GLANET: Genomic loci annotation and enrichment tool

Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. Results: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately. GLANET annotates and performs enrichment analysis on these loci with a rich library. We introduce and perform novel data-driven computational experiments for assessing the power and Type-I error of its enrichment procedure which show that GLANET has attained high statistical power and well-controlled Type-I error rate. As a key feature, users can easily extend its library with new gene sets and genomic intervals. Other key features include assessment of impact of single nucleotide variants (SNPs) on TF binding sites and regulation based pathway enrichment analysis. Availability and implementation: GLANET can be run using its GUI or on command line. GLANET's source code is available at https://github.com/burcakotlu/GLANET. Tutorials are provided at https://glanet.readthedocs.org. © 2017 The Author

Respiratory Health Symptoms among Students Exposed to Different Levels of Air Pollution in a Turkish City

In this study, we aimed to investigate the frequency of respiratory health symptoms among high school students attending schools at industrial, urban and rural areas in a Turkish city. Three schools located in different zones of the city having different pollution characteristics were chosen based on the pollutant distribution maps using Geographical Information Systems (GIS) software. A cross-sectional survey was performed among 667 high school students in the schools. Outdoor and indoor nitrogen dioxide (NO2) and ozone (O3) concentrations were also measured by passive samplers in the same schools to investigate possible routes of exposure. Chronic pulmonary disease (OR = 1.49; 95%CI: 1.11–1.99; p = 0.008), tightness in the chest (OR = 1.57; 95%CI: 1.22–2.02; p = 0.001), morning cough (OR = 1.81 95%CI: 1.19–2.75; p = 0.006) were higher among students in the industrial zone where nitrogen dioxide and ozone levels were also highest. There were no indoor sources of nitrogen dioxide and ozone exists in the schools except for the dining hall. As a conclusion, this study has noticed that air pollution and respiratory health problems among high school students are high in industrial zones and the use of passive samplers combined with GIS is an effective tool that may be used by public health researchers to identify pollutant zones and persons at risk

Magnetic crystals and helical liquids in alkaline-earth fermionic gases

The joint action of a synthetic gauge potential and of atomic contact repulsion in a one-dimensional alkaline-earth(-like) fermionic gas with nuclear spin I leads to the existence of a hierarchy of fractional insulating and conducting states with intriguing properties. We unveil the existence and the features of those phases by means of both analytical bosonization techniques and numerical methods based on the density-matrix renormalization group algorithm. In particular, we show that the gapless phases can support helical modes, whereas the gapped states, which appear under certain conditions, are characterised both by density and magnetic order. Several distinct features emerge solely for spin I larger than 1/2, thus making their study with cold-atoms unique. We will finally argue that these states are related to the properties of an unconventional fractional quantum Hall effect in the thin-torus limit. The properties of this hierarchy of states can be experimentally studied in state-of-the-art cold-atom laboratories

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

Palladium complexes with bis(diphenylphosphinomethyl)amino ligands and their application as catalysts for the Heck reaction

Aminomethylphosphine (P-C-N) type ligands, (Ph2PCH 2)2NR R = -(CH2)3Si(OEt 3)3 or -CH2CH2OH, and their Pd(II) complexes have been synthesized. All the compounds were characterized by 1H-, 31P-NMR, and elemental analysis. The complexes are proposed to have a square planar geometry. They were investigated as catalysts for the Heck reaction of aryl halides (I, Br, Cl) with methyl acrylate. Both complexes showed high activity to give methyl cinnamate in good yields, with the best turnover numbers found for [PdCl2(Ph2PCH 2)2N(CH2)3Si(OEt)3]. © 2008 Springer Science+Business Media B.V.Acknowledgments We would like to thank Dr Arif Hesenov for GC analysis. The authors are also thankful to Research Fund of C¸ ukurova University and the Scientific and Technological Research Council of Turkey for financial support to this project

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)

Synthesis and characterization of bis(diphenylphosphinomethyl)amino ligands and their Ni(II), Pd(II) complexes: Application to hydrogenation of styrene

Transition metal complexes of Ni(II) and Pd(II) with ditertiary bis(diphenylphosphinomethyl)amino ligands, (Ph2PCH2) 2NC(CH3)3 (1) and [(Ph2PCH 2)Nm-PhSO3]Na (2) (Ph = phenyl), have been synthesized in good yields under nitrogen atmosphere by Schlenk technique. All complexes have been characterized using elemental analyses and spectroscopic techniques such as atomic absorption, FT-IR, and NMR (1H, 31P). Atomic absorption spectroscopic analysis showed that the reactions of ligands 1 and 2 with NiCl2·6H2O and [PdCl2(COD)] occurred in 1:1 molar ratio. The metal complexes [NiCl2(Ph 2PCH2)2Nm-PhSO3Na] (4) and [PdCl2(Ph2PCH2)2Nm-PhSO 3Na] (6) were found to be soluble in ethanolic and aqueous solutions, as well as slightly soluble in water. Electrochemical behaviors of complexes were investigated by cyclic voltammetry. Catalytic effects of Pd(II) complexes were tested throughout the hydrogénation of styrene to ethylbenzene. © 2008 Wiley Periodicals, Inc

Hydrogenation of acetophenone and its derivatives with 2-propanol using aminomethylphosphine-ruthenium catalysis

The reaction of 3'-aminopropyltriethoxysilane with the phosphonium salt ([Ph2P(CH2OH)2]Cl) gives an aminomethylphosphine-type ligand ((CH3CH2O) 3Si(CH2)3N(CH2PPh2)2). Reaction of the ligand ((CH3CH2O)3Si(CH2) 3N(CH2PPh2)2) with silica gives silica supported aminomethylphosphine ligand (SiO2)-O-Si(CH 2)3N(CH2PPh2)2). The ligands were refluxed with [RuCl2(p-cymene)]2 in toluene to give [RuCl2((CH3CH2O)3Si(CH 2)3N(CH2PPh2)2)] and silica-supported SiO2)-O-[RuCl2((Si(CH2) 3N(CH2PPh2)2)2] complex, respectively. The catalytic studies show that the complexes [RuCl 2((CH3CH2O)3Si(CH2) 3N(CH2PPh2)2)] and SiO 2)-O-[RuCl2((CH3CH2O) 3Si(CH2)3N(CH2PPh2) 2)2] are very active catalysts for the transfer hydrogenation of acetophenone by 2-propanol in basic media. The best yield was observed in hydrogenation of m-methoxy acetophenone (95%) with catalyst [RuCl2((CH3CH2O)3Si(CH 2)3N(CH2PPh2)2)]

Catalytic synthesis of 2-methyl-1,4-naphthoquinone (vitamin K3) over silica-supported aminomethyl phosphine-Ru(II), Pd(II), and Co(II) complexes

Ru(II), Pd(II), and Co(II) complexes of the free ditertiary aminomethylphosphine ligand, N,N-bis(diphenylphosphinomethyl) aminopropyltriethoxysilane [(EtO)3Si(CH2)3 N(CH2PPh2)2] (DIPAPTES), and its SiO2-DIPAPES have been synthesized under a nitrogen atmosphere using Schlenk techniques. All the complexes were used as catalysts for the oxidation of 2-methyl naphthalene (2MN) to give 2-methyl-1,4-naphthoquinone (vitamin K3, menadione, 2MNQ) in the presence of hydrogen peroxide as a clean and cheap oxidant. The catalytic synthesis of vitamin K3 was investigated using both homogeneous catalysis with free complexes and heterogeneous catalysis with silica-supported complexes. [(DIPAPTES)PdCl2] and its silica-supported form showed the best catalytic activity for the selective oxidation of 2-methyl naphthalene to 2-methyl-1,4-naphtoquinone compared to the other metal complexes. 2MNQ yield reached 52.26% with the 2MN conversion of 90.52% using complex [(DIPAPTES)PdCl2] and 58.59% with the 2MN conversion of 99.56% using the silica supported [SiO2(DIPAPES)PdCl2] complex for 1 h. Recycling was investigated for the silica-supported Pd(II) complex and compared with the classical production of vitamin K3. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file. Copyright © Taylor & Francis Group, LLC