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https://www.readbyqxmd.com/read/28077647/sensitive-next-generation-sequencing-method-reveals-deep-genetic-diversity-of-hiv-1-in-the-democratic-republic-of-the-congo
#1
M A Rodgers, E Wilkerson, A Vallari, C McArthur, L Sthreshley, C A Brennan, G Cloherty, T de Oliveira
: As the epidemiological epicentre of the human immunodeficiency virus (HIV) pandemic, the Democratic Republic of the Congo (DRC) is a reservoir of circulating HIV strains exhibiting high levels of diversity and recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between 2001 and 2003 to identify rare strains of HIV. The env gp41 region was sequenced and characterized for 172 HIV-positive specimens. The env sequences were predominantly subtype A (43...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28064308/-structural-studies-of-chromatin-remodeling-factors
#2
O I Volokh, N I Derkacheva, V M Studitsky, O S Sokolova
Changes of chromatin structure require participation of chromatin remodeling factors (CRFs), which are ATP-dependent multisubunit complexes that change the structure of the nucleosome without covalently modifying its components. CRFs act together with other protein factors to regulate the extent of chromatin condensation. Four CRF families are currently distinguished based on their structural and biochemical characteristics: SWI/SNF, ISWI, Mi-2/CHD, and SWR/INO80. X-ray diffraction analysis and electron microscopy are the main methods to obtain structural information about macromolecules...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28062403/mutated-chromatin-regulatory-factors-as-tumor-drivers-in-cancer
#3
REVIEW
Carl Koschmann, Felipe J Nunez, Flor Mendez, Jacqueline A Brosnan-Cashman, Alan K Meeker, Pedro R Lowenstein, Maria G Castro
Genes encoding proteins that regulate chromatin structure and DNA modifications [i.e., chromatin regulatory factors (CRF)] and genes encoding histone proteins harbor recurrent mutations in most human cancers. These mutations lead to modifications in tumor chromatin and DNA structure and an altered epigenetic state that contribute to tumorigenesis. Mutated CRFs have now been identified in most types of cancer and are increasingly regarded as novel therapeutic targets. In this review, we discuss DNA alterations in CRFs and how these influence tumor chromatin structure and function, which in turn leads to tumorigenesis...
January 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28058575/study-on-reproductive-performance-of-holstein-x-lai-sind-crossbred-dairy-heifers-and-cows-at-smallholdings-in-ho-chi-minh-city-vietnam
#4
Cuong Nguyen-Kien, Nguyen Van Khanh, Christian Hanzen
The reproductive performance of Holstein x Lai Sind crossbred dairy heifers and cows was evaluated at smallholdings in Ho Chi Minh City (HCMC). The data of 232 heifers and 244 cows (261 lactations) from 35 small dairy farms was collected over a 2-year period, from 2013 to 2014. The overall mean for age at first service (AFS), days between first and last service (DFLS), and age at conception (AC) of heifers was 479 (±80), 38 (±80), and 517 (±114) days, respectively. Average number of services per conception (NSC), conception rate (CR), and conception rate at first service (CRFS) was 1...
January 5, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28045578/cytokinin-response-factor-5-has-transcriptional-activity-governed-by-its-c-terminal-domain
#5
Bernd Striberny, Anthony E Melton, Rainer Schwacke, Kirsten Krause, Karsten Fischer, Leslie R Goertzen, Aaron M Rashotte
Cytokinin Response Factors (CRFs) are AP2/ERF transcription factors involved in cytokinin signal transduction. CRF proteins consist of a N-terminal dimerization domain (CRF domain), an AP2 DNA-binding domain, and a clade-specific C-terminal region of unknown function. Using a series of sequential deletions in yeast-two-hybrid assays, we provide evidence that the C-terminal region of Arabidopsis CRF5 can confer transactivation activity. Although comparative analyses identified evolutionarily conserved protein sequence within the C-terminal region, deletion experiments suggest that this transactivation domain has a partially redundant modular structure required for activation of target gene transcription...
January 3, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28038337/common-data-elements-and-data-management-remedy-to-cure-underpowered-preclinical-studies
#6
Niina Lapinlampi, Esbjörn Melin, Eleonora Aronica, Jens P Bankstahl, Albert Becker, Cristophe Bernard, Jan A Gorter, Olli Gröhn, Anu Lipsanen, Katarzyna Lukasiuk, Wolfgang Löscher, Jussi Paananen, Teresa Ravizza, Paolo Roncon, Michele Simonato, Annamaria Vezzani, Merab Kokaia, Asla Pitkänen
Lack of translation of data obtained in preclinical trials to clinic has kindled researchers to develop new methodologies to increase the power and reproducibility of preclinical studies. One approach relates to harmonization of data collection and analysis, and has been used for a long time in clinical studies testing anti-seizure drugs. EPITARGET is a European Union FP7-funded research consortium composed of 18 partners from 9 countries. Its main research objective is to identify biomarkers and develop treatments for epileptogenesis...
November 22, 2016: Epilepsy Research
https://www.readbyqxmd.com/read/28017734/ex-vivo-cd34-selected-t-cell-depleted-tcd-peripheral-blood-stem-cell-grafts-for-allogeneic-hematopoietic-stem-cell-transplantation-in-acute-leukemia-and-myelodysplastic-syndrome-is-associated-with-low-incidence-of-acute-and-chronic-graft-versus-host-disease
#7
Pere Barba, Patrick Hilden, Sean M Devlin, Molly Maloy, Djamilia Dierov, Jimmy Nieves, Matthew D Garrett, Julie Sogani, Christina Cho, Juliet N Barker, Nancy A Kernan, Hugo Castro-Malaspina, Ann A Jakubowski, Guenther Koehne, Esperanza B Papadopoulos, Susan Prockop, Craig Sauter, Roni Tamari, Marcel R M van den Brink, Scott T Avecilla, Richard Meagher, Richard J O'Reilly, Jenna D Goldberg, James W Young, Sergio Giralt, Miguel-Angel Perales, Doris M Ponce
Ex vivo CD34+ selected T-cell depletion (TCD) has been developed as a strategy to reduce the incidence of graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Clinical characteristics, treatment responses, and outcomes of patients developing acute (a-) and chronic (c-) GVHD after TCD allo-HSCT have not been well established. We evaluated 241 consecutive patients (median age 57 years) with acute leukemia (n = 191, 79%) or myelodysplastic syndrome (MDS) (n = 50, 21%) undergoing CD34+ selected TCD allo-HSCT without post-HCST immunosuppression in a single institution...
December 22, 2016: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/27930384/the-endothelial-mineralocorticoid-receptor-mediator-of-the-switch-from-vascular-health-to-disease
#8
Ana P Davel, Imran J Anwar, Iris Z Jaffe
PURPOSE OF REVIEW: Endothelial dysfunction is an early feature of vascular disease induced by cardiovascular risk factors (CRFs). In growing populations with obesity, diabetes, hypertension, and heart failure, mineralocorticoid receptor antagonism improves endothelial function. This review summarizes recent advances in our understanding of the specific role of endothelial cell mineralocorticoid receptor in vascular function in health and disease. RECENT FINDINGS: Using transgenic mice with mineralocorticoid receptor expression specifically modulated in endothelial cells, recent studies support the emerging concept that while endothelial cell mineralocorticoid receptor may be protective in health, in the presence of CRFs, endothelial cell mineralocorticoid receptor activity contributes to endothelial dysfunction and progression of vascular disease...
December 7, 2016: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/27899162/design-of-case-report-forms-based-on-a-public-metadata-registry-re-use-of-data-elements-to-improve-compatibility-of-data
#9
Martin Dugas
BACKGROUND: Clinical trials use many case report forms (CRFs) per patient. Because of the astronomical number of potential CRFs, data element re-use at the design stage is attractive to foster compatibility of data from different trials. The objective of this work is to assess the technical feasibility of a CRF editor with connection to a public metadata registry (MDR) to support data element re-use. RESULTS: Based on the Medical Data Models portal, an ISO/IEC 11179-compliant MDR was implemented and connected to a web-based CRF editor...
November 29, 2016: Trials
https://www.readbyqxmd.com/read/27885364/bidirectional-rnn-for-medical-event-detection-in-electronic-health-records
#10
Abhyuday N Jagannatha, Hong Yu
Sequence labeling for extraction of medical events and their attributes from unstructured text in Electronic Health Record (EHR) notes is a key step towards semantic understanding of EHRs. It has important applications in health informatics including pharmacovigilance and drug surveillance. The state of the art supervised machine learning models in this domain are based on Conditional Random Fields (CRFs) with features calculated from fixed context windows. In this application, we explored recurrent neural network frameworks and show that they significantly out-performed the CRF models...
June 2016: Proceedings of the Conference
https://www.readbyqxmd.com/read/27882430/identification-of-cardiovascular-risk-factors-associated-with-bone-marrow-cell-subsets-in-patients-with-stemi-a-biorepository-evaluation-from-the-cctrn-time-and-latetime-clinical-trials
#11
Ariadna Contreras, Aaron F Orozco, Micheline Resende, Robert C Schutt, Jay H Traverse, Timothy D Henry, Dejian Lai, John P Cooke, Roberto Bolli, Michelle L Cohen, Lem Moyé, Carl J Pepine, Phillip C Yang, Emerson C Perin, James T Willerson, Doris A Taylor
Autologous bone marrow mononuclear cell (BM-MNC) therapy for patients with ST-segment elevation myocardial infarction (STEMI) has produced inconsistent results, possibly due to BM-MNC product heterogeneity. Patient-specific cardiovascular risk factors (CRFs) may contribute to variations in BM-MNC composition. We sought to identify associations between BM-MNC subset frequencies and specific CRFs in STEMI patients. Bone marrow was collected from 191 STEMI patients enrolled in the CCTRN TIME and LateTIME trials...
January 2017: Basic Research in Cardiology
https://www.readbyqxmd.com/read/27852214/time-scale-of-minor-hiv-1-complex-circulating-recombinant-forms-from-central-and-west-africa
#12
Edson Delatorre, Gonzalo Bello
BACKGROUND: Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method. RESULTS: The analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958-1979), CRF11_cpx (~1957: 1950-1966) and CRF13_cpx (~1965: 1958-1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964-1976); env = 1960 (1952-1969)]...
November 16, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27831948/hiv-surveillance-combining-an-assay-for-identification-of-very-recent-infection-and-phylogenetic-analyses-on-dried-spots
#13
Denys Brand, Jean Capsec, Antoine Chaillon, Françoise Cazein, Stéphane Le Vu, Alain Moreau, Josiane Pillonel, Sylvie Brunet, Damien Thierry, Leslie Guillon-Grammatico, Florence Lot, Francis Barin
BACKGROUND: Transmitted/founder (T/F) viruses isolated at the early stage of infection are indicators of the variants that are spreading within a population. The French reporting system for new HIV diagnoses is linked to a virological surveillance using dried serum spots (DSS). METHODS: We combined an immunoassay for very recent infection (VRI < 31 days) to a phylogenetic analysis of T/F viruses and sociodemographic information to analyze the dynamics of the HIV-1 epidemic during a 3-year period...
November 7, 2016: AIDS
https://www.readbyqxmd.com/read/27819152/blood-pressure-and-lipid-target-adherence-in-korean-patients-receiving-angiotensin-ii-receptor-blockers-statin-regimens
#14
Hyun-Jin Kim, Eugene Kim, Kyoung-Bok Min, Jin-Young Min
OBJECTIVES: Hypertension and dyslipidemia are important cardiovascular risk factors. Simultaneously controlling blood pressure (BP) and lipid levels is effective in preventing cardiovascular events and premature death. This study investigated the association between adherence to angiotensin II receptor blocker (ARB)/statin regimens and BP or low density lipoprotein-cholesterol (LDL-C) target attainment in Korean patients with concomitant hypertension and dyslipidemia. METHODS: In this retrospective, multicenter study, we collected case report forms (CRFs) of hypertensive patients with concomitant dyslipidemia who were prescribed an ARB/statin regimen between 1 April 2014 and 31 March 2015 from 51 outpatient clinics...
February 2017: Current Medical Research and Opinion
https://www.readbyqxmd.com/read/27789361/hematopoietic-cell-transplantation-comorbidity-index-predicts-outcomes-in-patients-with-acute-myeloid-leukemia-and-myelodysplastic-syndromes-receiving-cd34-selected-grafts-for-allogeneic-hematopoietic-cell-transplantation
#15
Pere Barba, Ravin Ratan, Christina Cho, Izaskun Ceberio, Patrick Hilden, Sean M Devlin, Molly A Maloy, Juliet N Barker, Hugo Castro-Malaspina, Ann A Jakubowski, Guenther Koehne, Esperanza B Papadopoulos, Doris M Ponce, Craig Sauter, Roni Tamari, Marcel R M van den Brink, James W Young, Richard J O'Reilly, Sergio A Giralt, Miguel-Angel Perales
To evaluate the association between the hematopoietic cell transplantation-comorbidity index (HCT-CI) and the recently developed age-adjusted HCT-CI (HCT-CI/age) and transplant outcomes in the setting of CD34-selected allogeneic HCT, we analyzed a homogeneous population of patients undergoing allogeneic HCT with CD34-selected grafts for acute myeloid leukemia and myelodysplastic syndrome (n = 346). Median HCT-CI and HCT-CI/age scores were 2 (percentile 25 to 75, 1 to 4) and 3 (percentile 25 to 75, 1 to 5), respectively...
January 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/27776866/effect-of-controlled-release-formulations-of-diuron-and-alachlor-herbicides-on-the-biochemical-activity-of-agricultural-soils
#16
Manuel Tejada, Esmeralda Morillo, Isidoro Gómez, Fernando Madrid, Tomás Undabeytia
The use of pesticides in agriculture is essential because it reduces the economic losses caused by pests, improving crop yields. In spite of the growing number of studies concerning the development and application of controlled release formulations (CRFs) of pesticides in agricultural soils, there are no studies about the effects of such formulations on the biochemical properties. In this paper the dissipation of diuron and alachlor in three agricultural soils for 127days, applied either as commercial or CRFs, was determined as well as their concomitant effects on soil biochemical properties...
October 14, 2016: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/27774303/hiv-1-transmission-between-msm-and-heterosexuals-and-increasing-proportions-of-circulating-recombinant-forms-in-the-nordic-countries
#17
Joakim Esbjörnsson, Mattias Mild, Anne Audelin, Jannik Fonager, Helena Skar, Louise Bruun Jørgensen, Kirsi Liitsola, Per Björkman, Göran Bratt, Magnus Gisslén, Anders Sönnerborg, Claus Nielsen, Patrik Medstrand, Jan Albert
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics...
January 2016: Virus Evolution
https://www.readbyqxmd.com/read/27773669/cytokinin-response-factors-gating-environmental-signals-and-hormones
#18
Jungmook Kim
CYTOKININ RESPONSE FACTORs (CRFs) encode transcription factors belonging to a small family within the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) superfamily. Recent studies have revealed the biological functions of some arabidopsis CRFs, providing insight into the role of these plant transcription factors in integrating environmental and hormonal signals for plant adaptation.
December 2016: Trends in Plant Science
https://www.readbyqxmd.com/read/27762600/trends-of-hiv-1-subtypes-among-young-people-in-hangzhou-china
#19
Wenjun Zhang, Junfang Chen, Xiaohong Pan, Jiafeng Zhang, Zhihong Guo, Yan Luo, Jiezhe Yang, Yan Xia, Lin He, Yun Xu, Ke Xu, Xiaobei Ding
To investigate the HIV-1 molecular epidemiology among young people (18 to 25 years old) in Hangzhou. Plasma samples from 262 newly diagnosed HIV-1-infected patients were collected between 2009 and 2013 from Hangzhou of Zhejiang province. HIV-1 nucleotide sequences of pol gene regions were amplified using a nested polymerase chain reaction method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. Based on all sequences generated, the subtype/circulating recombinant forms (CRFs) distribution was as follows: CRF01_AE (68...
November 9, 2016: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/27762598/identification-of-two-new-hiv-1-circulating-recombinant-forms-crf87_cpx-and-crf88_bc-from-reported-unique-recombinant-forms-in-asia
#20
Yihong Hu, Zhenzhou Wan, Yan-Heng Zhou, Davey Smith, Yong-Tang Zheng, Chiyu Zhang
The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3...
December 13, 2016: AIDS Research and Human Retroviruses
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