnot, Donald Mackay
The chemical dietary absorption efficiency (ED) quantifies the amount of chemical absorbed by an organism relative to the amount of chemical an organism is exposed to following ingestion. In particular, ED can influence the extent of bioaccumulation and biomagnification for hydrophobic chemicals. A new ED model is developed to quantify chemical process rates in the gastrointestinal tract (GIT). The new model is calibrated with critically evaluated measured ED values (n = 250) for 80 hydrophobic persistent chemicals...
January 4, 2018: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/29298879/combined-drug-therapeutic-strategies-for-the-effective-treatment-of-triple-negative-breast-cancer
#12
Naveen Kr Chalakur-Ramireddy, Suresh B Pakala
Triple negative breast cancer (TNBC) is a subtype of breast cancer with an aggressive phenotype which shows high metastatic capability and poor prognosis. Owing to its intrinsic properties like heterogeneity, lack of hormonal receptors, and aggressive phenotype leaves chemotherapy as a mainstay for the treatment of TNBC. Various studies have demonstrated that chemotherapy alone or therapeutic drugs targeting TNBC pathways, epigenetic mechanisms and immunotherapy alone have not shown significant improvement in TNBC patients...
January 3, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29297315/utilizing-random-forest-qsar-models-with-optimized-parameters-for-target-identification-and-its-application-to-target-fishing-server
#13
Kyoungyeul Lee, Minho Lee, Dongsup Kim
BACKGROUND: The identification of target molecules is important for understanding the mechanism of "target deconvolution" in phenotypic screening and "polypharmacology" of drugs. Because conventional methods of identifying targets require time and cost, in-silico target identification has been considered an alternative solution. One of the well-known in-silico methods of identifying targets involves structure activity relationships (SARs). SARs have advantages such as low computational cost and high feasibility; however, the data dependency in the SAR approach causes imbalance of active data and ambiguity of inactive data throughout targets...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29284404/multiple-functions-of-creb-binding-protein-during-postembryonic-development-identification-of-target-genes
#14
Amit Roy, Smitha George, Subba Reddy Palli
BACKGROUND: Juvenile hormones (JH) and ecdysteroids control postembryonic development in insects. They serve as valuable targets for pest management. Hence, understanding the molecular mechanisms of their action is of crucial importance. CREB-binding protein (CBP) is a universal transcriptional co-regulator. It controls the expression of several genes including those from hormone signaling pathways through co-activation of many transcription factors. However, the role of CBP during postembryonic development in insects is not well understood...
December 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29283579/how-inert-perturbing-or-interacting-are-cryogenic-matrices-a-combined-spectroscopic-infrared-electronic-and-x-ray-absorption-and-dft-investigation-of-matrix-isolated-iron-cobalt-nickel-and-zinc-dibromides
#15
Owen M Wilkin, Neil Harris, John F Rooms, Emma L Dixon, Adam J Bridgeman, Nigel Andrew Young
The interaction of FeBr2, CoBr2, NiBr2 and ZnBr2 with Ne, Ar, Kr, Xe, CH4 and N2 matrices has been investigated using IR, electronic absorption and X-ray absorption spectroscopies, as well as DFT calculations. ZnBr2 is linear in all the matrices. NiBr2 is linear in all but N2 matrices where it is severely bent. For FeBr2 and CoBr2 there is a more gradual change, with evidence of non-linearity in Xe and CH4 matrices as well as N2. In the N2 matrices the presence of νNN modes blue shifted from the "free" N2 values indicates the presence of physisorbed species, and the magnitude of the blue-shift correlates with the shift in the ν3 mode of the metal dibromide...
December 28, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29281985/deep-convolutional-neural-networks-for-pan-specific-peptide-mhc-class-i-binding-prediction
#16
Youngmahn Han, Dongsup Kim
BACKGROUND: Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, machine-learning-based methods have generated successful results by training large amounts of experimental data. However, many machine learning-based methods are generally less sensitive in recognizing locally-clustered interactions, which can synergistically stabilize peptide binding...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29274508/a-heparin-binding-motif-rich-in-arginine-and-lysine-is-the-functional-domain-of-ykl-40
#17
Nipaporn Ngernyuang, Wei Yan, Lawrence M Schwartz, Dennis Oh, Ying-Bin Liu, Hongzhuan Chen, Rong Shao
The heparin-binding glycoprotein YKL-40 (CHI3L1) is intimately associated with microvascularization in multiple human diseases including cancer and inflammation. However, the heparin-binding domain(s) pertinent to the angiogenic activity have yet been identified. YKL-40 harbors a consensus heparin-binding motif that consists of positively charged arginine (R) and lysine (K) (RRDK; residues 144-147); but they don't bind to heparin. Intriguingly, we identified a separate KR-rich domain (residues 334-345) that does display strong heparin binding affinity...
December 20, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29273814/the-crucial-role-of-the-trpm7-kinase-domain-in-the-early-stage-of-amelogenesis
#18
Kayoko Ogata, Tomoyuki Tsumuraya, Kyoko Oka, Masashi Shin, Fujio Okamoto, Hiroshi Kajiya, Chiaki Katagiri, Masao Ozaki, Masayuki Matsushita, Koji Okabe
Transient receptor potential melastatin-7 (TRPM7) is a bi-functional protein containing a kinase domain fused to an ion channel. TRPM7 is highly expressed in ameloblasts during tooth development. Here we show that TRPM7 kinase-inactive knock-in mutant mice (TRPM7 KR mice) exhibited small enamel volume with opaque white-colored incisors. The TRPM7 channel function of ameloblast-lineage cells from TRPM7 KR mice was normal. Interestingly, phosphorylation of intracellular molecules including Smad1/5/9, p38 and cAMP response element binding protein (CREB) was inhibited in ameloblasts from TRPM7 KR mice at the pre-secretory stage...
December 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29251441/monitoring-of-the-conformational-space-of-dipeptides-by-generative-topographic-mapping
#19
Dragos Horvath, Gilles Marcou, Alexandre Varnek
This work describes a procedure to build generative topographic maps (GTM) as 2D representation of the conformational space (CS) of dipeptides. GTMs with excellent propensities to support highly predictive landscapes of various conformational properties were reported for three dipeptides (AA, KE and KR). CS monitoring via GTMproceeds through the projection of conformer ensembles on the map, producing cumulated responsibility (CR) vectors characteristic of the CS areas covered by the ensemble. Overlap of the CS areas visited by two distinct simulations can be expressed by the Tanimoto coefficient Tc of the associated CRs...
December 18, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29249635/study-on-physical-properties-of-ayurvedic-nanocrystalline-tamra-bhasma-by-employing-modern-scientific-tools
#20
Rakesh Kr Singh, Sanjay Kumar, Abhay Kr Aman, S M Karim, Sunil Kumar, Manoranjan Kar
BACKGROUND: Tamra Bhasma is derived from metallic copper that is recommended for different ailments of liver and spleen, dropsy, abdominal pain, heart disease, colitis, tumors, anemia, loss of appetite, tuberculosis, as well as eye problems. OBJECTIVES: The knowledge of crystallite size and active ingredients in Bhasma materials is limited restricting its use as nanomedicine in the modern era. Also, the 2015 Nobel prize in medicine has motivated many researchers towards traditional medicines...
December 15, 2017: Journal of Ayurveda and Integrative Medicine
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