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https://www.readbyqxmd.com/read/29244056/cscoretool-fast-hi-c-compartment-analysis-at-high-resolution
#1
Xiaobin Zheng, Yixian Zheng
Summary: The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth...
December 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29243504/promoting-language-and-social-communication-development-in-babies-through-an-early-storybook-reading-intervention
#2
Michelle I Brown, Marleen F Westerveld, David Trembath, Gail T Gillon
PURPOSE: This study examined the effectiveness of low- and high-intensity early storybook reading (ESR) intervention workshops delivered to parents for promoting their babies language and social communication development. These workshops educated parents on how to provide a stimulating home reading environment and engage in parent-child interactions during ESR. METHOD: Parent-child dyads (n = 32); child age: 3-12 months, were assigned into two intervention conditions: low and high intensity (LI versus HI) groups...
December 15, 2017: International Journal of Speech-language Pathology
https://www.readbyqxmd.com/read/29240230/lc-ms-ms-profiling-of-polyphenol-enriched-leaf-stem-and-root-extracts-of-korean-humulus-japonicus-siebold-zucc-and-determination-of-their-antioxidant-effects
#3
Jin Young Choi, Kebede Taye Desta, Soo Jung Lee, Yun-Hi Kim, Sung Chul Shin, Gon-Sup Kim, Sung Joong Lee, Jae-Han Shim, Ahmet Hacımüftüo, A M Abd El-Aty
Polyphenols from ethyl acetate extracts from the leaves, stems, and roots of Korean Humulus japonicus were comprehensively profiled using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). A total of 36 polyphenols were detected, of which 26 were structurally characterized based on their [M-H]- peak, MS/MS fragmentation pattern, UV-Vis absorption, and published data. Validation data provided satisfactory results for the evaluated parameters. The determination coefficients (R2 ) exceeded or equal to 0...
December 14, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29238387/the-tight-interlocked-rhythm-section-production-and-perception-of-synchronisation-in-jazz-trio-performance
#4
Alex Hofmann, Brian C Wesolowski, Werner Goebl
This study investigates the production and perception of timing, synchronisation and dynamics in jazz trio performances. In a production experiment, six trio combinations of one saxophonist, two bassists, and three drummers were recorded while they performed three popular jazz songs. Onset timing and dynamics of each performer were extracted and analysed. Results showed that the tempo was significantly influenced by the timing of the drummers and all performers showed higher temporal precision on the backbeats...
2017: Journal of New Music Research
https://www.readbyqxmd.com/read/29237994/evaluation-of-operational-parameters-role-on-the-emission-of-fumes
#5
Javad Sajedifar, Amir Hossein Kokabi, Somayeh Farhang Dehghan, Ahmad Mehri, Kamal Azam, Farideh Golbabaei
Electric arc welding is a routine operation in the construction of metallic structures, but the fumes generated during the welding process can threaten the health of welders. Fumes are undesirable products of the majority of welding operations and may have various detrimental effects on health. The purpose of this study was to investigate the effect of operational parameters of the shielded metal arc welding (SMAW) process on the emission of fumes. A dust monitor was used to measure the number and mass concentration of fumes generated by SMAW...
December 12, 2017: Industrial Health
https://www.readbyqxmd.com/read/29236582/heavy-metals-in-eggs-and-chicken-and-the-associated-human-health-risk-assessment-in-the-mining-areas-of-singhbhum-copper-belt-india
#6
Soma Giri, Abhay Kumar Singh
Metal contamination was studied in locally rearing chicken and eggs in the environs of mining areas of Singhbhum copper belt. Concentrations of metals were below Indian standards except for Cu, Ni and Zn in the case of chicken at some locations. Estimated daily intake (EDI) and target hazard quotient (THQ) suggested that the metals did not pose risk individually. However, considering the geometric mean of the metals, hazard index (HI) was above unity. Cu, Pb and Co were the key components contributing to a potential noncarcinogenic risk...
December 13, 2017: Archives of Environmental & Occupational Health
https://www.readbyqxmd.com/read/29235849/all-small-molecule-solar-cells-incorporating-ndi-based-acceptors-synthesis-and-full-characterization
#7
Jisu Hong, Yeon Hee Ha, Hyojung Cha, Ran Kim, Yu Jin Kim, Chan Eon Park, James R Durrant, Soon-Ki Kwon, Tae Kyu An, Yun-Hi Kim
A series of naphthalene diimide (NDI)-based small molecules were synthesized as nonfullerene acceptors and incorporated in all-small-molecule solar cells. Three NDI-based small molecules, NDICN-T, NDICN-BT, and NDICN-TVT, were designed with different linkers between two NDI units to induce the different conjugation length and modulate the geometric structures of the NDI dimers. The small NDI-based dimer electron acceptors with slip-stacked structures that facilitate π-π stacking interactions and/or hinder excessive aggregation exhibited different morphological behaviors, such as miscibility or crystallinity in bulk heterojunction blends with 7,7'-(4,4-bis(2-ethylhexyl)-4H-silolo[3,2-b:4,5-b']dithiophene-2,6-diyl)bis(6-fluoro-4-(5'-hexyl-[2,2'-bithiophen]-5-yl)benzo[c][1,2,5]thiadiazole) (DTS-F) electron donors...
December 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29233143/relative-hyperglycemia-is-associated-with-complications-following-an-acute-myocardial-infarction-a-post-hoc-analysis-of-hi-5-data
#8
Tien F Lee, Morton G Burt, Leonie K Heilbronn, Arduino A Mangoni, Vincent W Wong, Mark McLean, N Wah Cheung
BACKGROUND: Hyperglycemia is associated with increased morbidity and mortality in patients with an acute myocardial infarction (AMI). We evaluated whether complications after AMI are associated with absolute or relative glycemia. METHODS: A total of 192 patients with AMI were randomized to intensive or conventional insulin therapy. Absolute glycemia was defined as mean blood glucose level (BGL) during the first 24 h following randomization. Relative glycemia was defined by the stress hyperglycaemia ratio (SHR), calculated as mean BGL divided by average glucose concentration over the prior 3 months estimated from glycosylated haemoglobin...
December 12, 2017: Cardiovascular Diabetology
https://www.readbyqxmd.com/read/29231514/-development-of-non-traumatic-pain-acupuncture-moxibustion-apparatus-and-its-industrialization
#9
Qian Ran, Xingpeng Jiang
In order to alleviate the discomforts induced by the invasive manipulation of acupuncture, improve the acceptability of acupuncture-moxibustion therapy and promote the application of it in healthcare, the research team developed the non-traumatic-pain acupuncture-moxibustion apparatus for disease treatment and prevention as well as healthcare, such as crude herbal moxibustion plus cupping device (cupping device), the healthcare cloth for warming the governor vessel (healthcare cloth) and the governor vessel intelligent diagnosis apparatus (diagnosis apparatus)...
June 12, 2017: Zhongguo Zhen Jiu, Chinese Acupuncture & Moxibustion
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#10
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229338/delayed-occurrence-of-diabetes-insipidus-following-transsphenoidal-surgery-with-radiological-evaluation-of-the-pituitary-stalk-on-magnetic-resonance-imaging
#11
Yasuhiko Hayashi, Yasuhiro Aida, Yasuo Sasagawa, Masahiro Oishi, Daisuke Kita, Osamu Tachibana, Fumiaki Ueda, Mitsutoshi Nakada
INTRODUCTION: Diabetes insipidus (DI) is a major complication of transsphenoidal surgery (TSS). DI usually occurs within a couple of days after TSS. Delayed occurrence of postoperative DI is rarely observed and its developing mechanisms remain unknown. Methods Six patients were identified as having postoperative delayed DI, which was defined as DI that first occurred two or more weeks after TSS. They consisted of one male and five females, and their mean age was 38.3 (range: 10-76) years...
December 8, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/29228241/speech-intelligibility-and-personality-peer-ratings-of-young-adults-with-cochlear-implants
#12
Valerie Freeman
Speech intelligibility, or how well a speaker's words are understood by others, affects listeners' judgments of the speaker's competence and personality. Deaf cochlear implant (CI) users vary widely in speech intelligibility, and their speech may have a noticeable "deaf" quality, both of which could evoke negative stereotypes or judgments from peers. In this study, college students with typical hearing (TH) used semantic differential scales to rate speech samples of highly-intelligible TH young adults and age-matched CI users with high or low intelligibility (CI-Hi, CI-Lo) on personality traits related to competence (intelligence, achievement), friendship skills (friendliness, popularity), and attractiveness as a friend (extraversion, dependability)...
December 8, 2017: Journal of Deaf Studies and Deaf Education
https://www.readbyqxmd.com/read/29227464/antibiotic-resistance-of-potential-otopathogens-isolated-from-nasopharyngeal-flora-of-children-with-acute-otitis-media-before-during-and-after-pneumococcal-conjugate-vaccines-implementation
#13
Alexis Rybak, Corinne Levy, Stéphane Bonacorsi, Stéphane Béchet, François Vié le Sage, Annie Elbez, Emmanuelle Varon, Robert Cohen
BACKGROUNDL: To re-evaluate antibiotic strategies for acute otitis media (AOM) in young children, we analyzed the trends of nasopharyngeal carriage and antibiotic resistance of Streptococcus pneumoniae (Sp), Haemophilus influenzae (Hi) and Moraxella catarrhalis (Mc) isolated from young children with AOM during a 16-year period. METHODS: This cross-sectional study analyzed from 2001 to 2016, the nasopharyngeal carriage of Sp, Hi and Mc of young children with AOM...
December 8, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/29226260/a-novel-rapid-direct-haemagglutination-inhibition-assay-for-measurements-of-humoral-immune-response-against-non-haemagglutinating-fowlpox-virus-strains-in-vaccinated-chickens
#14
Philemon N Wambura, Alexanda Mzula
Fowlpox (FP) is a serious disease in chickens caused by Fowlpox virus (FPV). One method currently used to control FPV is vaccination followed by confirmation that antibody titres are protective using the indirect haemagglutination assay (IHA). The direct haemagglutination inhibition (HI) assay is not done because most FPV strains do not agglutinate chicken red blood cells (RBCs). A novel FPV strain TPV-1 which agglutinates chicken RBCs was discovered recently and enabled a direct HI assay to be conducted using homologous sera...
October 2017: Heliyon
https://www.readbyqxmd.com/read/29224316/-effects-of-npm1-gene-expression-on-acute-myeloid-leukemia-cell-lines-and-its-mechanism
#15
S W Qiu, Y L Wan, M Wang, J X Wang
Objective: To investigate the impact and mechanism of NPM1 gene expression on acute myeloid leukemia (AML) cell lines. Methods: Human AML cell line U937 and HL-60 cells were transfected with NPM1 plasmid to establish stable clones, and the high NPM1 protein expression (NPM1(hi)) clones were screened by Western blot. The cell proliferation was assayed by methylthiazolyl tetrazolium bromide (MTT) , cell cycle and cell apoptosis by flow cytometric, cell colony formation by microscope count, the molecular pathways related to cell cycle by Western blot...
November 14, 2017: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/29224078/investigate-global-chromosomal-interaction-by-hi-c-in-human-naive-cd4-t-cells
#16
Xiangzhi Meng, Nicole Riley, Ryan Thompson, Siddhartha Sharma
Hi-C is a methodology developed to reveal chromosomal interactions from a genome-wide perspective. Here, we described a protocol for generating Hi-C sequencing libraries in resting and activated human naive CD4 T cells to investigate activation-induced chromatin structure re-arrangement in T cell activation followed by a section reviewing the general concepts of Hi-C data analysis.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224068/hi-plex-for-simple-accurate-and-cost-effective-amplicon-based-targeted-dna-sequencing
#17
Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J Park
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29219220/heart-rate-recovery-fast-to-slow-phase-transition-influence-of-physical-fitness-and-exercise-intensity
#18
Rhenan Bartels, Eliza Prodel, Mateus C Laterza, Jorge Roberto P de Lima, Tiago Peçanha
BACKGROUND: Postexercise heart rate (HR) recovery presents an exponential decay, with two distinct phases: a fast phase, characterized by abrupt decay of HR, and determined by parasympathetic reactivation; and a slow phase, characterized by gradual decay of HR, and predominantly determined by sympathetic withdrawal. Although several methods have been proposed to assess postexercise HR recovery, none of those methods selectively assesses the time of transition from the fast to the slow phase of the HR recovery curve (HRRPT ), and the magnitude of decay prior to (HRRFP ) and after this point (HRRSP )...
December 8, 2017: Annals of Noninvasive Electrocardiology
https://www.readbyqxmd.com/read/29217590/a-mechanism-of-cohesin-dependent-loop-extrusion-organizes-zygotic-genome-architecture
#19
Johanna Gassler, Hugo B Brandão, Maxim Imakaev, Ilya M Flyamer, Sabrina Ladstätter, Wendy A Bickmore, Jan-Michael Peters, Leonid A Mirny, Kikuë Tachibana
Fertilization triggers assembly of higher-order chromatin structure from a condensed maternal and a naïve paternal genome to generate a totipotent embryo. Chromatin loops and domains have been detected in mouse zygotes by single-nucleus Hi-C (snHi-C), but not bulk Hi-C. It is therefore unclear when and how embryonic chromatin conformations are assembled. Here, we investigated whether a mechanism of cohesin-dependent loop extrusion generates higher-order chromatin structures within the one-cell embryo. Using snHi-C of mouse knockout embryos, we demonstrate that the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and that are regulated in size and linear density by Wapl...
December 7, 2017: EMBO Journal
https://www.readbyqxmd.com/read/29217589/cohesin-building-loops-but-not-compartments
#20
Judith Hi Haarhuis, Benjamin D Rowland
No abstract text is available yet for this article.
December 7, 2017: EMBO Journal
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