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https://www.readbyqxmd.com/read/28334818/chromosomal-dynamics-predicted-by-an-elastic-network-model-explains-genome-wide-accessibility-and-long-range-couplings
#1
Natalie Sauerwald, She Zhang, Carl Kingsford, Ivet Bahar
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334776/structural-characterization-of-interactions-between-transactivation-domain-1-of-the-p65-subunit-of-nf-%C3%AE%C2%BAb-and-transcription-regulatory-factors
#2
Lauriane Lecoq, Luca Raiola, Philippe R Chabot, Normand Cyr, Geneviève Arseneault, Pascale Legault, James G Omichinski
p65 is a member of the NF-κB family of transcriptional regulatory proteins that functions as the activating component of the p65-p50 heterodimer. Through its acidic transactivation domain (TAD), p65 has the capacity to form interactions with several different transcriptional regulatory proteins, including TFIIB, TFIIH, CREB-binding protein (CBP)/p300 and TAFII31. Like other acidic TADs, the p65 TAD contains two subdomains (p65TA1 and p65TA2) that interact with different regulatory factors depending on the target gene...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334773/a-critical-assessment-of-topologically-associating-domain-prediction-tools
#3
Rola Dali, Mathieu Blanchette
Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available for TAD prediction, but their properties have never been thoroughly assessed. In this manuscript, we compare the output of seven different TAD prediction tools on two published Hi-C data sets. TAD predictions varied greatly between tools in number, size distribution and other biological properties...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28329082/aortic-elongation-and-the-risk-for-dissection-the-t%C3%A3-bingen-aortic-pathoanatomy-taipan-project%C3%A2
#4
Tobias Krüger, Alexandre Oikonomou, David Schibilsky, Mario Lescan, Katharina Bregel, Luise Vöhringer, Wilke Schneider, Henning Lausberg, Gunnar Blumenstock, Fabian Bamberg, Christian Schlensak
OBJECTIVES: We measured aortic dimensions, particularly length parameters, using 3D imaging with the aim of refining the risk-morphology for Stanford type A aortic dissection (TAD). METHODS: Computer tomography angiography studies were analysed using the curved multiplanar reformats. At defined landmarks, the diameters and lengths of aortic segments were recorded. Three groups were compared retrospectively: patients actually suffering from a TAD (TAD-group; n  = 150), patients before suffering a TAD (preTAD-group n  = 15) and a healthy control group ( n  = 215)...
February 16, 2017: European Journal of Cardio-thoracic Surgery
https://www.readbyqxmd.com/read/28326966/cognitive-load-during-route-selection-increases-reliance-on-spatial-heuristics
#5
Tad T Brunyé, Shaina B Martis, Holly A Taylor
Planning routes from maps involves perceiving the symbolic environment, identifying alternate routes, and applying explicit strategies and implicit heuristics to select an option. Two implicit heuristics have received considerable attention, the southern route preference and initial segment strategy. The current study tested a prediction from decision making theory, that increasing cognitive load during route planning will increase reliance on these heuristics. In two experiments, participants planned routes while under conditions of minimal (0-back) or high (2-back) working memory load...
March 22, 2017: Quarterly Journal of Experimental Psychology: QJEP
https://www.readbyqxmd.com/read/28323041/quantitative-analyses-of-the-3d-nuclear-landscape-recorded-with-super-resolved-fluorescence-microscopy
#6
Volker J Schmid, Marion Cremer, Thomas Cremer
Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction...
March 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28321275/features-of-hepatocellular-carcinoma-in-hispanics-differ-from-african-americans-and-non-hispanic-whites
#7
Neeta K Venepalli, Mary V Modayil, Stephanie A Berg, Tad D Nair, Mayur Parepally, Priyanka Rajaram, Ron C Gaba, James T Bui, Yue Huang, Scott J Cotler
AIM: To compare features of hepatocellular carcinoma (HCC) in Hispanics to those of African Americans and Whites. METHODS: Patients treated for HCC at an urban tertiary medical center from 2005 to 2011 were identified from a tumor registry. Data were collected retrospectively, including demographics, comorbidities, liver disease characteristics, tumor parameters, treatment, and survival (OS) outcomes. OS analyses were performed using Kaplan-Meier method. RESULTS: One hundred and ninety-five patients with HCC were identified: 80...
March 8, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28318949/wing-augmentation-reduces-femoral-head-cutting-out-of-dynamic-hip-screw
#8
Chih-Yu Chen, Shu-Wei Huang, Jui-Sheng Sun, Shin-Yiing Lin, Chih-Sheng Yu, Hsu-Pin Pan, Ping-Hung Lin, Fan-Chun Hsieh, Yang-Hwei Tsuang, Feng-Huei Lin, Rong-Sen Yang, Cheng-Kung Cheng
The dynamic hip screw (DHS) is commonly used in the treatment of femoral intertrochanteric fracture with high satisfactory results. However, post-operative failure does occur and result in poor prognosis. The most common failure is femoral head varus collapse, followed by lag screw cut-out through the femoral head. In this study, a novel-designed DHS with two supplemental horizontal blades was used to improve the fixation stability. In this study, nine convention DHS and 9 Orthopaedic Device Research Center (ODRC) DHSs were tested in this study...
March 17, 2017: Medical Engineering & Physics
https://www.readbyqxmd.com/read/28318311/treatment-of-vertical-maxillary-excess-without-open-bite-in-a-skeletal-class-ii-hyperdivergent-patient
#9
Cheol-Ho Paik, Hong-Sik Park, Hyo-Won Ahn
A 20-year-old woman visited the office complaining of a gummy smile and lip protrusion. She was diagnosed with vertical maxillary excess without open bite and skeletal Class II hyperdivergent pattern. She refused the surgical-orthodontic treatment option, although she wanted to correct the gummy smile and retruded chin. Differential intrusion of anterior and posterior teeth in both arches was necessary to maximize the skeletal treatment effects. In the maxilla, one palatal temporary anchorage device (TAD), an archwire with an accentuated curve of Spee, and a transpalatal arch were applied...
March 20, 2017: Angle Orthodontist
https://www.readbyqxmd.com/read/28299260/controlling-the-vector-of-distraction-osteogenesis-in-the-management-of-obstructive-sleep-apnea
#10
Dekel Shilo, Omri Emodi, Dror Aizenbud, Adi Rachmiel
BACKGROUND: Obstructive sleep apnea (OSA) in individuals with craniofacial anomalies can compromise airway and is a serious life-threatening condition. In many cases, tracheostomy is carried out as the treatment of choice. Distraction osteogenesis of the mandible as a treatment modality for OSA is very useful and may spare the need for tracheostomy or allow decannulation, yet controlling the vector of distraction is still a major challenge. We present a method for controlling the vector of distraction...
July 2016: Annals of Maxillofacial Surgery
https://www.readbyqxmd.com/read/28295210/cnvs-analysis-in-a-cohort-of-isolated-and-syndromic-dd-id-reveals-novel-genomic-disorders-position-effects-and-candidate-disease-genes
#11
Eleonora Di Gregorio, Evelise Riberi, Elga Fabia Belligni, Elisa Biamino, Malte Spielmann, Ugo Ala, Alessandro Calcia, Irene Bagnasco, Diana Carli, Giorgia Gai, Mara Giordano, Andrea Guala, Roberto Keller, Giorgia Mandrile, Carlo Arduino, Antonella Maffè, Valeria Giorgia Naretto, Fabio Sirchia, Lorena Sorasio, Silvana Ungari, Andrea Zonta, Giulia Zacchetti, Flavia Talarico, Patrizia Pappi, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Marta Ferrero, Alessandro Brussino, Elisa Savin, Marina Gandione, Alessandra Pelle, Daniela Francesca Giachino, Mario De Marchi, Gabriella Restagno, Paolo Provero, Margherita Cirillo Silengo, Enrico Grosso, Joseph D Buxbaum, Barbara Pasini, Silvia De Rubeis, Alfredo Brusco, Giovanni Battista Ferrero
Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect Copy Number Variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes...
March 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28290181/acute-type-a-aortic-dissection-beyond-the-diameter
#12
Calogera Pisano, Carmela Rita Balistreri, Oreste Fabio Triolo, Vincenzo Argano, Giovanni Ruvolo
Aortic dissection is a life-threatening condition in which early diagnosis, treatment and close follow up are critical for survival. Between 60% and 70% of patients with acute aortic dissection are affected at the ascending aorta, classified as Stanford type A (TAD). Preventive surgery of the aorta in asymptomatic patients on the basis of aortic size alone remains controversial among patient populations without known risk factors for aortic dissection. In fact, many dissection patients do not appear to have markedly dilated aortas at the time of presentation...
November 2016: Journal of Heart Valve Disease
https://www.readbyqxmd.com/read/28288607/influence-of-different-great-trochanteric-entry-points-on-the-outcome-of-intertrochanteric-fractures-a-retrospective-cohort-study
#13
Shuo Pan, Xiao-Hui Liu, Tao Feng, Hui-Jun Kang, Zhi-Guang Tian, Chun-Guang Lou
BACKGROUND: The Proximal Femoral Nail Antirotation (PFNA) system for treatment of intertrochanteric fractures is currently widely applied worldwide. However, even though the PFNA has produced good clinical outcomes, a poor introduction technique with an inappropriate entry point can cause surgical complications. Some researchers suggest improving clinical outcomes by modifying the entry point, but no research has focused on this issue. The purpose of the present study is to compare the clinical and radiological outcomes of two different trochanteric entry points for the treatment of intertrochanteric fractures using the PFNA system...
March 14, 2017: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/28282436/regions-of-very-low-h3k27me3-partition-the-drosophila-genome-into-topological-domains
#14
Sherif El-Sharnouby, Bettina Fischer, Jose Paolo Magbanua, Benjamin Umans, Rosalyn Flower, Siew Woh Choo, Steven Russell, Robert White
It is now well established that eukaryote genomes have a common architectural organization into topologically associated domains (TADs) and evidence is accumulating that this organization plays an important role in gene regulation. However, the mechanisms that partition the genome into TADs and the nature of domain boundaries are still poorly understood. We have investigated boundary regions in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing moderate-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive...
2017: PloS One
https://www.readbyqxmd.com/read/28272594/hospital-medicine-resident-training-tracks-developing-the-hospital-medicine-pipeline
#15
Joseph R Sweigart, Darlene Tad-Y, Patrick Kneeland, Mark V Williams, Jeffrey J Glasheen
BACKGROUND: Hospital medicine (HM) is rapidly evolving into new clinical and nonclinical roles. Traditional internal medicine (IM) residency training likely does not optimally prepare residents for success in HM. Hospital medicine residency training tracks may offer a preferred method for specialized HM education. METHODS: Internet searches and professional networks were used to identify HM training tracks. Information was gathered from program websites and discussions with track directors...
March 2017: Journal of Hospital Medicine: An Official Publication of the Society of Hospital Medicine
https://www.readbyqxmd.com/read/28263316/single-molecule-sequencing-and-chromatin-conformation-capture-enable-de-novo-reference-assembly-of-the-domestic-goat-genome
#16
Derek M Bickhart, Benjamin D Rosen, Sergey Koren, Brian L Sayre, Alex R Hastie, Saki Chan, Joyce Lee, Ernest T Lam, Ivan Liachko, Shawn T Sullivan, Joshua N Burton, Heather J Huson, John C Nystrom, Christy M Kelley, Jana L Hutchison, Yang Zhou, Jiajie Sun, Alessandra Crisà, F Abel Ponce de León, John C Schwartz, John A Hammond, Geoffrey C Waldbieser, Steven G Schroeder, George E Liu, Maitreya J Dunham, Jay Shendure, Tad S Sonstegard, Adam M Phillippy, Curtis P Van Tassell, Timothy P L Smith
The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping...
March 6, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28261389/bridging-leadership-roles-in-quality-and-patient-safety-experience-of-6-us-academic-medical-centers
#17
Jennifer S Myers, Anjala V Tess, Katherine McKinney, Glenn Rosenbluth, Vineet M Arora, Darlene Tad-Y, Arpana R Vidyarthi
No abstract text is available yet for this article.
February 2017: Journal of Graduate Medical Education
https://www.readbyqxmd.com/read/28251877/genomic-landscape-of-cpg-rich-elements-in-human
#18
Vladimir N Babenko, Irina V Chadaeva, Yuriy L Orlov
BACKGROUND: The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28251841/topologically-associated-domains-a-successful-scaffold-for-the-evolution-of-gene-regulation-in-animals
#19
REVIEW
Rafael D Acemel, Ignacio Maeso, José Luis Gómez-Skarmeta
The evolution of gene regulation is considered one of the main drivers causing the astonishing morphological diversity in the animal kingdom. Gene regulation in animals heavily depends upon cis-regulatory elements, discrete pieces of DNA that interact with target promoters to regulate gene expression. In the last years, Chromosome Conformation Capture experiments (4C-seq, 5C, and HiC) in several organisms have shown that the genomes of many bilaterian animals are organized in the 3D chromatin space in compartments called topologically associated domains (TADs)...
March 2, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28249171/cis-acting-complex-trait-associated-lincrna-expression-correlates-with-modulation-of-chromosomal-architecture
#20
Jennifer Yihong Tan, Adam Alexander Thil Smith, Maria Ferreira da Silva, Cyril Matthey-Doret, Rico Rueedi, Reyhan Sönmez, David Ding, Zoltán Kutalik, Sven Bergmann, Ana Claudia Marques
Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci...
February 28, 2017: Cell Reports
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