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https://www.readbyqxmd.com/read/28103239/identifying-t-cell-receptors-from-high-throughput-sequencing-dealing-with-promiscuity-in-tcr%C3%AE-and-tcr%C3%AE-pairing
#1
Edward S Lee, Paul G Thomas, Jeff E Mold, Andrew J Yates
Characterisation of the T cell receptors (TCR) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease. The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervariable CDR3 regions on the TCRα and TCRβ chains, and obtaining the paired sequences of these regions is a standard for functionally defining the TCR. A brute force approach to identifying the TCRs in a population of T cells is to use high-throughput single-cell sequencing, but currently this process remains costly and risks missing small clones...
January 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28103192/audio-visual-speaker-diarization-based-on-spatiotemporal-bayesian-fusion
#2
Israel Gebru, Sileye Ba, Xiaofei Li, Radu Horaud
Speaker diarization consists of assigning speech signals to people engaged in a dialogue. An audio-visual spatiotemporal diarization model is proposed. The model is well suited for challenging scenarios that consist of several participants engaged in multi-party interaction while they move around and turn their heads towards the other participants rather than facing the cameras and the microphones. Multiple-person visual tracking is combined with multiple speech-source localization in order to tackle the speech-to-person association problem...
January 5, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28101934/detection-of-neonatal-unit-clusters-of-candida-parapsilosis-fungaemia-by-microsatellite-genotyping-results-from-laboratory-based-sentinel-surveillance-south-africa-2009-2010
#3
Rindidzani E Magobo, Serisha D Naicker, Jeannette Wadula, Maphoshane Nchabeleng, Yacoob Coovadia, Anwar Hoosen, Shawn R Lockhart, Nelesh P Govender
Neonatal candidaemia is a common, deadly and costly hospital-associated disease. To determine the genetic diversity of Candida parapsilosis causing fungaemia in South African neonatal intensive care units (NICUs). From February 2009 through to August 2010, cases of candidaemia were reported through laboratory-based surveillance. C. parapsilosis isolates from neonatal cases were submitted for identification by internal transcribed spacer (ITS) region sequencing, antifungal susceptibility testing and microsatellite genotyping...
January 19, 2017: Mycoses
https://www.readbyqxmd.com/read/28101894/sleep-quality-and-body-mass-index-a-co-twin-study
#4
Juan J Madrid-Valero, José M Martínez-Selva, Juan R Ordoñana
There is a consistent relationship between body mass index and sleep quality. However, the directionality and possible confounding factors of this relationship are unclear. Our aim is to confirm the association between sleep quality and body mass index, independent of possible genetic confounding, as well as to provide some indirect inferences about the directionality of this association. The co-twin study design was used to analyse the body mass index-sleep relationship in a sample of 2150 twins. We selected two parallel sub-samples of twins discordant for body mass index (n = 430 pairs), or discordant for sleep quality (n = 316 pairs)...
January 19, 2017: Journal of Sleep Research
https://www.readbyqxmd.com/read/28101581/the-protein-arginine-methyltransferase-5-promotes-malignant-phenotype-of-hepatocellular-carcinoma-cells-and-is-associated-with-adverse-patient-outcomes-after-curative-hepatectomy
#5
Dai Shimizu, Mitsuro Kanda, Hiroyuki Sugimoto, Masahiro Shibata, Haruyoshi Tanaka, Hideki Takami, Naoki Iwata, Masamichi Hayashi, Chie Tanaka, Daisuke Kobayashi, Suguru Yamada, Goro Nakayama, Masahiko Koike, Michitaka Fujiwara, Tsutomu Fujii, Yasuhiro Kodera
The prognosis of advanced hepatocellular carcinoma (HCC) is dismal. Novel molecular targets for diagnosis and therapy is urgently required. This study evaluated expression and functions of the protein arginine methyltransferase 5 (PRMT5) in HCC. Using HCC cell lines, the expression levels of PRMT5 mRNA were determined using the quantitative real-time reverse-transcription polymerase chain reaction, and the effect of a small interfering PRMT5-siRNA on cell phenotype was evaluated. Further, PRMT5 expression was determined in 144 pairs of resected liver tissues to evaluate its clinical significance...
February 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#6
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100804/role-of-the-different-eyes-in-the-visual-odometry-in-the-wolf-spider-lycosa-tarantula-araneae-lycosidae
#7
Joaquin Ortega-Escobar, Miguel A Ruiz
The wolf spider Lycosa tarantula returns home by means of path integration. Previous studies demonstrated: (i) that the angular component of the outbound run is measured using a polarized-light compass associated with the anterior median eyes; (ii) changes in direction of the substratum are detected by the anterior lateral eyes (ALEs); and (iii) in relation to the linear component of the outbound run, an increase of optic flow, in either the lateral or ventral fields of view, caused spiders to search for the burrow at a point nearer to the goal...
January 15, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28100769/the-ubiquitin-like-with-phd-and-ring-finger-domains-1-uhrf1-dna-methyltransferase-1-dnmt1-axis-is-a-primary-regulator-of-cell-senescence
#8
Hyun-Jung Jung, Hae-Ok Byun, Byul A Jee, Seongki Min, Un-Woo Jeoun, Young-Kyoung Lee, Yonghak Seo, Hyun Goo Woo, Gyesoon Yoon
As senescence develops, cells sequentially acquire diverse senescent phenotypes, along with simultaneous multi-stage gene reprogramming. It remains unclear what acts as the key regulator of the collective changes in gene expression at initiation of senescent reprogramming. Here we analysed time-series gene expression profiles obtained in two different senescence models in human diploid fibroblasts (HDF): replicative senescence and H2O2-induced senescence. Our results demonstrated that suppression of DNA methyltransferase 1 (DNMT1)-mediated DNA methylation activity was an initial event prior to the display of senescent phenotypes...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100677/paired-siglec-receptors-generate-opposite-inflammatory-responses-to-a-human-specific-pathogen
#9
Flavio Schwarz, Corinna S Landig, Shoib Siddiqui, Ismael Secundino, Joshua Olson, Nissi Varki, Victor Nizet, Ajit Varki
Paired immune receptors display near-identical extracellular ligand-binding regions but have intracellular sequences with opposing signaling functions. While inhibitory receptors dampen cellular activation by recognizing self-associated molecules, the functions of activating counterparts are less clear. Here, we studied the inhibitory receptor Siglec-11 that shows uniquely human expression in brain microglia and engages endogenous polysialic acid to suppress inflammation. We demonstrated that the human-specific pathogen Escherichia coli K1 uses its polysialic acid capsule as a molecular mimic to engage Siglec-11 and escape killing...
January 18, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28100652/correlation-between-discharge-timings-of-pairs-of-motor-units-reveals-the-presence-but-not-the-proportion-of-common-synaptic-input-to-motor-neurons
#10
Javier Rodriguez-Falces, Francesco Negro, Dario Farina
We investigated whether correlation measures derived from pairs of motor unit (MU) spike trains are reliable indicators of the degree of common synaptic input to motor neurons. Several 50-s isometric contractions of the biceps brachii muscle were performed at different target forces ranging from 10 to 30% of the maximal voluntary contraction (MVC) relying on force feedback. 48 pairs of MUs were examined at various force levels. Motor unit synchrony was assessed by cross-correlation analysis using three indices: the output correlation as the peak of the cross-histogram (ρ), the number of synchronous spikes per second (CIS), and per trigger (E)...
January 18, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28100589/meiotic-consequences-of-genetic-divergence-across-the-murine-pseudoautosomal-region
#11
Beth L Dumont
The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X/Y segregation is buffered against the accumulation of homology-disrupting mutations...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28100521/perioperative-%C3%AE-receptor-blockade-in-phaeochromocytoma-surgery-an-observational-case-series
#12
H Groeben, B J Nottebaum, P F Alesina, A Traut, H P Neumann, M K Walz
BACKGROUND: Mortality associated with surgery for phaeochromocytoma has dramatically decreased over the last decades. Many factors contributed to the dramatic decline of the mortality rate, and the influence of an α-receptor blockade is unclear and has never been tested in a randomized trial. We evaluated intraoperative haemodynamic conditions and the incidence of complications in patients with and without α-receptor blockade undergoing surgery for catecholamine producing tumours. METHODS: Haemodynamic conditions and perioperative complications were assessed in 110 patients with (B) and 166 without (N) α-receptor blockade...
February 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28100511/higher-dietary-flavonoid-intakes-are-associated-with-lower-objectively-measured-body-composition-in-women-evidence-from-discordant-monozygotic-twins
#13
Amy Jennings, Alex MacGregor, Tim Spector, Aedín Cassidy
BACKGROUND: Although dietary flavonoid intake has been associated with less weight gain, there are limited data on its impact on fat mass, and to our knowledge, the contribution of genetic factors to this relation has not previously been assessed. OBJECTIVE: We examined the associations between flavonoid intakes and fat mass. DESIGN: In a study of 2734 healthy, female twins aged 18-83 y from the TwinsUK registry, intakes of total flavonoids and 7 subclasses (flavanones, anthocyanins, flavan-3-ols, flavonols, flavones, polymers, and proanthocyanidins) were calculated with the use of food-frequency questionnaires...
January 18, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28100477/inability-to-replete-white-adipose-tissue-during-the-recovery-phase-of-sepsis-is-associated-with-increased-autophagy-apoptosis-and-proteasome-activity
#14
Kristen T Crowell, David I Soybel, Charles H Lang
Adipose tissue is an important energy depot and endocrine organ, and the degree of adiposity impacts the host response to infection. However, little is known regarding the mechanisms by which white adipose tissue (WAT) is lost acutely and then restored after resolution of sepsis. Therefore, signaling pathways governing protein synthesis, autophagy, apoptosis and the ubiquitin-proteasome were investigated to identify potential mechanisms mediating the acute (24 h) loss of WAT after cecal ligation and puncture (CLP) as well as the failure to replenish WAT during recovery (day 10)...
January 18, 2017: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology
https://www.readbyqxmd.com/read/28100466/associations-of-accelerometer-measured-and-self-reported-sedentary-time-with-leukocyte-telomere-length-in-older-women
#15
Aladdin H Shadyab, Caroline A Macera, Richard A Shaffer, Sonia Jain, Linda C Gallo, Michael J LaMonte, Alexander P Reiner, Charles Kooperberg, Cara L Carty, Chongzhi Di, Todd M Manini, Lifang Hou, Andrea Z LaCroix
Few studies have assessed the association of sedentary time with leukocyte telomere length (LTL). In a cross-sectional study conducted in 2012-2013, we examined associations of accelerometer-measured and self-reported sedentary time with LTL in a sample of 1,481 older white and African-American women from the Women's Health Initiative and determined whether associations varied by level of moderate- to vigorous-intensity physical activity (MVPA). The association between sedentary time and LTL was evaluated using multiple linear regression models...
January 18, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28100207/rate-and-associated-factors-of-non-retention-of-mother-baby-pairs-in-hiv-care-in-the-elimination-of-mother-to-child-transmission-programme-gulu-uganda-a-cohort-study
#16
Gerald Obai, Ruth Mubeezi, Fredrick Makumbi
BACKGROUND: Poor retention in HIV care of mother-baby pairs remains a public health challenge in the elimination of mother-to-child transmission (eMTCT) of HIV. We determined the rate of non-retention and time to non-retention of mother-baby pairs and associated factors in Gulu district, Northern Uganda. METHODS: Mother-baby pairs enrolled into the eMTCT programme at Gulu Regional Referral Hospital (GRRH) and Lacor Hospital (LH) were retrospectively followed for 18 months...
January 18, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28100118/assessing-sexual-interest-in-children-using-the-go-no-go-association-test
#17
Ross M Bartels, Anthony R Beech, Leigh Harkins, David Thornton
The present study investigated whether a latency-based Go/No-Go Association Task (GNAT) could be used as an indirect measure of sexual interest in children. A sample of 29 individuals with a history of exclusive extrafamilial offenses against a child and 15 individuals with either a history of exclusive intrafamilial or mixed offenses (i.e., against both adults and children) were recruited from a treatment center in the United States. Also, a sample of 26 nonoffenders was recruited from a university in the United Kingdom...
January 1, 2017: Sexual Abuse: a Journal of Research and Treatment
https://www.readbyqxmd.com/read/28100029/isolation-with-asymmetric-gene-flow-during-the-nonsynchronous-divergence-of-dry-forest-birds
#18
Jessica A Oswald, Isaac Overcast, William M Mauck, Michael J Andersen, Brian Tilston Smith
Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of communities often results from dynamic processes linked to numerous population histories among co-distributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co-distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099921/stiehopus-japonieus-acidic-mucopolysaccharide-inhibits-the-proliferation-of-pancreatic-cancer-sw1990-cells-through-hippo-yap-pathway
#19
Xiaoyu Li, Yi Liu, Cuiping Zhang, Qinghui Niu, Hui Wang, Cong Che, Man Xie, Bin Zhou, Yonghong Xu, Qi Zhang, Jun Wu, Zibin Tian
Previous studies have indicated that stiehopus japonieus acidic mucopolysaccharide (SJAMP) could inhibit the proliferation of pancreatic cancer cell SW1990. However, the mechanism remains unclear. In our study, YAP expression was identified by immunohistochemistry and quantitative Real-time PCR from 45 pairs of human pancreatic ductal adenocarcinoma (PDAC) tissues and their adjacent non-tumor samples. We found that the YAP expression was associated with the histological differentiation degree, and negatively correlated with pancreatic cancer patients' survival...
January 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099324/interaction-of-isoflurane-tumor-necrosis-factor-%C3%AE-and-%C3%AE-amyloid-on-long-term-potentiation-in-rat-hippocampal-slices
#20
Ran Zhou, Philip Bickler
BACKGROUND: The relationship between inhalational anesthetics such as isoflurane and cognitive impairment in the elderly is controversial. Both β-amyloid peptide (Aβ), associated with Alzheimer disease, and tumor necrosis factor-α (TNF-α), a proinflammatory stress-related peptide, impair the synaptic function. We hypothesized that transient exposure to isoflurane and these peptides would impair synaptic function, manifest as a depression of long-term potentiation (LTP) and paired pulse facilitation (PPF), in the rat hippocampus...
February 2017: Anesthesia and Analgesia
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