bluuebunny/crossref_metadata_2025 huggingface dataset:
C‐reactive protein as a marker of the surgical stress reduction within an ERAS protocol (Enhanced Recovery After Surgery) in colorectal surgery: A prospective cohort study
Authors: Cabellos Olivares Mercedes , Labalde Martínez María , Torralba Miguel , Rodríguez Fraile José R. , Atance Martínez Juan C.
Published: January 2018

Background

The aim of this study is to evaluate the effectiveness of an Enhanced Recovery After Surgery Protocol (ERAS) in relation to reduce the Systemic Inflammatory Response (SIR) to surgery using C‐reactive protein (CRP) in the first (POD1), second (POD2) and third (POD3) postoperative day.

Methods

We enrolled 121 patients (ERAS group) that underwent elective colorectal surgery with ERAS, and compared them with 135 patients (preERAS group) that had undergone surgery prior to the implementation. We made a univariate analysis to compare the CRP values in POD1, POD2, and POD3 between preERAS/ERAS group, laparoscopic/open surgery and the presence or not of Clavien Dindo complications. Multivariable lineal regression was used to assess if the ERAS had a decreasing effect on the CRP in POD1, POD2, and POD3, and was adjusted by age, male sex, use of laparoscopy, and complications.

Results

The presence of complications was independently associated with an increase in CRP values ​​in POD1, POD2, and POD3. Laparoscopy in POD1 and POD2, and ERAS in POD2 was independently associated with a decrease in CRP values.

Conclusion

The analysis shows an increase in SIR measured as a CRP value in those patients that had complications. The SIR decreased with laparoscopy in POD1 and POD2 and with ERAS in POD2.
Deep learning for segmentation of brain tumors: Impact of cross‐institutional training and testing
Authors: AlBadawy Ehab A. , Saha Ashirbani , Mazurowski Maciej A.
Published: January 2018

Background and purpose

Convolutional neural networks (CNNs) are commonly used for segmentation of brain tumors. In this work, we assess the effect of cross‐institutional training on the performance of CNNs.

Methods

We selected 44 glioblastoma (GBM) patients from two institutions in The Cancer Imaging Archive dataset. The images were manually annotated by outlining each tumor component to form ground truth. To automatically segment the tumors in each patient, we trained three CNNs: (a) one using data for patients from the same institution as the test data, (b) one using data for the patients from the other institution and (c) one using data for the patients from both of the institutions. The performance of the trained models was evaluated using Dice similarity coefficients as well as Average Hausdorff Distance between the ground truth and automatic segmentations. The 10‐fold cross‐validation scheme was used to compare the performance of different approaches.

Results

Performance of the model significantly decreased (P < 0.0001) when it was trained on data from a different institution (dice coefficients: 0.68 ± 0.19 and 0.59 ± 0.19) as compared to training with data from the same institution (dice coefficients: 0.72 ± 0.17 and 0.76 ± 0.12). This trend persisted for segmentation of the entire tumor as well as its individual components.

Conclusions

There is a very strong effect of selecting data for training on performance of CNNs in a multi‐institutional setting. Determination of the reasons behind this effect requires additional comprehensive investigation.
Augmented nested sampling for stochastic programs with recourse and endogenous uncertainty
Authors: Ekin Tahir , Polson Nicholas G. , Soyer Refik
Published: January 2018

We propose a novel simulation‐based approach for solving two‐stage stochastic programs with recourse and endogenous (decision dependent) uncertainty. The proposed augmented nested sampling approach recasts the stochastic optimization problem as a simulation problem by treating the decision variables as random. The optimal decision is obtained via the mode of the augmented probability model. We illustrate our methodology on a newsvendor problem with stock‐dependent uncertain demand both in single and multi‐item (news‐stand) cases. We provide performance comparisons with Markov chain Monte Carlo and traditional Monte Carlo simulation‐based optimization schemes. Finally, we conclude with directions for future research.
Spatial modeling of permafrost distribution and properties on the Qinghai‐Tibet Plateau
Authors: Wu Xiaobo , Nan Zhuotong , Zhao Shuping , Zhao Lin , Cheng Guodong
Published: January 2018

Accurate information on the distribution of permafrost and its thermal and hydrological properties is critical for environmental management and engineering development. This study modeled the current state of permafrost on the Qinghai‐Tibet Plateau (QTP), including the spatial distribution of permafrost, active‐layer thickness (ALT), mean annual ground temperature (MAGT), depth of zero annual amplitude (DZAA) and ground‐ice content using an improved Noah land surface model (LSM). The improved model was examined at a typical permafrost site and then applied to the entire QTP using existing gridded meteorological data and newly developed soil data. The simulated permafrost distribution and properties were validated against existing permafrost maps in three representative survey areas and with measurements from 54 boreholes. The results indicate that the Noah LSM with augmented physics and proper soil data support can model permafrost over the QTP. Permafrost was simulated to underlie an area of 1.113 × 106 km2 in 2010, accounting for 43.8% of the entire area of the QTP. The modeled regional average ALT and MAGT were 3.23 m and −1.56°C, respectively. Spatially, MAGT increases and DZAA becomes shallower from north to south. Thermally unstable permafrost (MAGT above −0.5°C) is predominant, accounting for 38.75% of the whole permafrost area on the QTP. Ice‐rich permafrost was mainly simulated around lakes across the north‐central QTP.
Cardiopulmonary exercise test to quantify enzyme replacement response in pediatric Pompe disease
Authors: Bar‐Yoseph Ronen , Mandel Hanna , Mainzer Gur , Gur Michal , Tal Galit , Shalloufeh George , Bentur Lea
Published: January 2018

Introduction

Enzyme replacement therapy (ERT) with Myozyme improved the prospect of Pompe disease patients. Our aim was to evaluate ERT acute effect on exercise capacity in pediatric Pompe patients.

Methods

Five Pompe patients (10‐19 years, 4 infantile‐onset and 1 diagnosed at 5 years) were evaluated before and 2 days after ERT using cardiopulmonary exercise testing (CPET), 6 min walking test (6MWT) and motor function test (GMFM‐88).

Results

Preserved normal peak oxygen uptake, 6MWT and motor function were observed in the relative mild disease and impairment of these parameters in the more advanced disease. Two days following ERT, three patients demonstrated changes; one patient (relative mild disease) increased both oxygen uptake (11%) and walking distance (38%). Second patient (advanced disease) increased oxygen uptake (11%) while a small decrease in walking distance in the 6MWT (8%) was observed. Third patient (advanced disease) decreased oxygen uptake (39%) but increased walking distance (42%) and motor function score (27%).

Conclusions

CPET is safe for pediatric Pompe patients. ERT may benefit exercise capacity in patients with less advanced disease. Individualized assessment by CPET, 6MWT, and motor function may help ERT adjustment by providing precise quantification of the response to treatment. Additional studies are needed to clarify the benefit of this assessment protocol.
Printed Copper Nanoparticle Metal Grids for Cost‐Effective ITO‐Free Solution Processed Solar Cells
Authors: Georgiou Efthymios , Choulis Stelios. A. , Hermerschmidt Felix , Pozov Sergey M. , Burgués‐Ceballos Ignasi , Christodoulou Constantinos , Schider Gerburg , Kreissl Stefanie , Ward Richard , List‐Kratochvil Emil J. W. , Boeffel Christine
Published: January 2018

Copper nanoparticle inks have drawn much attention since they have the potential to constitute an alternative cost‐effective solution than other noble metals nanoparticle inks such as Ag for indium tin oxide (ITO)‐free printed electronic applications. Our research and development efforts have produced high conductivity copper nanoparticle inks which have excellent jetting and printing properties resulting in high quality inkjet‐printed (IJP) Cu nanoparticle‐based metal grids. We present ITO‐free, Si‐PCPDTBT: PC[70]BM organic photovoltaics (OPVs) processed in ambient low‐cost fabrication conditions comprising for the first time embedded and non embedded inkjet‐printed copper grid/Poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) as the bottom electrode with power conversion efficiencies (PCE) of 2.56 and 3.35%, respectively. The results of the ITO‐free OPVs using inkjet‐printed Cu nanoparticle current collecting grids are discussed relevant to reference ITO‐based OPVs with PCE of 4.92%.
EPIC framework for enterprise processes integrative collaboration
Authors: Sitton Miri , Reich Yoram
Published: January 2018

Enterprise System Engineering (ESE), an emerging practice arising in the last decades, aims to improve enterprise operational processes. Its main goal is to enable better collaboration between humans, operational processes, and technical subsystems, by using system engineering methods. However, this is challenging due to the enterprise's unique property as a system of unsynchronized arrays of systems. This property might lead to severe consequences, such as cross‐enterprise failures, lack of decision‐support information for cross‐enterprise decisions, long delays in integration tests, and unexpected emergent behavior. Existing approaches such as ESE frameworks and Systems of Systems (SOS) engineering methods do not fully address this property. This paper presents a new ESE framework named EPIC (Enterprise Processes Integrative Collaboration), that enables better coordination between unsynchronized arrays of systems within the enterprise and even further across several enterprises. This coordination contributes to cross‐enterprise operational processes effectiveness. The paper summarizes the results of two successful large‐scale implementations of EPIC in the aerospace and transportation disciplines. Results analysis of processes performance and effectiveness, confirm that EPIC leads to improvement in enterprise operational processes. Similarly, we contend that EPIC may be applicable in other disciplines in order to obtain better enterprises by improving cross‐enterprise operational processes collaboration.
A particular AC component protection scheme for bipolar HVDC transmission lines
Authors: Yang Yayu , Tai Nengling , Fan Chunju , Liu Jian , Chen Miao
Published: January 2018

The line protection methods for high‐voltage direct current (HVDC) transmission system in engineering applications are poor in sensitivity and reliability. In this paper, we introduce a new notion of energy, namely a particular AC energy, based on which a particular AC component protection scheme is proposed. The scheme is comprised of start‐up criterion, fault identification criterion, and faulty pole identification criterion. The start‐up criterion is based on the fact that particular AC component measured at both terminals increases rapidly when a fault occurs. The particular AC energy calculated by particular AC component at both terminals behaves differently in the face of an internal or external fault, and this characteristic is applied to construct the fault identification criterion. The particular AC energy on the non‐fault line is smaller than that on the faulty line, which can be used to establish the faulty pole identification criterion. Compared with other energy‐based protections, the proposed method does not require data synchronization and is not affected by the distributed capacitive current of the transmission line. Comprehensive simulation experiments including real‐time digital simulator (RTDS) tests indicate that this method is able to operate reliably under various fault conditions with satisfactory accuracy and high sensitivity. © 2018 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Machine learning methods for short‐term bid forecasting in the renewable energy market: A case study in Italy
Authors: Cocchi Guido , Galli Leonardo , Galvan Giulio , Sciandrone Marco , Cantù Matteo , Tomaselli Giuseppe
Published: January 2018

In liberalized markets, there usually exists a day‐ahead session where energy is sold and acquired for the following production day. Owing to the high uncertainty of its production, renewable energy (wind in particular) can significantly influence the network imbalance of the following day. In this work, we consider the problem of predicting the sum of the bid volumes for wind energy of all the producers inside the day‐ahead energy market. This is a valuable tool to be used by an energy provider in order to determine the imbalance of a market zone and, thus, properly size its bids. In particular, we focus on the estimation of the possible relationship between the meteorological forecasts and the wind power offered on the market by the companies for a market zone. We propose a machine learning model which is used to compute a 1‐day‐ahead forecast. The input‐output mapping is obtained by support vector regression. The input feature vector is defined by a suitable feature extraction technique since the meteorological forecasts are given on a lattice of thousands of geographical points. The computational experiments are performed considering the Italian market as a case study (years 2012‐2016). The results show that the proposed feature extraction technique, selecting only some geographical zones, manages to reduce the error attained using all the features. Moreover, classical statistical methods are shown to be outperformed by machine learning models. The analysis reveals also some weaknesses of the model, which may be due to other nonmeteorological factors at play.
Blood phospholipid fatty acid analysis of adults with and without attention deficit/hyperactivity disorder
Authors: Young Genevieve S. , Maharaj Nicole J. , Conquer Julie A.
Published: January 2018

Several psychiatric disorders, including juvenile Attention Deficit/Hyperactivity Disorder (ADHD), have been associated with abnormalities of certain long‐chain PUFA (LCPUFA). Despite this reported association, the FA levels of patients with the adult form of ADHD have not previously been evaluated. In this study we measured the total blood phospholipid FA concentrations in 35 control subjects and 37 adults with ADHD symptoms to determine whether adults with ADHD symptoms would show abnormalities of FA relative to control subjects. In the serum phospholipids, adults with ADHD symptoms had significantly lower levels of total saturated, total polyunsaturated, and total omega‐6 (n−6) FA, as well as the omega‐3 (n−3) LCPUFA DHA (22∶6n−3), and significantly higher levels of total monounsaturated FA and the n−3 LCPUFA docosapentaenoic acid (22∶5n−3). In the erythrocyte membrane phospholipids, adults with ADHD symptoms had significantly lower levels of total PUFA, total n−3 FA, and DHA, and significantly higher levels of total saturated FA. Neither serum nor erythrocyte membrane phospholipid DHA was related to ADHD symptom severity (as assessed by the Amen questionnaire) in ADHD subjects. Although the exact cause of these variations is unknown, both environmental and genetic factors may be involved.
Dioxirane oxidation of 3β‐substituted Δ5‐steroids
Authors: Parish Edward J. , Qiu Zhihai
Published: January 2018

This article reviews the utility of dioxiranes in the oxidation of 3β‐substituted Δ5‐sterols. Dioxiranes are the smallest cyclic peroxides that contain a carbon atom. They can be generated in situ from Oxone® (2KHSO5·KHSO4·K2SO4) and a ketone. Dioxiranes are versatile oxidizing agents. The most common reaction of dioxiranes is epoxidation, with nearly 1∶1 ratios of α/β isomer products in all cases. Δ5‐steroids with different side chains were epoxidized by dioxiranes generated in situ from several commercially available ketones. Although ketones function as catalyst, they were used in about an equivalent amount or large excess to accelerate the reaction.
Effect of salts on soy storage proteins defatted with supercritical CO2 and alcohols
Authors: Sessa David J. , Nelsen Terry C. , Snyder Janet M.
Published: January 2018

The primary objective was to determine whether salts will stabilize soy storage proteins against the denaturing effects of alcohols or the heat and pressure used in supercritical CO2 during the defatting process. Nitrogen solubility index (NSI) and differential scanning calorimetry (DSC) were used to monitor the denaturation of proteins. A variety of salt solutions used to hydrate full‐fat soy grits increased the thermal stability of both 7S and 11S storage proteins. DSC was used to monitor their denaturation temperature. Neutral salt hydrations followed the lyotropic series for protein stabilization. Of the salts evaluated, the test results indicate that the reducing salt, sodium sulfite, and the neutral salt, sodium sulfate, when used to steep beans, yielded significantly higher NSI than did the water‐steeped controls or other salt treatments after partial defatting with absolute isopropanol or ethanol and supercritical CO2. However, these same salt treatments did not as effectively stabilize the proteins against the denaturing effects of ethanol more aqueous than 84% when these alcohols were used as the defatting medium.
Enantioselective conversion of linoleate hydroperoxide to an α, β‐epoxy alcohol by niobium ethoxide
Authors: Piazza George J. , Foglia Thomas A. , Nuñez Alberto
Published: January 2018

Niobium (V) ethoxide [Nb(OC2H5)5] catalyzed the rearrangement of methyl 13(S)‐hydroperoxy‐9(Z),11(E)‐octadecadienoate (Me‐HPODE) to epoxy hydroxy isomers. At low temperature (5°C) in aprotic solvent, Me‐HPODE was converted to the diastereomeric α, β‐epoxy alcohols, methyl 11(R,S),12(R,S)‐epoxy‐13(S)‐hydroxy‐9(Z)octadecenoate. These products are referred to as oxylipids and structurally resemble those obtained from the vanadium‐ and epoxygenase‐catalyzed rearrangement of Me‐HPODE but are distinct from products obtained from ferrous iron‐, hematin‐, and hemoglobin‐catalyzed rearrangements. Because the product of the niobium‐catalyzed rearrangement of Me‐HPODE was predominantly the erythro diastereomer, the rearrangement is distinguished from that produced by a titanium catalyst, in which the threo diastereomer [methyl 11(R), 12(R)‐epoxy‐13(S)‐hydroxy‐9(Z)‐octadecenoate] predominates, and from that produced by a vanadium catalyst, in which both diastereomers are produced in equal proportion. The synthesis of alcohol epoxide by Nb(OC2H5)5 was inhibited by traces of water, but inclusion of molecular sieves in the reaction medium did not improve yield, as the alcohol epoxide rearranged to ketonic materials.
Lipase‐assisted concentration of n‐3 polyunsaturated fatty acids in acylglycerols from marine oils
Authors: Wanasundara Udaya N. , Shahidi Fereidoon
Published: January 2018

Preparation of n‐3 polyunsaturated fatty acid (PUFA) concentrates from seal blubber oil (SBO) and menhaden oil (MHO) in the form of acylglycerols was carried out by hydrolysis with a number of commercial microbial lipases. The lipases tested were Aspergillus niger, Candida cylindracea (CC), Chromobacterium viscosum, Geotrichum candidum, Mucor miehei, Pseudomonas sp., Rhizopus oryzae, and Rhizopus niveus. After lipase‐assisted hydrolysis of oils, free fatty acids were removed, and fatty acid composition of the mixture containing mono‐, di‐, and triacylglycerols was determined. All lipases were effective in increasing the n‐3 PUFA content of the remaining acylglycerols of both SBO and MHO. The highest concentration of n‐3 PUFA was provided by CC lipase; 43.5% in SBO [9.75% eicosapentaenoic acid (EPA), 8.61% docosapentaenoic acid (DPA), and 24.0% docosahexaenoic acid (DHA)] and 44.1% in MHO (18.5% EPA, 3.62% DPA, and 17.3% DHA) after 40 h of hydrolysis. Thus, CC lipase appears to be most suitable for preparation of n‐3 PUFA in the acylglycerol form from marine oils.
The incorporation of n‐3 polyunsaturated fatty acids into acylglycerols of borage oil via lipase‐catalyzed reactions
Authors: Ju Yi‐Hsu , Huang Fang‐Cheng , Fang Chia‐Hui
Published: January 2018

The purpose of this work was to add n‐3 polyunsaturated fatty acids (PUFA) into the acylglycerols of borage oil. The acidolysis reaction between borage oil and n‐3 PUFA was carried out with lipase (Lipozyme IM‐60) in organic solvent. The effects of temperature, solvent, and water content on the reaction product were investigated. For the acidolysis reaction between acylglycerols (product of the selective hydrolysis of borage oil, catalyzed by immobilized Candida rugosa lipase) and n‐3 PUFA, the total content of n‐3 and n‐6 PUFA in acylglycerols was 72.8% after a reaction time of 18 h. The contents of γ‐linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid were 26.5, 19.8, and 18.1%, respectively. By properly controlling the reaction time, acylglycerols with ca. 70–72% PUFA and a ratio of n‐3 PUFA to n‐6 PUFA from 0–1.09 can be obtained.
Study of the enantiomeric composition of chiral constituents in edible oils by simultaneous distillation‐extraction. Detection of adulterated olive oils
Authors: Caja M. M. , Ruiz del Castillo M. L. , Herraiz M. , Blanch G. P.
Published: January 2018

A method is proposed for detecting adulterations of olive oil with hazelnut oil at percentages as low as 5%. The method is based on the identification of R‐ and S‐enantiomers of E‐5‐methylhept‐2‐en‐4‐one (filbertone) and involves the use of simultaneous distillation‐solvent extraction in the sample preparation step and subsequent gas chromatographic analysis with a chiral stationary phase. Relative standard deviation values obtained from three replicates of adulterated mixtures of olive oil and hazelnut oil (95:5) were less than 9% for both R‐and S‐filbertone.
Impact on disease-free survival of the duration of ovarian function suppression, as postoperative adjuvant therapy, in premenopausal women with hormone receptor-positive breast cancer: a retrospective single-institution study
Authors: Ozaki Yukinori , Tanabe Yuko , Tamura Nobuko , Ogura Takuya , Kondoh Chihiro , Miura Yuji , Yoshimura Kenichi , Kawabata Hidetaka , Takano Toshimi
Published: January 2018

Introduction

Although tamoxifen (TAM) plus ovarian function suppression (OFS) is considered as a standard adjuvant treatment for premenopausal women with hormone receptor-positive breast cancer, the optimal duration of OFS has not yet been established. This retrospective study was designed to assess the duration of OFS and the impact of the duration of OFS on the DFS in these patients.

Methods

We retrospectively reviewed the data of premenopausal patients with breast cancer who received TAM + OFS (goserelin or leuprorelin) as adjuvant therapy between February 2004 and June 2015. The primary analysis was a comparison of the disease-free survival (DFS) between patients who received OFS for 3 years or less (OFS ≤ 3 years group) and those who received OFS for longer than 3 years (OFS > 3 years group).

Results

We analyzed the data of 215 premenopausal patients diagnosed as having hormone receptor-positive breast cancer. A propensity score-matched model showed the absence of any significant difference in the DFS between the OFS ≤ 3 years group and OFS > 3 years group (6-year DFS rate, 93.2 vs. 94.0%; log-rank test p = 0.767).

Conclusions

Our data showed that among premenopausal women with hormone receptor-positive breast cancer who received TAM + OFS as adjuvant endocrine therapy, there was no significant difference in the DFS between the OFS ≤ 3-year group and OFS > 3-year group. A randomized trial is needed to establish the optimal duration of OFS for these patients.
„Trauma First“ – ein ambulantes, kognitiv-behaviorales Behandlungsprogamm für Kinder und Jugendliche mit Traumafolgestörungen – Eine Pilotstudie
Authors: Sierau Susan , Knabe Alena , Ahrens-Eipper Sabine , Nelius Katrin , Glaesmer Heide
Published: January 2018

Zusammenfassung. Fragestellung: Obwohl traumatische Erfahrungen eine der wichtigsten Ursachen für psychische Erkrankungen in der Kindheit und im Erwachsenenalter sind, finden traumaspezifische Behandlungsansätze in der deutschen Versorgungspraxis momentan zu wenig Anwendung. Daher war das Ziel der vorliegenden Pilotstudie die Evaluation eines manualisierten, ambulanten, kognitiv-behavioralen Behandlungsangebots („Trauma First“) für Kinder und Jugendliche mit Traumafolgestörungen. Die Annahme war, dass sich die Symptomatik einer Posttraumatischen Belastungsstörung (PTBS) sowie depressive Symptome, Ängste und Verhaltensauffälligkeiten durch ein solches intensives, strukturiertes Behandlungsprogramm signifikant verbessern lassen. Methodik: In der Pilotstudie wurde ein Prä-Post-Testdesign ohne Kontrollgruppe durchgeführt. Die Symptombelastung von 33 Kindern und Jugendlichen (Alter: 10–15 Jahre; 54.5 % weiblich) mit traumatischen Erfahrungen wurde mittels störungsspezifischer Diagnostik und Breitbanddiagnostik vor und nach der Behandlung in Selbst- und Fremdeinschätzung erfasst. Ergebnisse: Nach der Behandlung wurde ein Rückgang von selbst- und fremdbeurteilten PTBS-Symptomen, Depressivität, Angst und Verhaltensauffälligkeiten der Kinder und Jugendlichen festgestellt (Cohens d: 0.51–1.49). In der selbst- und fremdbeurteilten Lebensqualität konnte eine Tendenz in Richtung einer positiven Veränderung verzeichnet werden. Die identifizierten Effektstärken unter Versorgungsbedingungen waren überwiegend vergleichbar mit denen aus Metaanalysen. Schlussfolgerungen: Die vorliegende Pilotstudie liefert erste Hinweise zur Effektivität des „Trauma First“-Programms unter ökologisch validen Bedingungen. Sie dient als Vorstufe der psychotherapeutischen Wirksamkeitsprüfung, die in einem randomisiert-kontrollierten Studiendesign weiterverfolgt werden sollte.
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

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

DNA 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

Many 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

Tin 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

Superconductivity 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

Antimicrobial 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

A 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

Land 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

The 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

The 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

On 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

While 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.
Publisher Correction: Observation of photobleaching in Ge-deficient Ge16.8Se83.2 chalcogenide thin film with prolonged irradiation
Authors: Zhang Sen , Chen Yimin , Wang Rongping , Shen Xiang , Dai Shixun
Published: January 2018

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
Flow-injection analysis coupled with electrochemical detection of poisonous inorganic arsenic(iii) species using a gold nanoparticle/carbon nanofiber/chitosan chemically modified carbon screen printed electrode in neutral pH solution
Authors: Nellaiappan Subramanian , Pillai K. Chandrasekara , Kumar Annamalai Senthil
Published: January 2018

Simple, selective and contentious fluidic detection of As(iii) species in drinking water has been demonstrated.
Combination of efficient charge separation with the assistance of novel dual Z-scheme system: self-assembly photocatalyst Ag@AgI/BiOI modified oxygen-doped carbon nitride nanosheet with enhanced photocatalytic performance
Authors: Liang Chao , Niu Cheng-Gang , Guo Hai , Huang Da-Wei , Wen Xiao-Ju , Yang Shi-Feng , Zeng Guang-Ming
Published: January 2018

The self-assembly dual Z-scheme photocatalyst Ag@AgI/BiOI/g-C3N4 was successfully fabricated with high charge separation efficiency.
Dihydroxyacetone conversion into lactic acid in an aqueous medium in the presence of metal salts: influence of the ionic thermodynamic equilibrium on the reaction performance
Authors: Jolimaitre E. , Delcroix D. , Essayem N. , Pinel C. , Besson M.
Published: January 2018

Different Lewis acid aluminium complexes catalyse the successive reactions to convert dihydroxyacetone into lactic acid in an aqueous medium.
Ionic liquids-coordinated Au catalysts for acetylene hydrochlorination: DFT approach towards reaction mechanism and adsorption energy
Authors: Xu Hao , Meng Shijun , Luo Guohua
Published: January 2018

A DFT study of Au–IL catalysts for acetylene hydrochlorination was carried out and consistency with experimental data was obtained.
Occurrence, biological activity and metabolism of 6-shogaol
Authors: Kou Xingran , Wang Xiaoqi , Ji Ruya , Liu Lang , Qiao Yening , Lou Zaixiang , Ma Chaoyang , Li Shiming , Wang Hongxin , Ho Chi-Tang
Published: January 2018

As one of the main bioactive compounds of dried ginger, 6-shogaol has been widely used to alleviate many ailments.
Impact of dietary supplementation with olive and thyme phenols on alpha-tocopherol concentration in the muscle and liver of adult Wistar rats
Authors: Bars-Cortina David , López de las Hazas María-Carmen , Benavent-Vallés Alfred , Motilva Maria-José
Published: January 2018

A preliminary study to evaluate the effect of dietary supplementation with olive phenols (oleuropein, hydroxytyrosol and secoiridoids), thyme phenols and a combination of these on the α-tocopherol concentrations in the muscle and liver of healthy adult Wistar rats over 21 days was conducted.
Discovery of 7-hydroxyaporphines as conformationally restricted ligands for beta-1 and beta-2 adrenergic receptors
Authors: Ku Angela F. , Cuny Gregory D.
Published: January 2018

Potent beta-1 and beta-2 adrenergic receptor antagonism via a conformationally restricted aporphine scaffold with defined stereochemistry has been developed.