bluuebunny/crossref_metadata_2025_split huggingface dataset:
The widespread dissemination of integrons throughout bacterial communities in a riverine system
Authors: Amos Gregory C A , Ploumakis Semina , Zhang Lihong , Hawkey Peter M , Gaze William H , Wellington Elizabeth M H 
Published: January 2018

Abstract
Anthropogenic inputs increase levels of antimicrobial resistance (AMR) in the environment, however, it is unknown how these inputs create this observed increase, and if anthropogenic sources impact AMR in environmental bacteria. The aim of this study was to characterise the role of waste water treatment plants (WWTPs) in the dissemination of class 1 integrons (CL1s) in the riverine environment. Using sample sites from upstream and downstream of a WWTP, we demonstrate through isolation and culture-independent analysis that WWTP effluent significantly increases both CL1 abundance and antibiotic resistance in the riverine environment. Characterisation of CL1-bearing isolates revealed that CL1s were distributed across a diverse range of bacteria, with identical complex genetic resistance determinants isolated from both human-associated and common environmental bacteria across connected sites. Over half of sequenced CL1s lacked the 3′-conserved sequence (‘atypical’ CL1s); surprisingly, bacteria carrying atypical CL1s were on average resistant to more antibiotics than bacteria carrying 3′-CS CL1s. Quaternary ammonium compound (QAC) resistance genes were observed across 75% of sequenced CL1 gene cassette arrays. Chemical data analysis indicated high levels of boron (a detergent marker) downstream of the WWTP. Subsequent phenotypic screening of CL1-bearing isolates demonstrated that ~90% were resistant to QAC detergents, with in vitro experiments demonstrating that QACs could solely select for the transfer of clinical antibiotic resistance genes to a naive Escherichia coli recipient. In conclusion, this study highlights the significant impact of WWTPs on environmental AMR, and demonstrates the widespread carriage of clinically important resistance determinants by environmentally associated bacteria.
GWAS of epigenetic aging rates in blood reveals a critical role for TERT
Authors: Lu Ake T. , Xue Luting , Salfati Elias L. , Chen Brian H. , Ferrucci Luigi , Levy Daniel , Joehanes Roby , Murabito Joanne M. , Kiel Douglas P. , Tsai Pei-Chien , Yet Idil , Bell Jordana T. , Mangino Massimo , Tanaka Toshiko , McRae Allan F. , Marioni Riccardo E. , Visscher Peter M. , Wray Naomi R. , Deary Ian J. , Levine Morgan E. , Quach Austin , Assimes Themistocles , Tsao Philip S. , Absher Devin , Stewart James D. , Li Yun , Reiner Alex P. , Hou Lifang , Baccarelli Andrea A. , Whitsel Eric A. , Aviv Abraham , Cardona Alexia , Day Felix R. , Wareham Nicholas J. , Perry John R. B. , Ong Ken K. , Raj Kenneth , Lunetta Kathryn L. , Horvath Steve 
Published: January 2018

AbstractDNA methylation age is an accurate biomarker of chronological age and predicts lifespan, but its underlying molecular mechanisms are unknown. In this genome-wide association study of 9907 individuals, we find gene variants mapping to five loci associated with intrinsic epigenetic age acceleration (IEAA) and gene variants in three loci associated with extrinsic epigenetic age acceleration (EEAA). Mendelian randomization analysis suggests causal influences of menarche and menopause on IEAA and lipoproteins on IEAA and EEAA. Variants associated with longer leukocyte telomere length (LTL) in the telomerase reverse transcriptase gene (TERT) paradoxically confer higher IEAA (P < 2.7 × 10−11). Causal modeling indicates TERT-specific and independent effects on LTL and IEAA. Experimental hTERT-expression in primary human fibroblasts engenders a linear increase in DNA methylation age with cell population doubling number. Together, these findings indicate a critical role for hTERT in regulating the epigenetic clock, in addition to its established role of compensating for cell replication-dependent telomere shortening.
Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain
Authors: Hirata Tetsuya , Mishra Sushil K. , Nakamura Shota , Saito Kazunobu , Motooka Daisuke , Takada Yoko , Kanzawa Noriyuki , Murakami Yoshiko , Maeda Yusuke , Fujita Morihisa , Yamaguchi Yoshiki , Kinoshita Taroh 
Published: January 2018

AbstractMany eukaryotic proteins are anchored to the cell surface via the glycolipid glycosylphosphatidylinositol (GPI). Mammalian GPIs have a conserved core but exhibit diverse N-acetylgalactosamine (GalNAc) modifications, which are added via a yet unresolved process. Here we identify the Golgi-resident GPI-GalNAc transferase PGAP4 and show by mass spectrometry that PGAP4 knockout cells lose GPI-GalNAc structures. Furthermore, we demonstrate that PGAP4, in contrast to known Golgi glycosyltransferases, is not a single-pass membrane protein but contains three transmembrane domains, including a tandem transmembrane domain insertion into its glycosyltransferase-A fold as indicated by comparative modeling. Mutational analysis reveals a catalytic site, a DXD-like motif for UDP-GalNAc donor binding, and several residues potentially involved in acceptor binding. We suggest that a juxtamembrane region of PGAP4 accommodates various GPI-anchored proteins, presenting their acceptor residue toward the catalytic center. In summary, we present insights into the structure of PGAP4 and elucidate the initial step of GPI-GalNAc biosynthesis.
Caging tin oxide in three-dimensional graphene networks for superior volumetric lithium storage
Authors: Han Junwei , Kong Debin , Lv Wei , Tang Dai-Ming , Han Daliang , Zhang Chao , Liu Donghai , Xiao Zhichang , Zhang Xinghao , Xiao Jing , He Xinzi , Hsia Feng-Chun , Zhang Chen , Tao Ying , Golberg Dmitri , Kang Feiyu , Zhi Linjie , Yang Quan-Hong 
Published: January 2018

AbstractTin and its compounds hold promise for the development of high-capacity anode materials that could replace graphitic carbon used in current lithium-ion batteries. However, the introduced porosity in current electrode designs to buffer the volume changes of active materials during cycling does not afford high volumetric performance. Here, we show a strategy leveraging a sulfur sacrificial agent for controlled utility of void space in a tin oxide/graphene composite anode. In a typical synthesis using the capillary drying of graphene hydrogels, sulfur is employed with hard tin oxide nanoparticles inside the contraction hydrogels. The resultant graphene-caged tin oxide delivers an ultrahigh volumetric capacity of 2123 mAh cm–3 together with good cycling stability. Our results suggest not only a conversion-type composite anode that allows for good electrochemical characteristics, but also a general synthetic means to engineering the packing density of graphene nanosheets for high energy storage capabilities in small volumes.
Pressure-induced superconductivity and topological quantum phase transitions in a quasi-one-dimensional topological insulator: Bi4I4
Authors: Qi Yanpeng , Shi Wujun , Werner Peter , Naumov Pavel G. , Schnelle Walter , Wang Lei , Rana Kumari Gaurav , Parkin Stuart , Medvedev Sergiy A. , Yan Binghai , Felser Claudia 
Published: January 2018

AbstractSuperconductivity and topological quantum states are two frontier fields of research in modern condensed matter physics. The realization of superconductivity in topological materials is highly desired; however, superconductivity in such materials is typically limited to two-dimensional or three-dimensional materials and is far from being thoroughly investigated. In this work, we boost the electronic properties of the quasi-one-dimensional topological insulator bismuth iodide β-Bi4I4 by applying high pressure. Superconductivity is observed in β-Bi4I4 for pressures, where the temperature dependence of the resistivity changes from a semiconducting-like behavior to that of a normal metal. The superconducting transition temperature Tc increases with applied pressure and reaches a maximum value of 6 K at 23 GPa, followed by a slow decrease. Our theoretical calculations suggest the presence of multiple pressure-induced topological quantum phase transitions as well as a structural–electronic instability.
AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest
Authors: Bhadra Pratiti , Yan Jielu , Li Jinyan , Fong Simon , Siu Shirley W. I. 
Published: January 2018

AbstractAntimicrobial peptides (AMPs) are promising candidates in the fight against multidrug-resistant pathogens owing to AMPs’ broad range of activities and low toxicity. Nonetheless, identification of AMPs through wet-lab experiments is still expensive and time consuming. Here, we propose an accurate computational method for AMP prediction by the random forest algorithm. The prediction model is based on the distribution patterns of amino acid properties along the sequence. Using our collection of large and diverse sets of AMP and non-AMP data (3268 and 166791 sequences, respectively), we evaluated 19 random forest classifiers with different positive:negative data ratios by 10-fold cross-validation. Our optimal model, AmPEP with the 1:3 data ratio, showed high accuracy (96%), Matthew’s correlation coefficient (MCC) of 0.9, area under the receiver operating characteristic curve (AUC-ROC) of 0.99, and the Kappa statistic of 0.9. Descriptor analysis of AMP/non-AMP distributions by means of Pearson correlation coefficients revealed that reduced feature sets (from a full-featured set of 105 to a minimal-feature set of 23) can result in comparable performance in all respects except for some reductions in precision. Furthermore, AmPEP outperformed existing methods in terms of accuracy, MCC, and AUC-ROC when tested on benchmark datasets.
Real-Time Characterization Using in situ RHEED Transmission Mode and TEM for Investigation of the Growth Behaviour of Nanomaterials
Authors: Jo Janghyun , Tchoe Youngbin , Yi Gyu-Chul , Kim Miyoung 
Published: January 2018

AbstractA novel characterization technique using both in situ reflection high-energy electron diffraction (RHEED) transmission mode and transmission electron microscopy (TEM) has been developed to investigate the growth behaviour of semiconductor nanostructures. RHEED employed in transmission mode enables the acquisition of structural information during the growth of nanostructures such as nanorods. Such real-time observation allows the investigation of growth mechanisms of various nanomaterials that is not possible with conventional ex situ analytical methods. Additionally, real-time monitoring by RHEED transmission mode offers a complete range of information when coupled with TEM, providing structural and chemical information with excellent spatial resolution, leading to a better understanding of the growth behaviour of nanomaterials. Here, as a representative study using the combined technique, the nucleation and crystallization of InAs nanorods and the epitaxial growth of InxGa1−xAs(GaAs) shell layers on InAs nanorods are explored. The structural changes in the InAs nanorods at the early growth stage caused by the transition of the local growth conditions and the strain relaxation processes that occur during epitaxial coating of the shell layers are shown. This technique advances our understanding of the growth behaviour of various nanomaterials, which allows the realization of nanostructures with novel properties and their application in future electronics and optoelectronics.
A ‘NanoSuit’ successfully protects petals of cherry blossoms in high vacuum: examination of living plants in an FE-SEM
Authors: Takehara Sayuri , Takaku Yasuharu , Suzuki Hiroshi , Ohta Isao , Shimomura Masatsugu , Hariyama Takahiko 
Published: January 2018

AbstractLand plants have evolved on dry land and developed surface barriers to protect themselves from environmental stresses. We have previously reported that polymerization of a natural extracellular substance (ECS) on the outer surface of animals by electron beam or plasma irradiation, can give rise to a nano-scale layer, termed the “NanoSuit”, which can keep small animals alive under the high vacuum of a scanning electron microscope (SEM). In the present research, we have focused on plants, using petals of cherry blossoms, as experimental specimens and examined their behavior under high vacuum conditions. Experiments on healthy living petals have demonstrated that without any pre-treatment, the overall morphology of specimens is well preserved and intact after imaging in an SEM, suggesting that natural substances on the petal surface behave like animal ECS and form a NanoSuit following irradiation with an electron beam. Furthermore, we have shown that the surface material can be extracted with chloroform and polymerized into a free-standing membrane by plasma irradiation. From our results, we conclude that surface materials, which have the ability to prevent water loss under natural conditions, increase the barrier ability and can protect plants under high vacuum conditions.
Monoclonal and oligoclonal TCR AV and BV gene usage in CD4+ T cells from pigs immunised with C-strain CSFV vaccine
Authors: Wang Chunyan , Li Shoujie , Jia Huaijie , Chen Guohua , Fang Yongxiang , Zeng Shuang , He Xiaobing , Yao Wenjuan , Jin Qiwang , Cheng Wenyu , Feng Yuan , Yin Hong , Jing Zhizhong 
Published: January 2018

AbstractThe classical swine fever virus C-strain vaccine (C-strain vaccine) plays a vital role in preventing and controlling the spread of classical swine fever (CSF). However, the protective mechanisms of C-strain vaccine and cellular immunity conferred by T cell receptors (TCRs) are less well defined. We aimed to analyse the association between the complementarity determining region 3 (CDR3) spectratype of αβTCR in CD4+ T cells and C-strain vaccine; and to find conserved CDR3 amino acid motifs in specific TCR α- and β-chains. We found that the CDR3 spectratype showed dynamic changes correlating with C-strain vaccine immunisation and that TCR AV5S/8–3S/8–4S/14/38 and BV4S/6S/7S/15S/30 gene families showed clonal expansion in immunised pigs. The sequences of CDR3 from these clonally expanded T cells indicated a high frequency of the ‘KLX’ motif in the TCR α chain and the ‘GGX’ motif in β chain, and Jα39, Jα43, Jβ2.5 and Jβ2.3 genes were also found in high frequency. To the best of our knowledge, this is the first report describing the dynamic changes of αβTCRs and conserved CDR3 amino acid motifs in CD4+ T cells from C-strain vaccine-immunised pigs, which will provide a basis for the development of high-efficiency epitope vaccines.
Long range haplotyping of paired-homologous chromosomes by single-chromosome sequencing of a single cell
Authors: Luo Deng , Zhang Meng , Liu Ting , Cao Wei , Guo Jiajie , Mao Caiping , Li Yifan , Wang Juanmei , Huang Weiren , Lu Daru , Zhang Shuo , Li Zhoufang , He Jiankui 
Published: January 2018

AbstractThe longest possible haplotype is chromosome haplotype that is a set of co-inherited alleles occurred on a single strand chromosome inherited from one parent. Standard whole-genome shotgun sequencing technologies are limited by the inability to independently study the haplotype of homologous chromosomes due to the short-reads sequencing strategy and disturbance of homologue chromosomes. Here, we investigated several types of chromosomal abnormalities by a dilution-based method to separate an intact copy of homologous chromosome from human metaphase cells, and then single chromosomes were independently amplified by whole-genome amplification methods, converted into barcoded sequencing libraries, and sequenced in multiplexed pools by Illumina sequencers. We analyzed single chromosome derived from single metaphase cells of one patient with balanced chromosomal translocation t(3;5)(q24;q13), one patient with (47, XXY) karyotype and one with (47, XY, 21+) Down syndrome. We determined the translocation region of chromosomes in patient with t(3;5)(q24;q13) balanced chromosomal translocation by shallow whole-genome sequencing, which is helpful to pinpoint the chromosomal break point. We showed that SCS can physically separate and independently sequence three copies of chromosome 21 of Down syndrome patient. SCS has potential applications in personal genomics, single-cell genomics, and clinical diagnosis, particularly in revealing chromosomal level of genetic diseases.
Impact of the huge 2011 Tohoku-oki tsunami on the phenotypes and genotypes of Japanese coastal threespine stickleback populations
Authors: Kume Manabu , Mori Seiichi , Kitano Jun , Sumi Tetsuya , Nishida Shotaro 
Published: January 2018

AbstractOn March 11, 2011, a large earthquake occurred, causing a tsunami which struck the Pacific coast of northeast Japan. We investigated the ecological and genetic effects of the large tsunami on the threespine stickleback (genusGasterosteus) populations in Otsuchi Town, which was one of the most severely damaged areas after the tsunami. Our environmental surveys showed that spring water may have contributed to the habitat recovery. Morphological analysis of the stickleback before and after the tsunami showed morphological shifts in the gill raker number, which is a foraging trait. Genetic analyses revealed that the allelic richness of one population was maintained after the tsunami, whereas that of another decreased in 2012 and then started to recover in 2013. Additionally, we found that the large tsunami and ground subsidence created new spring water-fed pools with sticklebacks, suggesting that the tsunami brought sticklebacks into these pools. Genetic analysis of this population showed that this population might be derived from hybridization between freshwaterGasterosteus aculeatusand anadromousG.nipponicus. Overall, our data indicate that tsunamis can influence morphologies and genetic structures of freshwater fishes. Furthermore, spring water may play important roles in the maintenance and creation of fish habitats, faced with environmental disturbance.
Resource control of epidemic spreading through a multilayer network
Authors: Jiang Jian , Zhou Tianshou 
Published: January 2018

AbstractWhile the amount of resource is an important factor in control of contagions, outbreaks may occur when they reach a finite fraction of the population. An unexplored issue is how much the resource amount is invested to control this outbreak. Here we analyze a mechanic model of epidemic spreading, which considers both resource factor and network layer. We find that there is a resource threshold, such that a significant fraction of the total population may be infected (i.e., an outbreak will occur) if the amount of resource is below this threshold, but the outbreak may be effectively eradicated if it is beyond the threshold. The threshold is dependent upon both the connection strength between the layers and their internal structure. We also find that the layer-layer connection strength can lead to the phase transition from the first-order phase to the continuous one or vice versa, whereas the internal connection can result in a different kind of phase transition (i.e., the so-called hybrid phase transition) apart from first-order and continuous one. Our results could have important implications for government decisions on public health resources devoted to epidemic disease control.
Surface structure evolution in a homologous series of ionic liquids
Authors: Haddad Julia , Pontoni Diego , Murphy Bridget M. , Festersen Sven , Runge Benjamin , Magnussen Olaf M. , Steinrück Hans-Georg , Reichert Harald , Ocko Benjamin M. , Deutsch Moshe 
Published: January 2018

Significance
This high-resolution X-ray study resolves the liquid–air interface structure for a long homologous series of room temperature ionic liquids (RTILs). RTILs are intensely studied for many potential “green” applications and for their intriguingly complex and rare combination of intermolecular interactions. Varying their cation’s alkyl chain length provides, therefore, an opportunity to tune the main interaction from mostly long-range electrostatic to mostly short-range van der Waals. This variation is found here to drive the interface structure from simple, to layered, to liquid crystalline. The quantitative results obtained constitute an accurate yardstick for testing simulations and theory, impact the bulk–surface structure relations in general, and provide currently scarce data for many RTIL applications, like batteries and supercapacitors.
Aberration-corrected cryoimmersion light microscopy
Authors: Faoro Raffaele , Bassu Margherita , Mejia Yara X. , Stephan Till , Dudani Nikunj , Boeker Christian , Jakobs Stefan , Burg Thomas P. 
Published: January 2018

Significance
Cryofluorescence imaging is of great interest in biological microscopy because vitrified samples (i.e., frozen without ice crystallization) are free from fixation artifacts, are highly photostable, and allow direct correlation with electron cryomicroscopy. Here, we show a concept for conducting cryo-light microscopy in immersion that provides a twofold to fivefold increase in image brightness and higher resolution than are attainable with air objectives. Spherical aberration at an imaging temperature below the glass transition of water (−135 °C) is corrected by our approach.
Prediction of inherited genomic susceptibility to 20 common cancer types by a supervised machine-learning method
Authors: Kim Byung-Ju , Kim Sung-Hou 
Published: January 2018

Significance
Prevention and early diagnosis of cancer are the most effective ways of avoiding psychological, physical, and financial suffering from cancer. We present a machine-learning method for statistically predicting individuals’ inherited susceptibility (and environmental/lifestyle factors by inference) for acquiring the most likely type among a panel of 20 major common cancer types plus 1 “healthy” type. The results show that, depending on the type, about 33–88% of a cancer cohort have acquired its cancer type primarily due to inherited genomic susceptibility factors and that the rest are primarily due to environmental/lifestyle factors. These personal genomic susceptibilities with associated probabilities may provide practical information for individuals, heath professionals, and health policymakers related to prevention and/or early intervention of cancer.
The dominance of foreign capital and its impact on indigenous technology development in the production of liquefied natural gas in Nigeria
Authors: Albert Okorie 
Published: January 2018

SUMMARY
The briefing argues that the Nigerian economy is foreign capital driven and that the rentier character of the state has facilitated dominance of foreign capital in the gas sector. Furthermore, that the control of the sector and consequent reliance on foreign technology have distorted and stagnated local initiatives toward development of indigenous technology in the production of liquefied natural gas.
Changes in hospital bond ratings after the transition to a new electronic health record
Authors: McEvoy Dustin , Barnett Michael L , Sittig Dean F , Aaron Skye , Mehrotra Ateev , Wright Adam 
Published: January 2018

Abstract

Objective
To assess the impact of electronic health record (EHR) implementation on hospital finances.

Materials and Methods
We analyzed the impact of EHR implementation on bond ratings and net income from service to patients (NISP) at 32 hospitals that recently implemented a new EHR and a set of controls.

Results
After implementing an EHR, 7 hospitals had a bond downgrade, 7 had a bond upgrade, and 18 had no changes. There was no difference in the likelihood of bond rating changes or in changes to NISP following EHR go-live when compared to control hospitals.

Discussion
Most hospitals in our analysis saw no change in bond ratings following EHR go-live, with no significant differences observed between EHR implementation and control hospitals. There was also no apparent difference in NISP.

Conclusions
Implementation of an EHR did not appear to have an impact on bond ratings at the hospitals in our analysis.