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https://www.readbyqxmd.com/read/29334377/detecting-hierarchical-genome-folding-with-network-modularity
#1
Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus, Shi Gu, Danielle S Bassett, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29318375/action-compatibility-in-spatial-knowledge-developed-through-virtual-navigation
#2
Qi Wang, Holly A Taylor, Tad T Brunyé
Action-compatibility effects (ACEs) arise due to incongruity between perceptuo-motor traces stored in memory and the perceptuo-motor demands of a retrieval task. Recent research has suggested that ACEs arising during spatial memory retrieval are additionally modulated by individual differences in how experienced participants are with a college campus environment. However, the extent and nature of experience with a real-world environment is difficult to assess and control, and characteristics of the retrieval task itself might modulate ACEs during spatial memory retrieval...
January 9, 2018: Psychological Research
https://www.readbyqxmd.com/read/29314090/development-and-validation-of-lc-ms-ms-method-for-simultaneous-determination-of-sofosbuvir-and-daclatasvir-in-human-plasma-application-to-pharmacokinetic-study
#3
Ola M Abdallah, Ahmed M Abdel-Megied, Amira S Gouda
The first simple and highly sensitive Liquid chromatography-tandem mass spectrometry (LC-MS/MS) bioanalytical method was developed and fully validated for the simultaneous determination of newly discovered antiviral drugs namely, Sofosbuvir (SOF) and Daclatasvir (DAC) in human plasma. Tadalafil (TAD) was used as internal standard (IS). SOF, DAC and TAD (IS) were extracted from plasma using liquid-liquid extraction technique with methyl tert-butyl ether. The chromatographic separation was carried out using ZorbaxSB-C18 column (4...
January 3, 2018: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29302776/epidemiological-situation-of-transboundary-animal-diseases-in-north-african-countries-proposition-of-a-regional-control-strategy
#4
REVIEW
Moustafa Kardjadj
The Food and Agricultural Organization (FAO) defined transboundary animal diseases (TADs) as those that are of significant economic, trade, and food security importance for a considerable number of countries. TADs can easily spread to other countries, reach epidemic proportions, and where control, management, or exclusion is required cooperation between several countries. The North African countries are vulnerable to several TADs by virtue of its geographical location, its borders with the Sahel region, and peculiar control constraints on the budgets of the national veterinary services of each country and on the livelihoods of livestock owners across the region...
January 5, 2018: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/29300141/exercise-induced-physiological-arousal-biases-attention-toward-threatening-scene-details
#5
Tad T Brunyé, Caroline R Mahoney
The present experiment examined whether physiological arousal induced by acute bouts of aerobic exercise would influence attention and memory for scenes depicting or not depicting weapons. In a repeated-measures design, participants exercised at either low or high exertion levels. During exercise, they were presented with images, some of which depicted weapons; immediately following exercise, they completed a recognition test for portions of central and peripheral scene regions. Two primary results emerged...
January 1, 2018: Psychological Reports
https://www.readbyqxmd.com/read/29290819/identification-of-type-iv-collagen-exposure-as-a-molecular-imaging-target-for-early-detection-of-thoracic-aortic-dissection
#6
Ke Xu, Chen Xu, Yanzhenzi Zhang, Feiran Qi, Bingran Yu, Ping Li, Lixin Jia, Yulin Li, Fu-Jian Xu, Jie Du
Thoracic aortic dissection (TAD) is an aggressive and life-threatening vascular disease and there is no effective means of early diagnosis of dissection. Type IV collagen (Col-IV) is a major component of the sub-endothelial basement membrane, which is initially exposed followed by endothelial injury as early-stage event of TAD. So, we want to build a noninvasive diagnostic method to detect early dissection by identifying the exposed Col-IV via MRI. METHODS: Col-IV-targeted magnetic resonance/ fluorescence dual probe (Col-IV-DOTA-Gd-rhodamine B; CDR) was synthesized by amide reaction and coordination reaction...
2018: Theranostics
https://www.readbyqxmd.com/read/29289958/regulatory-variants-of-foxg1-in-the-context-of-its-topological-domain-organisation
#7
Mana M Mehrjouy, Ana Carolina S Fonseca, Nadja Ehmke, Giorgio Paskulin, Antonio Novelli, Francesco Benedicenti, Maria Antonietta Mencarelli, Alessandra Renieri, Tiffany Busa, Chantal Missirian, Claus Hansen, Kikue Terada Abe, Carlos Eduardo Speck-Martins, Angela M Vianna-Morgante, Mads Bak, Niels Tommerup
FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD...
December 30, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29280970/background-registration-based-adaptive-noise-filtering-of-lwir-mwir-imaging-sensors-for-uav-applications
#8
Byeong Hak Kim, Min Young Kim, You Seong Chae
Unmanned aerial vehicles (UAVs) are equipped with optical systems including an infrared (IR) camera such as electro-optical IR (EO/IR), target acquisition and designation sights (TADS), or forward looking IR (FLIR). However, images obtained from IR cameras are subject to noise such as dead pixels, lines, and fixed pattern noise. Nonuniformity correction (NUC) is a widely employed method to reduce noise in IR images, but it has limitations in removing noise that occurs during operation. Methods have been proposed to overcome the limitations of the NUC method, such as two-point correction (TPC) and scene-based NUC (SBNUC)...
December 27, 2017: Sensors
https://www.readbyqxmd.com/read/29273922/predictors-of-cut-out-after-cephalomedullary-nail-fixation-of-pertrochanteric-fractures-a-retrospective-study-of-813-patients
#9
Luigi Murena, Antonio Moretti, Francesca Meo, Enrico Saggioro, Giulia Barbati, Chiara Ratti, Gianluca Canton
BACKGROUND: Cut-out is the most common mechanical complication of the osteosynthesis of pertrochanteric fractures. This complication determines a significant increase in morbidity in elderly patient. Cut-out is defined as the varus collapse of the femoral head-neck fragment with the extrusion of the cephalic screw. Surgical treatment of cut-out might lead to further complications, longer rehabilitation, increased social burden and healthcare system costs. The aim of the study is to identify the predictors of cut-out to prevent its occurrence...
December 23, 2017: Archives of Orthopaedic and Trauma Surgery
https://www.readbyqxmd.com/read/29273679/the-hoxd-cluster-is-a-dynamic-and-resilient-tad-boundary-controlling-the-segregation-of-antagonistic-regulatory-landscapes
#10
Eddie Rodríguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, Denis Duboule
The mammalian HoxD cluster lies between two topologically associating domains (TADs) matching distinct enhancer-rich regulatory landscapes. During limb development, the telomeric TAD controls the early transcription of Hoxd genes in forearm cells, whereas the centromeric TAD subsequently regulates more posterior Hoxd genes in digit cells. Therefore, the TAD boundary prevents the terminal Hoxd13 gene from responding to forearm enhancers, thereby allowing proper limb patterning. To assess the nature and function of this CTCF-rich DNA region in embryos, we compared chromatin interaction profiles between proximal and distal limb bud cells isolated from mutant stocks where various parts of this boundary region were removed...
December 22, 2017: Genes & Development
https://www.readbyqxmd.com/read/29273625/the-nuclear-matrix-protein-hnrnpu-maintains-3d-genome-architecture-globally-in-mouse-hepatocytes
#11
Hui Fan, Pin Lv, Xiangru Huo, Jicheng Wu, Qianfeng Wang, Lu Cheng, Yun Liu, Qiqun Tang, Ling Zhang, Feng Zhang, Xiaoqi Zheng, Hao Wu, Bo Wen
The eukaryotic chromosomes are folded into higher-order conformation to coordinate genome functions. Besides long-range chromatin loops, recent chromosome conformation capture (3C)-based studies indicated the higher level of chromatin structures including compartments and topologically associating domains (TADs), which may serve as units of genome organization and functions. However, the molecular machinery underlying these hierarchically three-dimensional (3D) chromatin architectures remains poorly understood...
December 22, 2017: Genome Research
https://www.readbyqxmd.com/read/29250502/outcomes-of-cephalomedullary-nailing-in-basicervical-fracture
#12
Seok Hyun Kweon, Sung Hyun Lee, Seng Hwan Kook, Young Chae Choi
Purpose: A basicervical femoral fracture is defined as a fracture of base of neck of femur that occurs medially from intertrochanteric line above lesser trochanter. In this study, we intended to evaluate radiological and clinical results of basicervical femoral fractures treated by intramedullary nailing. Materials and Methods: Fifteen patients, who underwent intramedullary nailing among 50 patients, out of 50 who were diagnosed with basicervical femoral fractures from July 2012 to May 2015 were studied...
December 2017: Hip & Pelvis
https://www.readbyqxmd.com/read/29249537/chromatographic-performance-of-microfluidic-liquid-chromatography-devices-experimental-evaluation-of-straight-versus-serpentine-packed-channels
#13
Martin Gilar, Thomas S McDonald, Fabrice Gritti, Gregory T Roman, Jay S Johnson, Bernard Bunner, Joseph D Michienzi, Robert A Collamati, Jim P Murphy, Devesh D Satpute, Matthew P Bannon, Dennis DellaRovere, Robert A Jencks, Tad A Dourdeville, Keith E Fadgen, Geoff C Gerhardt
We prepared a series of planar titanium microfluidic (μLC) columns, each 100 mm long, with 0.15, 0.3 and 0.5 mm i.d.'s. The microfluidic columns were packed with 1.8 μm C18 sorbent and tested under isocratic and gradient conditions. The efficiency and peak capacity of these devices were monitored using a micro LC instrument with minimal extra column dispersion. Columns with serpentine channels were shown to perform worse than those with straight channels. The loss of efficiency and peak capacity was more prominent for wider i...
December 14, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29248484/is-there-any-role-for-direct-repair-of-extensor-mechanism-disruption-following-total-knee-arthroplasty
#14
P Maxwell Courtney, Tori A Edmiston, Caleb T Pflederer, Brett R Levine, Tad L Gerlinger
BACKGROUND: Extensor mechanism disruption remains a challenging problem in total knee arthroplasty (TKA) with historically poor outcomes. The purpose of our study is to determine if patients undergoing acute extensor mechanism repair had different outcomes than patients undergoing allograft reconstruction. METHODS: We reviewed a series of 126 total knee arthroplasty patients requiring surgical repair or reconstruction of an extensor mechanism injury from 2005 to 2014 with a minimum of 24 months of follow-up...
December 2, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/29237330/influence-of-cationic-polyacrilamide-flocculant-on-high-solids-anaerobic-digestion-of-sewage-sludge-under-thermophilic-condition
#15
Yuri Litti, Anna Nikitina, Dmitriy Kovalev, Artem Ermoshin, Rishi Mahajan, Gunjan Goel, Alla Nozhevnikova
Treatment of sewage sludge (SS) by biodegradable polyacrylamide-based flocculants (PAM) is considered to be an effective way to increase total solids (TS) content prior to anaerobic digestion (AD). However, data on how PAM addition influences the efficiency of AD process are quite contradictory; moreover no data is available for thermophilic AD (TAD). This study showed that at optimal inoculum to substrate ratio (ISR, 55/45), PAM addition resulted in some decrease in initial methane production during TAD of SS due to formation of large flocs (up to 2-3 mm in diameter) which deteriorated the mass transfer...
December 14, 2017: Environmental Technology
https://www.readbyqxmd.com/read/29235706/a-conserved-tad-pilus-promotes-vibrio-vulnificus-oyster-colonization
#16
Meng Pu, Patrick Duriez, Mattan Arazi, Dean A Rowe-Magnus
Vibrio vulnificus has the highest death rate (>35%) and per-case economic burden ($3.3 million) of any foodborne pathogen in the US. Infections occur via open wounds or following ingestion of contaminated seafood, most infamously oysters. We isolated a 1000th generation descendant, designated NT, that exhibited increased biofilm and aggregate formation relative to its parent. We identified two significant causal changes underlying these NT phenotypes. First, the entire 24-kb capsular polysaccharide biosynthesis locus, which is essential for virulence but inhibits biofilm formation, had been purged from the genome...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29233569/continuous-adductor-canal-blocks-provide-superior-ambulation-and-pain-control-compared-to-epidural-analgesia-for-primary-knee-arthroplasty-a-randomized-controlled-trial
#17
Erdan Kayupov, Kamil Okroj, Adam C Young, Mario Moric, Timothy J Luchetti, Gilat Zisman, Asokumar Buvanendran, Tad L Gerlinger, Craig J Della Valle
BACKGROUND: Adductor canal blocks (ACBs) are an alternative to femoral nerve blocks that minimize lower extremity weakness. However, it is unclear whether this block will provide analgesia that is equivalent to techniques, such as epidural analgesia. The purpose of this randomized controlled trial was to compare continuous ACBs with epidural analgesia for primary total knee arthroplasty. METHODS: Following institutional review board approval, 145 patients were randomized to 1 of 3 groups: combined spinal-epidural (CSE), spinal + continuous ACB (CACB), or general + CACB...
November 13, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/29229219/computer-assisted-navigation-for-intramedullary-nail-fixation-of-intertrochanteric-femur-fractures-a-randomized-controlled-trial
#18
Ryan J Lilly, Denise M Koueiter, Kelly C Graner, Gregory P Nowinski, Jason Sadowski, Kevin D Grant
INTRODUCTION: Lag screw cutout is one of the most commonly reported complications following intramedullary nail fixation of intertrochanteric femur fractures. However, its occurrence can be minimized by a well-positioned implant, with a short Tip-to-Apex Distance (TAD). Computer-assisted navigation systems provide surgeons with the ability to track screw placement in real-time. This could allow for improved lag screw placement and potentially reduce radiation exposure to the patient and surgeon...
December 7, 2017: Injury
https://www.readbyqxmd.com/read/29226300/a-novel-method-for-treatment-of-class-iii-malocclusion-in-growing-patients
#19
Saad A Al-Mozany, Oyku Dalci, Mohammed Almuzian, Carmen Gonzalez, Nour E Tarraf, M Ali Darendeliler
BACKGROUND: Management of Class III malocclusion is one of the most challenging treatments in orthodontics, and several methods have been advocated for treatment of this condition. A new treatment protocol involves the use of an alternating rapid maxillary expansion and constriction (Alt-RAMEC) protocol, in conjunction with full-time Class III elastic wear and coupled with the use of temporary anchorage devices (TADs). The aim of this study was to evaluate the dento-skeletal and profile soft tissue effects of this novel protocol in growing participants with retrognathic maxilla...
December 11, 2017: Progress in Orthodontics
https://www.readbyqxmd.com/read/29217591/topologically-associating-domains-and-chromatin-loops-depend-on-cohesin-and-are-regulated-by-ctcf-wapl-and-pds5-proteins
#20
Gordana Wutz, Csilla Várnai, Kota Nagasaka, David A Cisneros, Roman R Stocsits, Wen Tang, Stefan Schoenfelder, Gregor Jessberger, Matthias Muhar, M Julius Hossain, Nike Walther, Birgit Koch, Moritz Kueblbeck, Jan Ellenberg, Johannes Zuber, Peter Fraser, Jan-Michael Peters
Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops...
December 7, 2017: EMBO Journal
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