Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Pediyatrik medulla spinalis yaralanmalarinda epidemiyoloji ve patofizyoloji

It is essential to know the incidence and etiology of pediatric spinal cord injury (SCI) in order to identify risk groups, improve prevention and plan care and rehabilitation. SCI significantly and usually irreversibly alters every aspect of a person's life. Pediatric SCI is relatively uncommon, with distinctive manifestations due to the characteristic anatomical and physiologic features of the growing child. The interaction of growth and development, modified by injury, is responsible for the various clinical deformities frequently seen in pediatric patients. The incidence of pediatric SCI is lower than in adults, varying from 1 to 10% of all spinal injuries. However, the diagnostic studies and images differ from adults and require particular consideration. This article provides a review of epidemiologic data from different countries and also the pathophysiology of pediatric SCI with unique aspects in outline

Adsorption and inhibitive properties of aminobiphenyl and its Schiff base on mild steel corrosion in 0.5 M HCl medium

Electrochemical measurements were performed to investigate the effectiveness and adsorption behaviour of aminobiphenyl (Aph) and 2-(3-hydroxybenzylideneamino)biphenyl (Aph-S), as corrosion inhibitors for mild steel (MS) in 0.5 M HCl solution. Potentiodynamic polarization, linear polarization resistance (LP) and electrochemical impedance spectroscopy (EIS) techniques were applied to study the metal corrosion behaviour in the absence and presence of different concentrations of Aph and Aph-S. In order to gain more information about adsorption mechanism the AC impedance technique was used to evaluate the potential of zero charge (PZC) from polarization resistance (Rp) versus voltage (E) plot. Potentiodynamic polarization measurements showed that Aph act as cathodic type inhibitor where as Aph-S act mixed type. The inhibition efficiency (IE%) increases with increasing concentration of compounds and reached 92.6% for Aph and 97.2% for Aph-S at 5 × 10-3 M. Double layer capacitance (Cdl) and polarization resistance (Rp) values are derived from Nyquist plots obtained from AC impedance studies. The experimental data fit Langmuir isotherm for both Aph and Aph-S, and from the adsorption isotherm some thermodynamic data for the adsorption processes are calculated and discussed. The effect of exposure time on the corrosion behaviour of mild steel in the absence and presence of inhibitor over 168 h was also studied. © 2008 Elsevier B.V. All rights reserved.FEF2004D13This study has been financially supported by Cukurova University research fund (Project number: FEF2004D13)

Mesane rehabi?li?tasyonunda taşinabi?li?r ultrasoni?k haci?m ölçüm ci?hazlarinin yararlari

Post-void residuel urine volume and bladder capacity measurements are important in the diagnosis and the follow up of bladder disfunction. Portable ultrasound-based measurement devices (PU) offer the possibility of making these measurements accuretly, in a short time, without discomfort. This non-invasive method doesn't have the risk of urethral trauma and urinary tract infection. In the highlights of this knowledge PU will simplify the daily routine and will be useful in the neurogenic bladder rehabilitation

Electrochemical synthesis of poly-6-amino-m-cresol (poly-AmC)

The electropolymerization of 6-amino-m-cresol (AmC) on a platinum electrode was studied in 0.1 M Na 2 SO 4 solution containing 5 × 10 -3 M 6-amino-m-cresol at different pHs using cyclic voltammetry technique. Voltammetric results showed that oxidation of 6-amino-m-cresol produced a passivating polymeric film on the platinum surface at all pHs studied. Synthesized polymer has bronze color on platinum. To investigate the structure of poly-6-amino-m-cresol (poly-AmC) films FTIR technique was employed. The spectroscopic results indicate that polymer chain consist of ring opened units rather than phenoxazine structure. © 2005 Elsevier B.V. All rights reserved.FEF2004D13This study has been financially supported by Cukurova University research fund (Project number: FEF2004D13). The authors are grateful to Cukurova University research fund