keyword
MENU ▼
Read by QxMD icon Read
search

Tads

keyword
https://www.readbyqxmd.com/read/28087711/ctcf-mediated-topological-boundaries-during-development-foster-appropriate-gene-regulation
#1
Varun Narendra, Milica Bulajić, Job Dekker, Esteban O Mazzoni, Danny Reinberg
The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087402/accuracy-is-in-the-eyes-of-the-pathologist-the-visual-interpretive-process-and-diagnostic-accuracy-with-digital-whole-slide-images
#2
Tad T Brunyé, Ezgi Mercan, Donald L Weaver, Joann G Elmore
Digital whole slide imaging is an increasingly common medium in pathology, with application to education, telemedicine, and rendering second opinions. It has also made it possible to use eye tracking devices to explore the dynamic visual inspection and interpretation of histopathological features of tissue while pathologists review cases. Using whole slide images, the present study examined how a pathologist's diagnosis is influenced by fixed case-level factors, their prior clinical experience, and their patterns of visual inspection...
January 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28087167/lingering-questions-about-enhancer-rna-and-enhancer-transcription-coupled-genomic-instability
#3
REVIEW
Gerson Rothschild, Uttiya Basu
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes...
January 10, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28070687/predicting-chromatin-architecture-from-models-of-polymer-physics
#4
REVIEW
Simona Bianco, Andrea M Chiariello, Carlo Annunziatella, Andrea Esposito, Mario Nicodemi
We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches...
January 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28069653/the-molecular-epidemiology-of-pf-k13-mutations-in-senegal-using-targeted-amplicon-deep-sequencing
#5
Eldin Talundzic, Yaye D Ndiaye, Awa B Deme, Christian Olsen, Dhruviben S Patel, Shweta Biliya, Rachel Daniels, Fredrik O Vannberg, Sarah K Volkman, Venkatachalam Udhayakumar, Daouda Ndiaye
The emergence of Plasmodium falciparum (Pf) resistance to artemisinin in Southeast Asia threatens malaria control and elimination activities worldwide. Multiple polymorphisms in the Pf kelch gene found in chromosome 13 (Pfk13) have been associated with artemisinin resistance. Surveillance of potential drug resistance loci within a population that may emerge under increasing drug pressure is an important public health activity. In this context, P. falciparum infections from an observational surveillance study in Senegal were genotyped using targeted amplicon deep sequencing (TADS) for Pfk13 polymorphisms...
January 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28060840/an-isochore-framework-underlies-chromatin-architecture
#6
Kamel Jabbari, Giorgio Bernardi
A recent investigation showed the existence of correlations between the architectural features of mammalian interphase chromosomes and the compositional properties of isochores. This result prompted us to compare maps of the Topologically Associating Domains (TADs) and of the Lamina Associated Domains (LADs) with the corresponding isochore maps of mouse and human chromosomes. This approach revealed that: 1) TADs and LADs correspond to isochores, i.e., isochores are the genomic units that underlie chromatin domains; 2) the conservation of TADs and LADs in mammalian genomes is explained by the evolutionary conservation of isochores; 3) chromatin domains corresponding to GC-poor isochores (e...
2017: PloS One
https://www.readbyqxmd.com/read/28060558/the-connection-between-brg1-ctcf-and-topoisomerases-at-tad-boundaries
#7
A Rasim Barutcu, Jane B Lian, Janet L Stein, Gary S Stein, Anthony N Imbalzano
The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries...
January 6, 2017: Nucleus
https://www.readbyqxmd.com/read/28060229/repeat-two-stage-exchange-arthroplasty-for-periprosthetic-knee-infection-is-dependent-on-host-grade
#8
Keith A Fehring, Matthew P Abdel, Matthieu Ollivier, Tad M Mabry, Arlen D Hanssen
BACKGROUND: Two-stage exchange arthroplasty after a previous, failed 2-stage exchange procedure is fraught with difficulties, and there are no clear guidelines for treatment or prognosis given the heterogeneous group of patients in whom this procedure has been performed. The Musculoskeletal Infection Society (MSIS) staging system was developed in an attempt to stratify patients according to infection type, host status, and local soft-tissue status. The purpose of this study was to report the results of 2-stage exchange arthroplasty following a previous, failed 2-stage exchange protocol for periprosthetic knee infection as well as to identify risk factors for failure...
January 4, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28057745/reciprocal-insulation-analysis-of-hi-c-data-shows-that-tads-represent-a-functionally-but-not-structurally-privileged-scale-in-the-hierarchical-folding-of-chromosomes
#9
Yinxiu Zhan, Luca Mariani, Iros Barozzi, Edda G Schulz, Nils Bluthgen, Michael Stadler, Guido Tiana, Luca Giorgetti
Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs) and sub-TAD contact domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions...
January 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28056762/hic-bench-comprehensive-and-reproducible-hi-c-data-analysis-designed-for-parameter-exploration-and-benchmarking
#10
Charalampos Lazaris, Stephen Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
BACKGROUND: Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28054892/primary-infected-left-ventricular-pseudoaneurysm-and-the-use-of-omental-flap
#11
Giorgio Maria Aru, Tad Kim, Roberto Giorgio Aru, Mary Carolyn Vinson
A 55-year-old man with autoimmune deficiency syndrome presented with an infected left ventricular pseudoaneurysm and sepsis. The aneurysmectomy consisted of a Dor-style pericardial patch plus debridement of the abscess cavities. The infected pseudoaneurysm recurred, much larger, within five months due to persistent infected abscess cavities. The second repair was done without a Dor-style patch and with an omental flap. No recurrence has occurred one year after the second repair, but the patient has asymptomatic, partial gastric herniation inside the pericardium...
December 1, 2016: Heart Surgery Forum
https://www.readbyqxmd.com/read/28048767/su-f-i-77-radiation-dose-in-cardiac-catheterization-procedures-impact-of-a-systematic-reduction-in-pulsed-fluoroscopy-frame-rate
#12
C Schultz, S Dixon
PURPOSE: To evaluate whether one small systematic reduction in fluoroscopy frame rate has a significant effect on the total air kerma and/or dose area product for diagnostic and interventional cardiac catheterization procedures. METHODS: The default fluoroscopy frame rate (FFR) was lowered from 15 to 10 fps in 5 Siemens™ Axiom Artis cardiac catheterization labs (CCL) on July 1, 2013. A total of 7212 consecutive diagnostic and interventional CCL procedures were divided into two study groups: 3602 procedures from 10/1/12 -6/30/13 with FFR of 15 fps; and 3610 procedures 7/1/13 - 3/31/14 at 10 fps...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28045068/elucidating-the-genetic-basis-of-an-oligogenic-birth-defect-using-whole-genome-sequence-data-in-a-non-model-organism-bubalus-bubalis
#13
Lynsey K Whitacre, Jesse L Hoff, Robert D Schnabel, Sara Albarella, Francesca Ciotola, Vincenzo Peretti, Francesco Strozzi, Chiara Ferrandi, Luigi Ramunno, Tad S Sonstegard, John L Williams, Jeremy F Taylor, Jared E Decker
Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by absence of a variable distal portion of the hindlimbs. Limited genomic resources available for water buffalo required an original approach to identify genetic variants associated with the disease. The genomes of 4 bilateral and 7 unilateral affected cases and 14 controls were sequenced...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28044450/caffeine-and-theanine-exert-opposite-effects-on-attention-under-emotional-arousal
#14
Grace E Giles, Caroline R Mahoney, Tad T Brunyé, Holly A Taylor, Robin B Kanarek
Tea is perceived as more relaxing than coffee, even though both contain caffeine. L-theanine in tea may account for the difference. Consumed together, caffeine and theanine exert similar cognitive effects to that of caffeine alone, but exert opposite effects on arousal, in that caffeine accentuates and theanine mitigates physiological and felt stress responses. We evaluated whether caffeine and theanine influenced cognition under emotional arousal. Using a double-blind, repeated-measures design, 36 participants received 4 treatments (200 mg caffeine + 0 mg theanine, 0 mg caffeine + 200 mg theanine, 200 mg caffeine + 200 mg theanine, 0 mg caffeine + 0 mg theanine) on separate days...
January 2017: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/28043839/primary-pediatric-care-psychopharmacology-focus-on-medications-for-adhd-depression-and-anxiety
#15
Jeffrey R Strawn, Eric T Dobson, Lisa L Giles
The evidence base for psychopharmacologic interventions in youth with depressive and anxiety disorders as well as attention/deficit hyperactivity disorder (ADHD) has dramatically increased over the past two decades. Psychopharmacologic interventions commonly utilized in the pediatric primary care setting-selective serotonin (norepinephrine) reuptake inhibitors (SSRIs/SSNRIs), stimulants and α2 agonists-are reviewed. General pharmacologic principles are summarized along with class-related side effects and tolerability concerns (e...
December 30, 2016: Current Problems in Pediatric and Adolescent Health Care
https://www.readbyqxmd.com/read/28042267/comparison-of-temporary-anchorage-devices-and-transpalatal-arch-mediated-anchorage-reinforcement-during-canine-retraction
#16
Defne Kecik
OBJECTIVE: The purpose of this study was to compare the dental and skeletal effects of canine retraction using conventional anchorage reinforcement systems and comparing them with the usage of TADs. MATERIALS AND METHODS: The sample consisted of 50 patients having Class I malocclusions with bimaxillary protrusion indicated for first premolar extraction, and allocated into two groups. The first group consisted of 25 patients with a mean age of 18,7 years (min:14, max:22 years, 16 girls and 9 boys) that TADs were applied as an anchorage mechanic between attached gingiva of upper second premolar and first molar teeth...
October 2016: European Journal of Dentistry
https://www.readbyqxmd.com/read/28042256/are-temporary-anchorage-devices-truly-effective-in-the-treatment-of-skeletal-open-bites
#17
Hakan Turkkahraman, Mehmet Sarioglu
OBJECTIVE: The aims of this study were to evaluate the effects of temporary anchorage devices (TADs) in the treatment of skeletal open bites and to compare the results with untreated controls. MATERIALS AND METHODS: A total of forty patients with skeletal anterior open bites were assigned to two groups of twenty each. The mean chronological age for the treatment group (14 female, 6 male) was 16.68 ± 2.80 years old, compared with 16.63 ± 2.83 years old for the control group (11 female, 9 male)...
October 2016: European Journal of Dentistry
https://www.readbyqxmd.com/read/28039827/determinants-of-personal-exposure-to-ozone-in-school-children-results-from-a-panel-study-in-greece
#18
Konstantina Dimakopoulou, Georgios Grivas, Evangelia Samoli, Sophia Rodopoulou, Dionisis Spyratos, Despoina Papakosta, Anna Karakatsani, Archontoula Chaloulakou, Klea Katsouyanni
BACKGROUND: In the wider framework of the RESPOZE (ReSPiratory effects of OZone Exposure in Greek children) panel study, we investigated possible determinants of O3 exposure of school children, measured with personal passive samplers, in Athens and Thessaloniki, Greece. METHODS: Personal exposure to O3 was measured for five weeks spread along the academic year 2013-14, in 186 school children in Athens and Thessaloniki, Greece. At the same time, at-school outdoor measurements were performed and ambient levels of 8-h daily maximum O3 from fixed sites were collected...
December 28, 2016: Environmental Research
https://www.readbyqxmd.com/read/28024223/relationships-between-self-reported-childhood-traumatic-experiences-attachment-style-neuroticism-and-features-of-borderline-personality-disorders-in-patients-with-mood-disorders
#19
Ilya Baryshnikov, Grigori Joffe, Maaria Koivisto, Tarja Melartin, Kari Aaltonen, Kirsi Suominen, Tom Rosenström, Petri Näätänen, Boris Karpov, Martti Heikkinen, Erkki Isometsä
BACKGROUND: Co-occurring borderline personality disorder (BPD) features have a marked impact on treatment of patients with mood disorders. Overall, high neuroticism, childhood traumatic experiences (TEs) and insecure attachment are plausible aetiological factors for BPD. However, their relationship with BPD features specifically among patients with mood disorders remains unclear. We investigated these relationships among unipolar and bipolar mood disorder patients. METHODS: As part of the Helsinki University Psychiatric Consortium study, the McLean Screening Instrument (MSI), the Experiences in Close Relationships-Revised (ECR-R), the Short Five (S5) and the Trauma and Distress Scale (TADS) were filled in by patients with mood disorders (n=282) in psychiatric care...
December 14, 2016: Journal of Affective Disorders
https://www.readbyqxmd.com/read/27986921/development-of-a-cancer-marker-activated-enzymatic-switch-from-the-herpes-simplex-virus-thymidine-kinase
#20
Nirav Y Shelat, Sidhartha Parhi, Marc Ostermeier
Discovery of new cancer biomarkers and advances in targeted gene delivery mechanisms have made gene-directed enzyme prodrug therapy (GDEPT) an attractive method for treating cancer. Recent focus has been placed on increasing target specificity of gene delivery systems and reducing toxicity in non-cancer cells in order to make GDEPT viable. To help address this challenge, we have developed an enzymatic switch that confers higher prodrug toxicity in the presence of a cancer marker. The enzymatic switch was derived from the herpes simplex virus thymidine kinase (HSV-TK) fused to the CH1 domain of the p300 protein...
December 15, 2016: Protein Engineering, Design & Selection: PEDS
keyword
keyword
115509
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"