bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thiol/disulfide homeostasis as a novel indicator of oxidative stress in obstructive sleep apnea patients
Authors: Dinc Mehmet Emre , Ozdemir Cengiz , Ayan Nilhan Nurlu , Bozan Nazım , Ulusoy Seckin , Koca Cemile , Erel Ozcan 
Published: December 2016

ObjectivesThe aim of the present study was to assess thiol/disulfide (SS) homeostasis as a novel indicator of oxidative stress in patients with obstructive sleep apnea (OSA) and to investigate the effect of continuous positive airway pressure (CPAP) therapy on oxidative parameters.Study DesignProspective clinical study.MethodsA total of 104 subjects, 44 in an OSA group and 60 in two control groups (control simple snoring group, control OSA group) were included. The levels of parameters were measured using the Erel and Neselioglu method in patients with moderate or severe OSA before and after CPAP therapy.ResultsThe serum native thiol (SH) and total SH levels as well as the %SH/total SH ratio were significantly lower (P < 0.05) in OSA patients compared to controls, and the SS level and %SS/SH and %SS/total SH ratios were significantly higher (P < 0.05). After CPAP therapy, the native SH level and %SH/total SH ratio were significantly higher (P < 0.05) than before CPAP therapy, and the SS level and %SS/SH and %SS/total SH ratios were significantly lower (P < 0.05). Significant negative correlations were evident between the apnea/hypopnea index (AHI) and the native SH level and %SH/total SH ratio (P < 0.05) before CPAP therapy; and significant positive correlations were seen between the AHI and the %SS/SH and %SS/total SH ratios but not with the SS level.ConclusionWe found that oxidative stress was increased and CPAP therapy had a positive effect in patients with moderate or severe OSA.Level of Evidence3b. Laryngoscope, 127:E244–E250, 2017
A Robust and Efficient Feature Selection Algorithm for Microarray Data
Authors: Bari Mehrab Ghanat , Salekin Sirajul , Zhang Jianqiu (Michelle) 
Published: December 2016

AbstractIn the past decades, a few synergistic feature selection algorithms have been published, which includes Cooperative Index (CI) and K‐Top Scoring Pair (k‐TSP). These algorithms consider the synergistic behavior of features when they are included in a feature panel. Although promising results have been shown for these algorithms, there is lack of a comprehensive and fair comparison with other feature selection algorithms across a large number of microarray datasets in terms of classification accuracy and computational complexity. There is a need in evaluating their performance and reducing the complexity of such algorithms. We compared the performance of synergistic feature selection algorithms with 11 other commonly used algorithms based on 22 microarray gene expression binary class datasets. The evaluation confirms that synergistic algorithms such as CI and k‐TSP will gradually increase the classification performance as more features are used in the classifiers. Also, in order to cut down computational cost, we proposed a new feature selection ranking score called Positive Synergy Index (PSI). Testing results show that features selected using PSI as well as synergistic feature selection algorithms provide better performance compared to with all other methods, while PSI has a computational complexity significantly lower than that of other synergistic algorithms.
Identification of CLK1 Inhibitors by a Fragment–linking Based Virtual Screening
Authors: Walter Anne , Chaikuad Apirat , Loaëc Nadège , Preu Lutz , Knapp Stefan , Meijer Laurent , Kunick Conrad , Koch Oliver 
Published: December 2016

AbstractAlternative splicing plays an important role in the regulation of protein biosynthesis. CDC2‐like kinases (CLKs) phosphorylate splicing factors rendering them a potential target for treating diseases caused by splicing dysregulation. As selective and potent inhibitors of CLK1 are still lacking, a fragment‐linking based virtual screening campaign was successfully applied to identify new inhibitors showing activity on CLK1. These inhibitors exhibit a novel 2,4‐substituted 1,3‐thiazole scaffold that is suitable for further modification. A subsequently performed docking and protein structure based analysis revealed first hints for inhibitors showing preferred binding activity for CLK1 and DYRK2 over other splicing kinases.
Adipocyte lipopolysaccharide binding protein (LBP) is linked to a specific lipidomic signature
Authors: Moreno‐Navarrete José María , Jové Mariona , Padró Teresa , Boada Jordi , Ortega Francisco , Ricart Wifredo , Pamplona Reinald , Badimón Lina , Portero‐Otín Manuel , Fernández‐Real José Manuel 
Published: December 2016

ObjectiveLipopolysaccharide binding protein (LBP) is part of a family of structurally and functionally related lipid transfer proteins. This study aimed to investigate the associations of LBP with the lipid composition of human adipose tissue.MethodsLipidomic analysis was performed in whole adipose tissue. To validate the associations found, LBP was knocked down (KD) in 3T3‐L1 adipocytes, and lipidomic profile was evaluated by nontargeted lipidomics.ResultsLBP gene expression was negatively associated with phosphatidylcholine, phosphatidylserine, and sphingomyelin relative abundance in vivo. LBP expression was also decreased in those samples with the highest docosahexanoic content, implicated in the resolution of inflammation. The KD of LBP (by ∼70%) led to sharp changes in the lipidome of adipocytes. Of note, specific plasmalogen species PE(O‐16:0/22:5), PE(38:2), odd chain glycerolipids, and cholesteryl linoleate were upregulated by LBP KD. In contrast, GM3 gangliosides, several ceramides, a triacylglycerol potentially containing arachidonate, and cholesteryl palmitate were downregulated by LBP KD.ConclusionsLBP seems to play a role in the regulation of lipid composition of adipose tissue linked to resilience to inflammation.
Metabolites distinguishing visceral fat obesity and atherogenic traits in individuals with overweight
Authors: Baek Seung Han , Kim Minkyung , Kim Minjoo , Kang Miso , Yoo Hye Jin , Lee Nan Hee , Kim Yong Hwan , Song Min , Lee Jong Ho 
Published: December 2016

ObjectiveTo screen the metabolomes of both overweight subjects with low visceral fat area (LFO) and high visceral fat area (HFO) to identify potential metabolites that are associated with the different metabolic characteristics.MethodsThe metabolic characteristics of 112 overweight (25 kg/m2 ≤ BMI < 30 kg/m2) Korean individuals aged 30 to 65 years were examined. Plasma metabolomic profiling of HFO [visceral fat area (VFA) at L4 ≥ 100 cm2] and LFO (L4 VFA <100 cm2) individuals matched for age, gender, and BMI was performed.ResultsHFO subjects showed higher VFA at L1 and L4 than LFO subjects. The HFO group showed higher blood pressure, lipid profile, high‐sensitivity C‐reactive protein, malondialdehyde, oxidized low‐density lipoprotein (LDL), and homeostasis model assessment‐insulin resistance and lower high‐density lipoprotein‐cholesterol levels. In plasma metabolite identification, the HFO group showed significantly higher levels of long‐chain (C14:1, C16:1, C16) acylcarnitines (ACs), medium‐chain (C12:1, C12) ACs, urobilinogen, docosahexaenoic acid (C22:6ω3), lysoPE (22:6), lysoPC (22:6), lysoPC (22:5), methoxybenzenepropanoic acid, and isodesmosine. All five ACs correlated positively with VFA and oxidized LDL levels and negatively with high‐density lipoprotein‐cholesterol levels and LDL particle size.ConclusionsTwelve major metabolites, including three long‐chain fatty acids and two medium‐chain ACs, are important for distinguishing HFO and LFO. Chronic lipid surplus from visceral fat in HFO is likely associated with substantial increases in plasma medium‐chain ACs and long‐chain fatty acids, which are closely related to atherogenic traits.
Role of Anions in Assembling the Coordination Polymers of Bis–pyridyl–alkanediamides
Authors: Suman Kumari , Khullar Sadhika , Mandal Sanjay K. , Sarkar Madhushree 
Published: December 2016

AbstractFormation of Coordination Polymers (CPs) of an amide based flexible ligand, bis(3‐pyridyl)butanediamide, has been found to be directed by the anion of the starting metal salt: a 1D network with rectangular loops was obtained with CuSO4 while a 2D network having two‐fold parallel interpenetration was obtained with Cu(ClO4)2. In the 1D network, a π•••π interaction between C=O groups of the amide is present whereas the 2D network shows self‐complementary amide‐to‐amide hydrogen bond. The reaction of the ligand with Cu(C6H5COO)2 results in a 1D chain, where the benzoate units are also coordinated to the Cu(II) centres. The conformational adjustments of the butyl spacer of the ligand in the CPs according to the requirements of the counter anions is observed in the present study. The role of the counter anions (ClO4−, SO42− and C6H5COO−) towards the formation of the CPs was monitored through the competitive reactions, where the ligand was allowed to react with Cu(NO3)2 in the presence of other three counter anions altogether at a time. Further, an understanding on the network stability was gained by studying the counter anion exchange reactions.
CNT@MnO2 Hybrid as Cathode Catalysts Toward Long‐Life Lithium Oxygen Batteries
Authors: Wang Fan , Wen Zhaoyin , Wu Xiangwei 
Published: December 2016

AbstractRechargeable lithium‐oxygen (Li–O2) battery has attracted enormous research attention due to its remarkably high theoretical energy capacity. However, due to the sluggish oxygen reduction and oxygen evolution reaction (ORR and OER) kinetics and incidental side reactions in Li–O2 battery, cycle life is much shorter than that of lithium ion battery. Here, in‐situ growth of branched MnO2 nanosheets on carbon nanotubes (CNTs) were generated and applied as cathode catalyst in Li–O2 battery. The MnO2 with the morphology of petal‐like nanosheets were homogeneously coated outside the CNTs to form core‐shell nanowires. This structure can effectively prevent direct contact between the CNTs and Li2O2, thus avoiding or reducing the decomposition of CNTs and the formation of Li2CO3 during charge process, which can also improve the conductivity of the cathode and increase the cycling performance. As a promising cathode catalyst in Li–O2 batteries, the branched CNT@MnO2 nanocomposite cathode exhibits a stable deep discharge and charge cycling performance over 50 cycles, and more than 200 cycles with a fixed capacity of 500 mAh g–1 at a current density of 200 mA g–1.
Synthesis, Characterization and Catalytic Studies of Heterogeneous Oxo‐Vanadium(IV) Schiff base Catalyst for Activation of Benzylic C‐H bonds of Alkanes
Authors: Dey Ram C. , Islam Md. Mominul , Halder Mita , Roy Anupam Singha , Islam Sk. Manirul 
Published: December 2016

AbstractHere, polymer grafted vanadium(IV) Schiff base catalyst was prepared and applied in the oxidation of benzylic C‐H bonds of alkanes. The solid complex was characterized by some modern techniques i. e. FT‐IR, TGA, SEM‐EDX and solid state UV‐Vis spectroscopy (DRS). This heterogeneous complex showed excellent activity for the oxidation of toluene to benzaldehyde using 30% H2O2 as an oxidantin acetonitrile (ACN) medium at 70oC. This vanadium catalyst was also active for the oxidation of various substituted toluenes. It showed good conversion as well as selectivity for the production of aldehydes from alkanes. The reported catalyst was easily recovered and reused for at least eight times with similar activity.
Synthesis, Solvatochromism, Antibacterial Activity and Dyeing Performance of Tricyanofuran‐Hydrazone Analogues
Authors: Khattab Tawfik A. , Gaffer Hatem E. , Aly Sherif Abdelmoez , Klapötke Thomas M. 
Published: December 2016

AbstractFour novel tricyanofuran disperse dyestuffs 3a‐d bearing hydrazone moiety were synthesized in order to investigate their possible antibacterial activity. The hydrazone moiety was introduced via azo‐coupling of the tricyanofuran with the appropriately functionalized diazonium salt. The optical properties of these compounds showed interesting solvatochromic properties. The absorption peaks are observed in the wavelength range 454–513 nm. It can also be seen that they display different maximum emissions in the wavelength range 528–615 nm. The functional groups attached to the hydrazone moiety influenced both on absorption and emission maxima. The prepared hydrazone‐based disperse dyes were applied for dyeing polyester fabrics, affording satisfactory results. Furthermore, compounds 3a and 3c demonstrated a relatively strong antibacterial activity against some selected gram positive Staphylococcus aureus and Bacillus subtilis; and gram negative Escherichia coli and Pseudomonas aeuroginosa employing Ampicillin as standard drug.
Doubly, Triply and Multiply Pleated Sheets of Bipyridinium Radical Cation‐Incorporated Polymers Tuned by Four Cucurbiturils
Authors: Qi Qi , Yang Bo , Xi Cheng‐Gang , Yang Xiran , Zhang Dan‐Wei , Liu Simin , Li Zhan‐Ting 
Published: December 2016

AbstractDepending on the size of their cavity, cucurbit[n]urils (CB[n], n=5, 7, 8, and 10) exhibit very different encapsulation selectivity. This feature has been utilized to tune the formation and switching of three kinds of pleated sheets of bipyridinium radical cation (BIPY•+)‐based polymers in water. Driven by the dimerization of the BIPY•+ units, the polymers spontaneously form multiply pleated sheets. These pleated foldamers can be reversibly converted into flexible pseudopoly‐rotaxanes, doubly and triply pleated sheets by CB[7], CB[8] and CB[10], respectively, through selective encapsulation of the macrocycles for one, two or three stacked BIPY•+ units. Adding adamantamonium (ADMT), hexamethylenetetramine (HMTA) or CB[5] to the respective solutions leads to taking away of the CB rings from the polymers due to the formation of more stable 1:1 complexes and as a result, multiply pleated sheets are recovered. UV‐vis absorption spectroscopy has been used to investigate the formation and conversion of the pleated and extended states of the polymers.
Zinc Dialkylhydroxybenzoates with Unusual Structures: First Example of a Discrete Three‐Blade Paddle‐Wheel and a Solvent Engulfed Coordination Polymer
Authors: Vishnoi Pratap , Sharma Sunil K. , Kaleeswaran D. , Murugavel Ramaswamy 
Published: December 2016

AbstractSterically encumbered 4‐hydroxy‐3,5‐diisopropylbenzoic acid (H2diphba), bearing a carboxylic acid, a phenol and two iso‐propyl substituents, has been investigated for the first time as a ligand and supramolecular synthon to isolate eight Zn(II) complexes, [Zn2(Hdiphba)3(OAc)(L)] (L=DMF(1) or pyz (2)), [Zn(Hdiphba)2(2,2′‐bpy)] (3), [Zn(Hdiphba)2(1,10‐phen)] (4), [Zn(Hdiphba)2(pz)2] (5) and [Zn2(Hdiphba)2(μ2‐dmpz)2(Hdmpz)2] (6), [Zn(Hdiphba)2(4,4′‐bpy)]n⋅4nCH3OH (7.4nCH3OH), [Zn2(Hdiphba)4(4,4′‐azobpy)(H2O)2] (8⋅H2diphba), which have been structurally characterized. Compounds 1 and 2 are rare examples of symmetrically bridged triple‐blade molecular tricarboxylate paddle‐wheels which self‐assemble into hexameric units. Compounds 3, 4 and 5 are mononuclear complexes, bearing two exposed phenolic –OH groups self‐assembled into 2‐D arrays via both hydrogen bonding and π‐π stacking interactions. Compound 6 is a rare example of bis‐pyrazolate bridged dinuclear Zn(II) complex with two pyrazole N−H and two phenolic ‐OH groups on the molecular periphery to form hydrogen bonds. The use of 4,4’‐bpy leading to a zig‐zag 1‐D polymer 7 composed of [Zn(Hdiphba)2(4,4’‐bpy)]n chains, positioned 10.77 Å apart. The 1‐D channels of 7 are occupied by hydrogen bonded methanol with a rare (CH3OH)4 cluster as the repeating unit. Compound 8 is a discrete bimetallic complex, isolated with a free H2diphba ligand. The photoluminescence spectra of 1–8 exhibit ligand centered emission at around 325 nm.
VTA DA neuron excitatory synapses in Shank3 Δex4–9 mouse line
Authors: Bariselli Sebastiano , Bellone Camilla 
Published: December 2016

AbstractSeveral mutations within SHANK3 gene have been identified in Autism Spectrum Disorder patients and several studies have now started to show that those mutations could impact different brain circuits leading to the heterogeneity of the disease. Here we show that, compared to a mouse model lacking SHANK3 proline‐rich containing isoforms, in a mouse model lacking SHANK3 ANK(yrin)‐domain containing isoforms, the excitatory synaptic transmission within the Ventral Tegmental Area is not affected. We discuss about the possibility that different domains of SHANK3 are involved in regulating the synapses in a circuit‐specific manner resulting in different behavioral and synaptic phenotypes.
Emerging topological states in quasi‐two‐dimensional materials
Authors: Huang Huaqing , Xu Yong , Wang Jianfeng , Duan Wenhui 
Published: December 2016

Inspired by the discovery of graphene, various two‐dimensional (2D) materials have been experimentally realized, which exhibit novel physical properties and support promising applications. Exotic topological states in 2D materials (including quantum spin Hall and quantum anomalous Hall insulators), which are characterized by nontrivial metallic edge states within the insulating bulk gap, have attracted considerable attentions in the past decade due to their great importance for fundamental research and practical applications. They also create a surge of research activities and attract extensive efforts to search for new topological materials in realistic 2D/quasi‐2D systems. This review presents a comprehensive survey of recent progress in designing of topological states in quasi‐2D materials, including various quantum well heterostructures and 2D atomic lattice structures. In particular, the possibilities of constructing topological nontrivial states from commonly used materials are discussed and the ways of enlarging energy gaps of topological states and realizing different topological states in a single material are presented. WIREs Comput Mol Sci 2017, 7:e1296. doi: 10.1002/wcms.1296This article is categorized under:

Structure and Mechanism > Computational Materials Science
Quantitative approaches for investigating the spatial context of gene expression
Authors: Lee Je H. 
Published: December 2016

The spatial information associated with gene expression is important for elucidating the context‐dependent transcriptional regulation during development. Recently, high‐resolution sampling approaches, such as RNA tomography or single‐cell RNA‐seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images. This article will examine the basic principle of modern in situ and single‐cell genetic methods, hurdles in quantifying intrinsic and extrinsic forces that influence cell decision‐making, and technological requirements for making a visual map of gene regulation, form, and function. Successfully addressing these challenges will be essential for investigating the functional evolution of regulatory sequences during growth, development, and cancer progression. WIREs Syst Biol Med 2017, 9:e1369. doi: 10.1002/wsbm.1369This article is categorized under:

Developmental Biology > Developmental Processes in Health and Disease
Laboratory Methods and Technologies > Genetic/Genomic Methods
Laboratory Methods and Technologies > Imaging
Prediction of femoral strength using 3D finite element models reconstructed from DXA images: validation against experiments
Authors: Grassi Lorenzo , Väänänen Sami P. , Ristinmaa Matti , Jurvelin Jukka S. , Isaksson Hanna 
Published: December 2016

Abstract
Computed tomography (CT)-based finite element (FE) models may improve the current osteoporosis diagnostics and prediction of fracture risk by providing an estimate for femoral strength. However, the need for a CT scan, as opposed to the conventional use of dual-energy X-ray absorptiometry (DXA) for osteoporosis diagnostics, is considered a major obstacle. The 3D shape and bone mineral density (BMD) distribution of a femur can be reconstructed using a statistical shape and appearance model (SSAM) and the DXA image of the femur. Then, the reconstructed shape and BMD could be used to build FE models to predict bone strength. Since high accuracy is needed in all steps of the analysis, this study aimed at evaluating the ability of a 3D FE model built from one 2D DXA image to predict the strains and fracture load of human femora. Three cadaver femora were retrieved, for which experimental measurements from ex vivo mechanical tests were available. FE models were built using the SSAM-based reconstructions: using only the SSAM-reconstructed shape, only the SSAM-reconstructed BMD distribution, and the full SSAM-based reconstruction (including both shape and BMD distribution). When compared with experimental data, the SSAM-based models predicted accurately principal strains (coefficient of determination >0.83, normalized root-mean-square error <16%) and femoral strength (standard error of the estimate 1215 N). These results were only slightly inferior to those obtained with CT-based FE models, but with the considerable advantage of the models being built from DXA images. In summary, the results support the feasibility of SSAM-based models as a practical tool to introduce FE-based bone strength estimation in the current fracture risk diagnostics.
Mineralogy and Chemical Composition of the Clay Fraction of Neogene Shales from the Surma Group in the Bengal Basin, Bangladesh
Authors: Rahman M. Julleh Jalalur , Yeasmin Rumana , Mccann Tom 
Published: December 2016

Abstract:
Mineralogical and chemical investigations (&lt;2µm clay separates) of shale samples from the Neogene-age Surma Group obtained from four wells (Habiganj-11, Shahbazpur-1, Titas-11, Titas-15) in the Bengal basin, Bangladesh, were carried out in order to reveal the clay mineral composition as reservoir exploration and exploitation requires a good understanding of the clay minerals. The samples were analyzed by X-ray diffraction (XRD), scanning electron microscope (SEM) and X-Ray fluorescence spectrometry (XRF). Mineralogically, the sub-surface Surma Group shales comprise predominantly quartz, plagioclase, illite, chlorite, kaolinite, with lesser amounts of K-feldspar, dolomite and smectite, and minor to trace amounts of calcite, siderite and pyrite. The chemical composition of the &lt;2 µm clay separates also suggests an illite and chlorite-rich composition. With increasing burial depth, the Surma Group shales are enriched in illite. The gradual decreasing of the smectite clays with depth and ultimate disappearance at greater depths (≥ 3000 m) may have been responsible for the presence of the diagenetic illite. Based on the mineralogical composition it is most likely that the illite-chlorite associations together with quartz and feldspar were predominantly detrital in origin and thus reflect the presence of a rapidly-rising source terrain not subjected to intense weathering.