bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence of Anomalously Low δ13C of Marine Organic Matter in an Arctic Fjord
Authors: Kumar Vikash , Tiwari Manish , Nagoji Siddhesh , Tripathi Shubham 
Published: November 2016

AbstractAccurate estimation of relative carbon deposition (marine vs. terrestrial) is required for understanding the global carbon budget, particularly in the Arctic region, which holds disproportionate importance with respect to global carbon cycling. Although the sedimentary organic matter (SOM) concentration and its isotopic composition are important tools for such calculations, uncertainties loom over estimates provided by organic-geochemical bulk parameters. We report carbon and nitrogen concentrations and isotopes (δ13C and δ15N) of SOM at an Arctic fjord namely Kongsfjorden. We find that the bound inorganic nitrogen (ammonium attached to the clay minerals) forms a significant proportion of total nitrogen concentration (~77% in the inner fjord to ~24% in the outer part). On removing the bound nitrogen, the C/N ratio shows that the SOM in the inner fjord is made up of terrestrial carbon while the outer fjord shows mixed marine-terrestrial signal. We further show that the marine organic matter is unusually more depleted in 13C (~−24‰) than the terrestrial organic matter (~−22.5‰). This particular finding also helps explain high δ13C values of SOM as noted by earlier studies in central Arctic sediments despite a high terrestrial contribution.
Crosslinked polyarylene ether nitrile film as flexible dielectric materials with ultrahigh thermal stability
Authors: Yang Ruiqi , Wei Renbo , Li Kui , Tong Lifen , Jia Kun , Liu Xiaobo 
Published: November 2016

AbstractDielectric film with ultrahigh thermal stability based on crosslinked polyarylene ether nitrile is prepared and characterized. The film is obtained by solution-casting of polyarylene ether nitrile terminated phthalonitrile (PEN-Ph) combined with post self-crosslinking at high temperature. The film shows a 5% decomposition temperature over 520 °C and a glass transition temperature (Tg) around 386 °C. Stable dielectric constant and low dielectric loss are observed for this film in the frequency range of 100–200 kHz and in the temperature range of 25–300 °C. The temperature coefficient of dielectric constant is less than 0.001 °C−1 even at 400 °C. By cycling heating and cooling up to ten times or heating at 300 °C for 12 h, the film shows good reversibility and robustness of the dielectric properties. This crosslinked PEN film will be a potential candidate as high performance film capacitor electronic devices materials used at high temperature.
High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A β-lactamase, PenL
Authors: Yi Hyojeong , Choi Jin Myung , Hwang Junghyun , Prati Fabio , Cao Thinh-Phat , Lee Sung Haeng , Kim Heenam Stanley 
Published: November 2016

AbstractThe omega loop in β-lactamases plays a pivotal role in substrate recognition and catalysis, and some mutations in this loop affect the adaptability of the enzymes to new antibiotics. Various mutations, including substitutions, deletions, and intragenic duplications resulting in tandem repeats (TRs), have been associated with β-lactamase substrate spectrum extension. TRs are unique among the mutations as they cause severe structural perturbations in the enzymes. We explored the process by which TRs are accommodated in order to test the adaptability of the omega loop. Structures of the mutant enzymes showed that the extra amino acid residues in the omega loop were freed outward from the enzyme, thereby maintaining the overall enzyme integrity. This structural adjustment was accompanied by disruptions of the internal α-helix and hydrogen bonds that originally maintained the conformation of the omega loop and the active site. Consequently, the mutant enzymes had a relaxed binding cavity, allowing for access of new substrates, which regrouped upon substrate binding in an induced-fit manner for subsequent hydrolytic reactions. Together, the data demonstrate that the design of the binding cavity, including the omega loop with its enormous adaptive capacity, is the foundation of the continuous evolution of β-lactamases against new drugs.
Band gap modulation in polythiophene and polypyrrole-based systems
Authors: Kaloni Thaneshwor P. , Schreckenbach Georg , Freund Michael S. 
Published: November 2016

AbstractIn this paper, the structural and electronic properties of polythiophene and polyprrrole-based systems have been investigated using first-principles calculations both in periodic and oligomer forms. Of particular interest is the band gap modulation through substitutions and bilayer formation. Specifically, S has been substituted by Se and Te in polythiophene, leading to polyseleophene and polytellurophene, respectively, and N has been substituted by P and As in polypyrrole. The values obtained of the binding energy suggest that all the systems studied can be realized experimentally. Stacking (bilayer formation) of pure polythiophene, polypyrrole and their derivatives leads to linear suppression of the band gap or HOMO-LUMO gap as a function of the stacking. Mixed bilayers, including one formed from polythiophene on top of polypyrrole, have also been considered. Overall, a wide range of band gaps can be achieved through substitutions and stacking. Hybrid (B3LYP) calculations also suggest the same trend in the band gap as PBE calculations. Trends in the binding energy are similar for both periodic and molecular calculations. In addition, Γ-point phonon calculations were performed in order to check the stability of selected systems.
Alcohol consumption, genetic variants in the alcohol- and folate metabolic pathways and colorectal cancer risk: the JPHC Study
Authors: Svensson Thomas , Yamaji Taiki , Budhathoki Sanjeev , Hidaka Akihisa , Iwasaki Motoki , Sawada Norie , Inoue Manami , Sasazuki Shizuka , Shimazu Taichi , Tsugane Shoichiro 
Published: November 2016

AbstractThe association between alcohol intake and colorectal cancer (CRC) may vary secondary to single nucleotide polymorphisms (SNPs) in two pathways related to alcohol intake. 375 cases of CRC were identified among 38 373 Japan Public Health Center-based prospective Study (JPHC Study) participants who had returned a baseline questionnaire, reported no diagnosis of any cancer and provided blood samples. For each case, two controls were selected on matching variables. Logistic regression models were used to determine matched Odds Ratios (OR) and 95% Confidence Intervals (CI) for the association between alcohol consumption, genetic polymorphisms of enzymes in the alcohol- and folate metabolic pathways (e.g. methylenetetrahydrofolate reductase (MTHFR) rs1801133) and CRC risk. Compared to never/occasional alcohol intake, moderate to heavy alcohol intake was associated with CRC (OR = 2.12, 95% CI, 1.34–3.36). When compared to the CC genotype, the MTHFR rs1801133 CT/TT genotype was inversely associated with CRC (OR = 0.72, 95% CI, 0.54–0.97). Never/occasional consumers of alcohol with the MTHFR rs1801133 CT/TT genotype were also at a reduced risk of CRC compared to never/occasional drinkers with the CC genotype (OR = 0.68, 95% CI, 0.47–0.98) (P for interaction = 0.27). The results indicate that the folate pathway is likely to be involved in alcohol-related CRC development.
Clean thermal decomposition of tertiary-alkyl metal thiolates to metal sulfides: environmentally-benign, non-polar inks for solution-processed chalcopyrite solar cells
Authors: Heo Jungwoo , Kim Gi-Hwan , Jeong Jaeki , Yoon Yung Jin , Seo Jung Hwa , Walker Bright , Kim Jin Young 
Published: November 2016

AbstractWe report the preparation of Cu2S, In2S3, CuInS2 and Cu(In,Ga)S2 semiconducting films via the spin coating and annealing of soluble tertiary-alkyl thiolate complexes. The thiolate compounds are readily prepared via the reaction of metal bases and tertiary-alkyl thiols. The thiolate complexes are soluble in common organic solvents and can be solution processed by spin coating to yield thin films. Upon thermal annealing in the range of 200–400 °C, the tertiary-alkyl thiolates decompose cleanly to yield volatile dialkyl sulfides and metal sulfide films which are free of organic residue. Analysis of the reaction byproducts strongly suggests that the decomposition proceeds via an SN1 mechanism. The composition of the films can be controlled by adjusting the amount of each metal thiolate used in the precursor solution yielding bandgaps in the range of 1.2 to 3.3 eV. The films form functioning p-n junctions when deposited in contact with CdS films prepared by the same method. Functioning solar cells are observed when such p-n junctions are prepared on transparent conducting substrates and finished by depositing electrodes with appropriate work functions. This method enables the fabrication of metal chalcogenide films on a large scale via a simple and chemically clear process.
Associated factors for visibility and width of retrobulbar subarachnoid space on swept-source optical coherence tomography in high myopia
Authors: Fan Hua , Ma Hongjie , Gao Rulong , Ng Danny Siu-Chun , Cheung Carol Y. , Li Shuangnong , Wu Dezheng , Tang Shibo 
Published: November 2016

AbstractSubarachnoid space (SAS) around optic nerve can be visible with swept-source optical coherence tomography (SS-OCT). However, the relevant factors for its visibility and width have not been reported. In this prospective study, 193 eyes with high myopia were evaluated by SS-OCT. The relationship between age, gender, axial length, optic disc area, parapapillary atrophy (PPA) area, peripapillary choroidal thickness with the visibility and width of SAS were assessed. The results showed that SAS was observed in 125 (64.8%) and not observed in 68 (35.2%) eyes. Visibility of SAS is associated with long axial length, high myopia, thin choroid, large PPA and large optic disc areas. Among these associations, PPA area was the only independent factor (b = 0.177, p < 0.001). The width of SAS was associated with thin choroid, long axial length, large optic disc area and large PPA area. Multivariant analysis showed that optic disc area and PPA area were independent factors for the width of SAS (b = 30.8, p = 0.016 and 16.2, p < 0.001 respectively). These results suggested that SAS was extended into the peripapillary region possibly due to extension of posterior sclera in high myopia.
GDNF-expressing STO feeder layer supports the long-term propagation of undifferentiated mouse spermatogonia with stem cell properties
Authors: Wei Xiang , Jia Yuanyuan , Xue Yuanyuan , Geng Lei , Wang Min , Li Lufan , Wang Mei , Zhang Xuemei , Wu Xin 
Published: November 2016

AbstractThe development of a stem cell culture system would expedite our understanding of the biology of tissue regeneration. Spermatogonial stem cell (SSC) is the foundation for lifelong male spermatogenesis and the SSC culture has been optimized continuously in recent years. However, there have been many inconveniences to reconstruct SSC self-renewal and proliferation in vitro, such as the frequent refreshment of recombinant cytokines, including GDNF, the essential growth factor for SSC maintenance. In the present study, we observed that both STO and MEF cells, which were previously used as feeders for SSC growth, did not express GDNF, but a GDNF-expressing STO feeder could support undifferentiated mouse spermatogonia propagation in vitro for three months without the refreshment of recombinant growth factor GDNF. The cell morphology, growth rate and SSC-associated gene expression remained identical to the SSCs cultured using previous methods. The transplantation of SSCs growing on these GDNF-expressing STO feeders could generate extensive colonies of spermatogenesis in recipient testes, functionally validating the stemness of these cells. Collectively, our data indicated that the further modification of feeder cells might facilitate the self-renewal and propagation of SSCs in vitro.
Intraprostatic locations of tumor foci of higher grade missed by diagnostic prostate biopsy among potential candidates for active surveillance
Authors: Kim Kwangmo , Lee Jung Keun , Choe Gheeyoung , Hong Sung Kyu 
Published: November 2016

AbstractTo establish optimal biopsy scheme for selection of candidates for active surveillance (AS) among prostate cancer (PCa) patients, information on topographical distribution of tumor foci of higher grade missed by contemporary biopsy amongst potential candidates of AS would certainly be useful. Thus we analyzed topographic distribution of tumor foci by examining prostatectomy specimens in 444 patients who underwent radical prostatectomy for low risk PCa. Anterior and posterior prostate areas were demarcated by a horizontal line drawn at midpoint of prostatic urethra. Among 444 subjects, patients with upgrading showed relatively higher prevalence of index tumor foci in anterior prostate than those without upgrading, though not reaching statistical significance (p = 0.252). Meanwhile, among 135 (30.4%) patients with very low risk PCa, patients with upgrading showed significantly higher prevalence of index tumor foci in anterior prostate than those without upgrading (52.2% vs 33.8%; p = 0.031). In conclusions, tumor foci of higher grade missed by diagnostic biopsy were mostly located in anterior prostate among very low risk PCa patients. Such finding would be concrete evidence to support the notion that more efforts are needed to increase accuracy in detecting tumor foci in anterior prostate among potential candidates for AS.
The role of water molecules in stereoselectivity of glucose/galactose-binding protein
Authors: Kim Minsup , Cho Art E. 
Published: November 2016

AbstractUsing molecular dynamics (MD) simulation methods, we attempted to explain the experimental results on ligand specificity of glucose/galactose-binding protein (GGBP) to β-D-glucose and β-D-galactose. For the simulation, a three-dimensional structure of GGBP was prepared, and homology modeling was performed to generate variant structures of GGBP with mutations at Asp14. Then, docking was carried out to find a reasonable β-D-glucose and β-D-galactose binding conformations with GGBP. Subsequent molecular dynamics simulations of β-D-glucose–GGBP and β-D-galactose–GGBP complexes and estimation of the orientation and stability of water molecules at the binding site revealed how water molecules influence ligand specificity. In our simulation, water molecules mediated interactions of β-D-glucose or β-D-galactose with residue 14 of GGBP. In this mechanism, the Phe16Ala mutant leaves both sugar molecules free to move, and the specific role of water molecules were eliminated, while the wild type, Asp14Asn mutant, and Asp14Glu mutant make hydrogen bond interactions with β-D-glucose more favorable. Our results demonstrate that bound water molecules at the binding site of GGBP are related to localized conformational change, contributing to ligand specificity of GGBP for β-D-glucose over β-D-galactose.
Synthetic genome readers target clustered binding sites across diverse chromatin states
Authors: Erwin Graham S. , Grieshop Matthew P. , Bhimsaria Devesh , Do Truman J. , Rodríguez-Martínez José A. , Mehta Charu , Khanna Kanika , Swanson Scott A. , Stewart Ron , Thomson James A. , Ramanathan Parameswaran , Ansari Aseem Z. 
Published: November 2016

Significance
Targeting specific genomic loci with synthetic molecules remains a major goal in chemistry, biology, and precision medicine. Identifying how synthetic genome readers bind the chromatinized genome in cells would facilitate their development, but doing so remains a formidable challenge. We map the genome-wide binding patterns for two structurally distinct synthetic molecules. To achieve this goal, we couple our cross-linking of small molecules to isolate chromatin approach to next-generation sequencing. In addition to binding high-affinity sites, these molecules, surprisingly, bind clustered low-affinity sites. The data also show that these genome readers target sites in both open and closed chromatin. Our findings highlight the importance of genome-guided design for molecules that will serve as precision-targeted therapeutics.
Optimal prediction of the number of unseen species
Authors: Orlitsky Alon , Suresh Ananda Theertha , Wu Yihong 
Published: November 2016

SignificanceMany scientific applications ranging from ecology to genetics use a small sample to estimate the number of distinct elements, known as ”species,” in a population. Classical results have shown thatnsamples can be used to estimate the number of species that would be observed if the sample size were doubled to2n. We obtain a class of simple algorithms that extend the estimate all the way ton log nsamples, and we show that this is also the largest possible estimation range. Therefore, statistically speaking, the proverbial bird in the hand is worth lognin the bush. The proposed estimators outperform existing ones on several synthetic and real datasets collected in various disciplines.
tranSMART-XNAT Connector tranSMART-XNAT connector—image selection based on clinical phenotypes and genetic profiles
Authors: He Sijin , Yong May , Matthews Paul M , Guo Yike 
Published: November 2016

Abstract

Motivation
TranSMART has a wide range of functionalities for translational research and a large user community, but it does not support imaging data. In this context, imaging data typically includes 2D or 3D sets of magnitude data and metadata information. Imaging data may summarise complex feature descriptions in a less biased fashion than user defined plain texts and numeric numbers. Imaging data also is contextualised by other data sets and may be analysed jointly with other data that can explain features or their variation.

Results
Here we describe the tranSMART-XNAT Connector we have developed. This connector consists of components for data capture, organisation and analysis. Data capture is responsible for imaging capture either from PACS system or directly from an MRI scanner, or from raw data files. Data are organised in a similar fashion as tranSMART and are stored in a format that allows direct analysis within tranSMART. The connector enables selection and download of DICOM images and associated resources using subjects’ clinical phenotypic and genotypic criteria.

Availability and Implementation
tranSMART-XNAT connector is written in Java/Groovy/Grails. It is maintained and available for download at https://github.com/sh107/transmart-xnat-connector.git
A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases
Authors: Chen Xing , Huang Yu-An , You Zhu-Hong , Yan Gui-Ying , Wang Xue-Song 
Published: November 2016

Abstract

Motivation
Accumulating clinical observations have indicated that microbes living in the human body are closely associated with a wide range of human noninfectious diseases, which provides promising insights into the complex disease mechanism understanding. Predicting microbe–disease associations could not only boost human disease diagnostic and prognostic, but also improve the new drug development. However, little efforts have been attempted to understand and predict human microbe–disease associations on a large scale until now.

Results
In this work, we constructed a microbe-human disease association network and further developed a novel computational model of KATZ measure for Human Microbe–Disease Association prediction (KATZHMDA) based on the assumption that functionally similar microbes tend to have similar interaction and non-interaction patterns with noninfectious diseases, and vice versa. To our knowledge, KATZHMDA is the first tool for microbe–disease association prediction. The reliable prediction performance could be attributed to the use of KATZ measurement, and the introduction of Gaussian interaction profile kernel similarity for microbes and diseases. LOOCV and k-fold cross validation were implemented to evaluate the effectiveness of this novel computational model based on known microbe–disease associations obtained from HMDAD database. As a result, KATZHMDA achieved reliable performance with average AUCs of 0.8130 ± 0.0054, 0.8301 ± 0.0033 and 0.8382 in 2-fold and 5-fold cross validation and LOOCV framework, respectively. It is anticipated that KATZHMDA could be used to obtain more novel microbes associated with important noninfectious human diseases and therefore benefit drug discovery and human medical improvement.

Availability and Implementation
Matlab codes and dataset explored in this work are available at http://dwz.cn/4oX5mS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Bringing Rounds Back to the Patient: A One-Year Evaluation of the Chiefs’ Service Model for Inpatient Teaching
Authors: Bennett Nadia L. , Flesch Judd D. , Cronholm Peter , Reilly James B. , Ende Jack 
Published: November 2016

Purpose
The Chiefs’ Service (CS), a structured approach to inpatient teaching rounds, focuses on resident education and patient-centered care without disrupting patient census sizes or admitting cycles. It has five key elements: morning huddles; bedside rounds; diagnostic “time-outs”; day-of-discharge rounds; and postdischarge follow-up rounds. The authors hypothesized the CS model would be well received by residents and considered more effective than more-traditional rounds.

Method
The CS was implemented on Penn Presbyterian Medical Center’s general medicine inpatient service using a quasi-experimental design. Its first year (January 2013–January 2014) was evaluated with a mixed-methods approach. Residents completed end-of-rotation evaluation questionnaires; 20 CS and 10 traditional service (TS) residents were interviewed. Measures of resident agreement on questionnaire items were compared across groups using independent sample t testing. A modified grounded theory approach was used to assess CS residents’ perspectives on the CS elements and identify emergent themes.

Results
The questionnaires were completed by 183/188 residents (response rate 97%). Compared with TS residents, CS residents reported significantly greater satisfaction in the domains of resident education and patient care, and they rated the overall value of the rotation significantly higher. The majority of CS residents found the CS elements to be effective. CS residents described the CS as focused on resident education, patient-centered care, and collaboration with an interdisciplinary team.

Conclusions
The CS approach to inpatient rounding is seen by residents as valuable and is associated with positive outcomes in terms of residents’ perceptions of learning, interdisciplinary communication, and patient care.