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Mustafa Sancar Ataç, Yeliz Kilinç
The bony augmentation of severely atrophied mandible is generally required for the purposes of prosthetic rehabilitations. The treatment strategies have been well defined in the literature ranging from osteotomy techniques to distraction osteogenesis. Visor osteotomy is the milestone of the reconstructive surgery for the atrophied mandible which has received some modifications. In the present study, the authors describe a new modification of visor osteotomy in which a complete coronal split osteotomy down to the inferior border at the mental region has been performed...
October 14, 2016: Journal of Craniofacial Surgery
Xingqi Chen, Ying Shen, Will Draper, Jason D Buenrostro, Ulrike Litzenburger, Seung Woo Cho, Ansuman T Satpathy, Ava C Carter, Rajarshi P Ghosh, Alexandra East-Seletsky, Jennifer A Doudna, William J Greenleaf, Jan T Liphardt, Howard Y Chang
Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis...
October 17, 2016: Nature Methods
Nina Koenecke, Jeff Johnston, Bjoern Gaertner, Malini Natarajan, Julia Zeitlinger
BACKGROUND: Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear...
September 27, 2016: Genome Biology
Edwin Garcia, Annette Hayden, Charles Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, Clarisa Choh, Mathieu Derouet, Patrick Duriez, Fergus Noble, Michael J White, John N Primrose, Jonathan C Strefford, Matthew Rose-Zerilli, Gareth J Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C Fitzgerald, Timothy J Underwood
New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a 55-year-old male with OAC without recombinant-DNA transformation. Somatic genetic variations from MFD-1, tumour, normal oesophagus, and leucocytes were analysed with SNP6. WGS was performed in tumour and leucocytes. RNAseq was performed in MFD-1, and two classic OAC cell lines FLO1 and OE33...
September 7, 2016: Scientific Reports
E Ozan, G K Atac, T Evrin, K Alisar, L O Sonmez, A Alhan
The value of abdominal computed tomography in non-traumatic abdominal pain has been well established. On the other hand, to manage computed tomography, appropriateness has become more of an issue as a result of the concomitant increase in patient radiation exposure with increased computed tomography use. The purpose of this study was to investigate whether C-reactive protein, white blood cell count, and pain location may guide the selection of patients for computed tomography in non-traumatic acute abdomen...
September 2, 2016: Emergency Radiology
Meital Gury-BenAri, Christoph A Thaiss, Nicolas Serafini, Deborah R Winter, Amir Giladi, David Lara-Astiaso, Maayan Levy, Tomer Meir Salame, Assaf Weiner, Eyal David, Hagit Shapiro, Mally Dori-Bachash, Meirav Pevsner-Fischer, Erika Lorenzo-Vivas, Hadas Keren-Shaul, Franziska Paul, Alon Harmelin, Gérard Eberl, Shalev Itzkovitz, Amos Tanay, James P Di Santo, Eran Elinav, Ido Amit
Innate lymphoid cells (ILCs) are critical modulators of mucosal immunity, inflammation, and tissue homeostasis, but their full spectrum of cellular states and regulatory landscapes remains elusive. Here, we combine genome-wide RNA-seq, ChIP-seq, and ATAC-seq to compare the transcriptional and epigenetic identity of small intestinal ILCs, identifying thousands of distinct gene profiles and regulatory elements. Single-cell RNA-seq and flow and mass cytometry analyses reveal compartmentalization of cytokine expression and metabolic activity within the three classical ILC subtypes and highlight transcriptional states beyond the current canonical classification...
August 25, 2016: Cell
Arif Arısoy, Fatih Altunkaş, Kayıhan Karaman, Metin Karayakalı, Ataç Çelik, Köksal Ceyhan, Çağrı Zorlu
Intracoronary thrombus burden is associated with some adverse events and poor prognosis in patients with ST-segment elevation myocardial infarction (STEMI). Identifying predictors of the intracoronary thrombus burden may contribute to the management of STEMI. In this study, we evaluated whether monocyte count to high-density lipoprotein cholesterol ratio (MHR) is a predictor of intracoronary thrombus burden in patients with STEMI. The study population consisted of 414 patients with STEMI who underwent primary percutaneous coronary intervention (PCI)...
August 16, 2016: Clinical and Applied Thrombosis/hemostasis
Elif Bozçal, Gürkan Yiğittürk, Ataç Uzel, Sabire Şöhret Aydemir
BACKGROUND/AIM: The purpose of this study was to investigate Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) strains originating from diarrheagenic patients. MATERIALS AND METHODS: A total of 102 patients with diarrhea between October 2012 and January 2013 were enrolled in this study. Multiplex and standard polymerase chain reactions were performed to detect and distinguish STEC and EPEC strains. O serotyping of EPEC was carried out by monovalent antisera...
2016: Turkish Journal of Medical Sciences
A Fernández-Miñán, J Bessa, J J Tena, J L Gómez-Skarmeta
Accurate transcriptional control of genes is fundamental for the correct functioning of organs and developmental processes. This control depends on the interplay between the promoter of genes and other noncoding sequences, whose interaction is mediated by 3D chromatin arrangements. Thus, the detailed description of transcriptional regulatory landscapes is essential to understand the mechanisms of transcriptional regulation. However, to achieve that, two important challenges have to be faced: (1) the identification of the noncoding sequences that contribute to gene transcription and (2) the association of these sequences to the respective genes they control...
2016: Methods in Cell Biology
S Yang, C J Ott, M P Rossmann, M Superdock, L I Zon, Y Zhou
Zebrafish is an excellent genetic and developmental model for the study of vertebrate development and disease. Its ability to produce an abundance of transparent, externally developed embryos has facilitated large-scale genetic and chemical screens for the identification of critical genes and chemical factors that modulate developmental pathways. These studies can have profound implications for the diagnosis and treatment of a variety of human diseases. Recent advancements in molecular and genomic studies have provided valuable tools and resources for comprehensive and high-resolution analysis of epigenomes during cell specification and lineage differentiation throughout development...
2016: Methods in Cell Biology
Luca Giorgetti, Bryan R Lajoie, Ava C Carter, Mikael Attia, Ye Zhan, Jin Xu, Chong Jian Chen, Noam Kaplan, Howard Y Chang, Edith Heard, Job Dekker
X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed...
July 28, 2016: Nature
Burçe Ataç Mogol, Vural Gökmen
Chitosan has been popular as a natural food preservative due to its antibacterial and antifungal activities. It may be used in thermally processed foods such as bread to delay staling and improve the microbial stability during the shelf-life. However, the thermal process could lead to the formation of harmful compounds in bakery products through chemical reactions, in which chitosan could take part. Therefore, this study aims to investigate the effect of chitosan on the formation of acrylamide and hydroxymethylfurfural (HMF) in different model systems...
August 10, 2016: Food & Function
İmran Aydoğdu, Yavuz Atar, Ziya Saltürk, Hüseyin Sarı, Enes Ataç, Zeynep Aydoğdu, Muzaffer İnan, Gökhan Mersinlioğlu, Yavuz Uyar
OBJECTIVE: The goal of this study was to evaluate the effects of radioactive iodine ablation therapy on voice quality of patients diagnosed with well-differentiated thyroid carcinoma. METHODS: We enrolled 36 patients who underwent total or subtotal thyroidectomy due to well-differentiated thyroid carcinoma. Voice recordings from patients were analyzed for acoustic and aerodynamic voice. The Voice Handicap Index-10 was used for subjective analysis. The control group consisted of 36 healthy participants...
July 1, 2016: Journal of Voice: Official Journal of the Voice Foundation
Gülizar Demirok, Yasemin Topalak, Mustafa M Başaran, Gökçe K Ataç, Sertaç Öztürk, Ahmet Sengün
INTRODUCTION: The choroid receives about 65-85% of ocular blood flow, which comes from the ophthalmic artery (OA), the first branch of the internal carotid artery (ICA). In the foveal avascular zone, there is no retinal vascular supply; therefore, choroidal blood supply plays a significant role in this subfoveal region. The ocular pulse amplitude (OPA) provides useful information about intraocular blood flow and is an indirect indicator of choroidal perfusion. In this study, we aimed to assess the correlation between the OPA, subfoveal choroidal thickness (CT), and ICA Doppler ultrasound findings in healthy eyes...
July 1, 2016: Seminars in Ophthalmology
Ebru Ozan, Gokce Kaan Atac
BACKGROUND: Adult intussusception is a rare phenomenon, acute appendicitis accompanying multiple transient intussusceptions are much more uncommon. Satisfaction and quiting imaging studies after finding an intussusception on ultrasound, may lead diagnostic errors. Radiologists should raise their awareness of imaging findings in intussusception and keep in their mind coexistent troubles in the belly. This unique case presents unusual imaging findings of a rare dual abdominal emergency condition, particularly highlighting the value of abdominal computed tomography...
2016: Polish Journal of Radiology
Laura J Scott, Michael R Erdos, Jeroen R Huyghe, Ryan P Welch, Andrew T Beck, Brooke N Wolford, Peter S Chines, John P Didion, Narisu Narisu, Heather M Stringham, D Leland Taylor, Anne U Jackson, Swarooparani Vadlamudi, Lori L Bonnycastle, Leena Kinnunen, Jouko Saramies, Jouko Sundvall, Ricardo D'Oliveira Albanus, Anna Kiseleva, John Hensley, Gregory E Crawford, Hui Jiang, Xiaoquan Wen, Richard M Watanabe, Timo A Lakka, Karen L Mohlke, Markku Laakso, Jaakko Tuomilehto, Heikki A Koistinen, Michael Boehnke, Francis S Collins, Stephen C J Parker
Type 2 diabetes (T2D) results from the combined effects of genetic and environmental factors on multiple tissues over time. Of the >100 variants associated with T2D and related traits in genome-wide association studies (GWAS), >90% occur in non-coding regions, suggesting a strong regulatory component to T2D risk. Here to understand how T2D status, metabolic traits and genetic variation influence gene expression, we analyse skeletal muscle biopsies from 271 well-phenotyped Finnish participants with glucose tolerance ranging from normal to newly diagnosed T2D...
2016: Nature Communications
Cornelis J Boogerd, Ivy Aneas, Noboru Sakabe, Ralph J Dirschinger, Quen J Cheng, Bin Zhou, Ju Chen, Marcelo A Nobrega, Sylvia M Evans
Mutations in the T-box transcription factor TBX20 are associated with multiple forms of congenital heart defects, including cardiac septal abnormalities, but our understanding of the contributions of endocardial TBX20 to heart development remains incomplete. Here, we investigated how TBX20 interacts with endocardial gene networks to drive the mesenchymal and myocardial movements that are essential for outflow tract and atrioventricular septation. Selective ablation of Tbx20 in murine endocardial lineages reduced the expression of extracellular matrix and cell migration genes that are critical for septation...
August 1, 2016: Journal of Clinical Investigation
André F Rendeiro, Christian Schmidl, Jonathan C Strefford, Renata Walewska, Zadie Davis, Matthias Farlik, David Oscier, Christoph Bock
Chronic lymphocytic leukaemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, here we present genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients measured by the ATAC-seq assay. We also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting data set, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations...
2016: Nature Communications
Jingyi Wu, Bo Huang, He Chen, Qiangzong Yin, Yang Liu, Yunlong Xiang, Bingjie Zhang, Bofeng Liu, Qiujun Wang, Weikun Xia, Wenzhi Li, Yuanyuan Li, Jing Ma, Xu Peng, Hui Zheng, Jia Ming, Wenhao Zhang, Jing Zhang, Geng Tian, Feng Xu, Zai Chang, Jie Na, Xuerui Yang, Wei Xie
In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion...
June 30, 2016: Nature
Hande Ezerarslan, Ebru Ozan Sanhal, Selma Kurukahvecioğlu, Gökçe Kaan Ataç, Sinan Kocatürk
OBJECTIVES/HYPOTHESIS: To analyze whether there is correlation between branching patterns of anterior inferior cerebellar artery/posterior inferior cerebellar artery (AICA/PICA) in cerebellopontine angle (CPA) area, as demonstrated by three-dimensional fast imaging employing steady-state acquisition (3D FIESTA) magnetic resonance imaging (MRI) and 1) idiopathic sudden sensorineural hearing loss (ISSNHL) outcomes and 2) recovery of ISSNHL. STUDY DESIGN: We evaluated patients with idiopathic SSNHL for branching patterns of AICA/PICA in CPA area, as demonstrated by 3D FIESTA MRI...
June 10, 2016: Laryngoscope
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