bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diatom diversity through HTS-metabarcoding in coastal European seas
Authors: Piredda Roberta , Claverie Jean-Michel , Decelle Johan , de Vargas Colomban , Dunthorn Micah , Edvardsen Bente , Eikrem Wenche , Forster Dominik , Kooistra Wiebe H. C. F. , Logares Ramiro , Massana Ramon , Montresor Marina , Not Fabrice , Ogata Hiroyuki , Pawlowski Jan , Romac Sarah , Sarno Diana , Stoeck Thorsten , Zingone Adriana 
Published: December 2018

AbstractDiatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities.
Fate of bacterial indicators and Salmonella in biofilm developed on ultrafiltration membranes treating secondary effluents of domestic wastewater
Authors: Jadoun Jeries , Mreny Raghda , Saad Ons , Azaizeh Hassan 
Published: December 2018

AbstractThe fate of representative indicator and pathogenic bacteria on ultrafiltration (UF)-membrane surfaces treating secondary wastewater effluent, as well as their reaction to common biofouling-removal techniques was investigated. Field-condition experiments showed that the number of heterotrophic bacteria, fecal coliforms, E. coli and Salmonella on membrane surface increased rapidly and continuously until the end of the experiment, reaching 9, 6.5, 6, and 2.4 logs, respectively. Similar results were obtained under controlled laboratory conditions. However, the increase in the bacterial numbers was dependent on the supply of fresh wastewater. Quantitative real-time PCR verified the behavior of attached E. coli cells, although the numbers were 1–2 logs higher compared to the standard culture-based method. The number of attached bacteria was positively correlated to increases in DNA and protein content and negatively correlated to the membrane flux. In-situ membrane cleaning using sodium hypochlorite significantly reduced the number of attached bacteria. However, the effect was temporary and affected bacterial cell cultivability rather than viability. Taken together, these findings suggest that, under the studied conditions, indicator and pathogenic bacteria can initiate rapid biofilm development, persist on UF membrane surfaces, and survive membrane cleaning with sodium hypochlorite.
Adhesive-free adhesion between heat-assisted plasma-treated fluoropolymers (PTFE, PFA) and plasma-jet-treated polydimethylsiloxane (PDMS) and its application
Authors: Ohkubo Yuji , Endo Katsuyoshi , Yamamura Kazuya 
Published: December 2018

AbstractConventional low-temperature plasma treatment was reported to minimally improve the adhesion property of polytetrafluoroethylene (PTFE), whereas heat-assisted plasma (HAP) treatment significantly improved the same. An unvulcanized rubber was previously used as an adherent for PTFE. This study aimed to achieve strong adhesive-free adhesion between PTFE and vulcanized polydimethylsiloxane (PDMS) rubber. As-received vulcanized PDMS rubber did not adhere to HAP-treated PTFE, and as-received PTFE did not adhere to vulcanized rubber of plasma-jet (PJ) treated PDMS rubber; however, HAP-treated PTFE strongly adhered to vulcanized PJ-treated PDMS rubber, and both PTFE and PDMS exhibited cohesion failure in the T-peel test. The surface chemical compositions of the PTFE and PDMS sides were determined using X-ray photoelectron spectroscopy. The strong PTFE/PDMS adhesion was explained via hydrogen and covalent bond formation (C–O–Si and/or C(=O)–O–Si) between hydroxyl (C–OH) or carboxyl (C(=O)–OH) groups of the HAP-treated PTFE. This process was also applied to adhesive-free adhesion between a tetrafluoroethylene–perfluoroalkylvinylether copolymer (PFA) and PDMS; subsequently, a translucent PFA/PDMS assembly with strong adhesion was realized together with the PTFE/PDMS assembly. Strong adhesive-free adhesion between fluoropolymers (PTFE, PFA) and vulcanized PDMS rubber without using any adhesives and graft polymer was successfully realized upon plasma treatment of both the fluoropolymer and PDMS sides. Additionally, a PDMS sheet, which was PJ-treated on both sides, was applied to strongly adhere fluoropolymers (PTFE, PFA) to materials such as metal and glass. PJ-treated PDMS was used as an intermediate layer rather than a strong adhesive, achieving PTFE/PDMS/metal and PTFE/PDMS/glass assemblies. The PTFE/PDMS, PDMS/metal, and PDMS/glass adhesion strengths exceeded 2 N/mm.
Incident wavelength and polarization dependence of spectral shifts in β-Ga2O3 UV photoluminescence
Authors: Wang Yunshan , Dickens Peter T. , Varley Joel B. , Ni Xiaojuan , Lotubai Emmanuel , Sprawls Samuel , Liu Feng , Lordi Vincenzo , Krishnamoorthy Sriram , Blair Steve , Lynn Kelvin G. , Scarpulla Michael , Sensale-Rodriguez Berardi 
Published: December 2018

AbstractWe report polarization dependent photoluminescence studies on unintentionally-, Mg-, and Ca-doped β-Ga2O3 bulk crystals grown by the Czochralski method. In particular, we observe a wavelength shift of the highest-energy UV emission which is dependent on the pump photon energy and polarization. For 240 nm (5.17 eV) excitation almost no shift of the UV emission is observed between E||b and E||c, while a shift of the UV emission centroid is clearly observed for 266 nm (4.66 eV), a photon energy lying between the band absorption onsets for the two polarizations. These results are consistent with UV emission originating from transitions between conduction band electrons and two differentially-populated self-trapped hole (STH) states. Calcuations based on hybrid and self-interaction-corrected density functional theories further validate that the polarization dependence is consistent with the relative stability of two STHs. This observation implies that the STHs form primarily at the oxygen atoms involved in the original photon absorption event, thus providing the connection between incident polarization and emission wavelength. The data imposes a lower bound on the energy separation between the self-trapped hole states of ~70–160 meV, which is supported by the calculations.
Obstetric and perinatal outcomes for twin pregnancies in adolescent girls
Authors: Robson Danielle , Daniels Samuel , Flatley Christopher , Kumar Sailesh 
Published: December 2018

AbstractThis was a nine-year retrospective cohort study to investigate obstetric and perinatal outcomes in a cohort of adolescent girls with twin pregnancies from a major Australian tertiary centre in Brisbane, Australia. The adolescent cohort was aged <19 years and the control group was aged 20–24 years. The total study cohort comprised of 183 women. Of these, the adolescent cohort contained 29 girls (15.8%) and the control group comprised of 154 women (84.2%). Adolescent girls were less likely to delivery via an elective caesarean section compared to women in the control group (10.3% vs. 25.7%, p < 0.001). There were no differences in duration of labour, post-partum haemorrhage or perineal trauma rates. After controlling for the confounding effects of parity, chronicity and birth weight, birth <28 weeks remained significant (aOR 11.20, 95% CI 2.97–42.18, p < 0.001) for the adolescent cohort. There was a higher proportion of adolescents whose babies had an adverse composite perinatal outcome (87.9% vs. 69.5%, OR 3.20 95% CI: 1.40–7.31, p = 0.01) however significance was lost after adjusting for parity, chorionicity, birthweight and gestation at birth (aOR 3.27 95% CI: 0.95–11.31, p = 0.06). Our results show that obstetric and perinatal outcomes for twin pregnancies in teenagers were broadly similar compared to controls although the risk of extreme preterm birth was increased after controlling for confounders.
Shaoyao-Gancao Decoction alleviated hyperandrogenism in a letrozole-induced rat model of polycystic ovary syndrome by inhibition of NF-κB activation
Authors: Shao Yun-yun , Chang Zhuang-peng , Cheng Yao , Wang Xin-chun , Zhang Jing-ping , Feng Xiao-juan , Guo Yi-ting , Liu Jun-jin , Hou Rui-gang 
Published: December 2018

Abstract
Shaoyao-Gancao Decoction (SGD) has been widely used for the treatment of gynopathy. The present study aimed to evaluate the therapeutic effect and potential mechanism of SGD on hyperandrogenism in polycystic ovary syndrome (PCOS) rats. In the present work, SGD was orally administrated to the PCOS rats at the dose of 12.5, 25, and 50 g/kg/d for 14 consecutive days. UPLC–MS/MS was performed to identify the main chemical components of SGD. Body weight, ovarian weight, cystic dilating follicles, and serum levels of steroid hormones were tested to evaluate the therapeutic effect of SGD. In order to further clarify the underlying mechanism, we also measured mRNA and the protein levels of NF-κB, NF-κB p65, P-NF-κB p65, and IκB by RT-qPCR and Western blotting techniques. Our results showed that SGD treatment significantly alleviated hyperandrogenism in PCOS rats as evidenced by reduced serum levels of T and increased E2 and FSH levels. In addition, SGD effectively reduced the phosphorylation of NF-κB p65 and increased the expression of IκB. Results of the present study demonstrated that SGD could ameliorate hyperandrogenism in PCOS rats, and the potential mechanism may relate to the NF-κB pathway.
Impact analysis of traction loads on power grid based on probabilistic three‐phases load flow
Authors: Che Yulong , Wang Xiaoru , Lv Xiaoqin , Hu Yi , Li Longyuan , Chen Haoyue 
Published: December 2018

Electrified railway traction power supply system is directly powered by 110 kV or 220 kV (some 330 kV) high‐voltage power grid. The uncertainty, non‐linearity, and asymmetry of traction loads like the electric locomotives and electric multiple units (EMUs) exert the negative sequence and harmonics impact on the high‐voltage transmission network. In order to evaluate the impact of the uncertainty and asymmetry of traction loads on the high‐voltage transmission grid, a probabilistic three‐phase power flow model of transmission network considering the probability model of traction loads is proposed. First, the power probability model of traction loads is established according to the running characteristics of traction loads. Second, the Monte Carlo simulation method is applied for the probabilistic three‐phase power flow model calculation considering the traction loads. Finally, the simulation calculation is carried out on the balanced IEEE‐14 bus three‐phase test system. The results show that the asymmetric traction loads cause the unbalance of the grid nearby to deteriorate. The further away from the traction substation, the smaller impact of the traction loads.
(Semi-)global analytic hypoellipticity for a class of “sums of squares” which fail to be locally analytic hypoelliptic
Authors: Chinni Gregorio 
Published: December 2018

The global and semi-global analytic hypoellipticity on the torus is proved for two classes of sums of squares operators, introduced by P. Albano, A. Bove, and M. Mughetti, satisfying the Hörmander condition and which fail to be either locally or microlocally analytic hypoelliptic.
Widespread Cognitive Deficits in Alcoholism Persistent Following Prolonged Abstinence: An Updated Meta-analysis of Studies That Used Standardised Neuropsychological Assessment Tools
Authors: Crowe Simon F , Cammisuli Davide M , Stranks Elizabeth K 
Published: December 2018

Abstract

Objective
This study presents an updated meta-analysis replicating the study of (Stavro, K., Pelletier, J., & Potvin, S. (2013). Widespread and sustained cognitive deficits in alcoholism: A meta-analysis. Addiction Biology, 18, 203–213. doi:10.1111/j.1369-1600.2011.00418.x) regarding the cognitive functioning of alcoholics as a function of time abstinent.

Methods
A total of 34 studies (including a total of 2,786 participants) that met pre-determined inclusion and exclusion criteria were included in the analyses. The alcoholics were categorised into recently detoxified alcoholics (0–31 days sober), alcoholics 32–365 days sober and alcoholics &gt;365 days sober consistent with the previous study. The current study employed more stringent control on the tests included in the analysis to include only those tasks described in contemporary neuropsychological test compendia. Forty-seven percent of the papers surveyed were not include in the previous meta-analysis.

Results
The results indicated that there was a diffuse and pervasive pattern of cognitive deficit among recently detoxified alcoholics and that these deficits, particularly with regard to memory functioning, persisted even in longer term abstinent alcoholics. This was inconsistent with the prior meta-analysis which contended that significant cognitive recovery was possible after as little as 1 year.

Conclusion
The persisting cognitive deficits were noted across a wide range of cognitive functions, supporting the notion of a diffuse rather than a specific compromise of cognition in alcoholism following discontinuation, as measured using standardised neuropsychological tests. Limitations on the finding included the fact that it was a cross-sectional rather than a longitudinal analysis, was subject to heterogeneity of method, had low representation of females in the samples, and had fewer studies of long-term sober samples.
Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy
Authors: Gilad Topaz , Reyes Jose , Chen Jia-Yun , Lahav Galit , Riklin Raviv Tammy 
Published: December 2018

AbstractMotivationCell microscopy datasets have great diversity due to variability in cell types, imaging techniques and protocols. Existing methods are either tailored to specific datasets or are based on supervised learning, which requires comprehensive manual annotations. Using the latter approach, however, poses a significant difficulty due to the imbalance between the number of mitotic cells with respect to the entire cell population in a time-lapse microscopy sequence.ResultsWe present a fully unsupervised framework for both mitosis detection and mother–daughters association in fluorescence microscopy data. The proposed method accommodates the difficulty of the different cell appearances and dynamics. Addressing symmetric cell divisions, a key concept is utilizing daughters’ similarity. Association is accomplished by defining cell neighborhood via a stochastic version of the Delaunay triangulation and optimization by dynamic programing. Our framework presents promising detection results for a variety of fluorescence microscopy datasets of different sources, including 2D and 3D sequences from the Cell Tracking Challenge.Availability and implementationCode is available in github (github.com/topazgl/mitodix).Supplementary informationSupplementary data are available at Bioinformatics online.
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization
Authors: Yu Jialin , Shi Shaoping , Zhang Fang , Chen Guodong , Cao Man 
Published: December 2018

Abstract

Motivation
Protein glycation is a familiar post-translational modification (PTM) which is a two-step non-enzymatic reaction. Glycation not only impairs the function but also changes the characteristics of the proteins so that it is related to many human diseases. It is still much more difficult to systematically detect glycation sites due to the glycated residues without crucial patterns. Computational approaches, which can filter supposed sites prior to experimental verification, can extremely increase the efficiency of experiment work. However, the previous lysine glycation prediction method uses a small number of training datasets. Hence, the model is not generalized or pervasive.

Results
By searching from a new database, we collected a large dataset in Homo sapiens. PredGly, a novel software, can predict lysine glycation sites for H.sapiens, which was developed by combining multiple features. In addition, XGboost was adopted to optimize feature vectors and to improve the model performance. Through comparing various classifiers, support vector machine achieved an optimal performance. On the basis of a new independent test set, PredGly outperformed other glycation tools. It suggests that PredGly can provide more instructive guidance for further experimental research of lysine glycation.

Availability and implementation
https://github.com/yujialinncu/PredGly

Supplementary information
Supplementary data are available at Bioinformatics online.
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation
Authors: Manavalan Balachandran , Basith Shaherin , Shin Tae Hwan , Wei Leyi , Lee Gwang 
Published: December 2018

Abstract

Motivation
Cardiovascular disease is the primary cause of death globally accounting for approximately 17.7 million deaths per year. One of the stakes linked with cardiovascular diseases and other complications is hypertension. Naturally derived bioactive peptides with antihypertensive activities serve as promising alternatives to pharmaceutical drugs. So far, there is no comprehensive analysis, assessment of diverse features and implementation of various machine-learning (ML) algorithms applied for antihypertensive peptide (AHTP) model construction.

Results
In this study, we utilized six different ML algorithms, namely, Adaboost, extremely randomized tree (ERT), gradient boosting (GB), k-nearest neighbor, random forest (RF) and support vector machine (SVM) using 51 feature descriptors derived from eight different feature encodings for the prediction of AHTPs. While ERT-based trained models performed consistently better than other algorithms regardless of various feature descriptors, we treated them as baseline predictors, whose predicted probability of AHTPs was further used as input features separately for four different ML-algorithms (ERT, GB, RF and SVM) and developed their corresponding meta-predictors using a two-step feature selection protocol. Subsequently, the integration of four meta-predictors through an ensemble learning approach improved the balanced prediction performance and model robustness on the independent dataset. Upon comparison with existing methods, mAHTPred showed superior performance with an overall improvement of approximately 6–7% in both benchmarking and independent datasets.

Availability and implementation
The user-friendly online prediction tool, mAHTPred is freely accessible at http://thegleelab.org/mAHTPred.

Supplementary information
Supplementary data are available at Bioinformatics online.
Fast nonconvex deconvolution of calcium imaging data
Authors: Jewell Sean W , Hocking Toby Dylan , Fearnhead Paul , Witten Daniela M 
Published: December 2018

Summary
Calcium imaging data promises to transform the field of neuroscience by making it possible to record from large populations of neurons simultaneously. However, determining the exact moment in time at which a neuron spikes, from a calcium imaging data set, amounts to a non-trivial deconvolution problem which is of critical importance for downstream analyses. While a number of formulations have been proposed for this task in the recent literature, in this article, we focus on a formulation recently proposed in Jewell and Witten (2018. Exact spike train inference via $\ell_{0} $ optimization. The Annals of Applied Statistics12(4), 2457–2482) that can accurately estimate not just the spike rate, but also the specific times at which the neuron spikes. We develop a much faster algorithm that can be used to deconvolve a fluorescence trace of 100 000 timesteps in less than a second. Furthermore, we present a modification to this algorithm that precludes the possibility of a “negative spike”. We demonstrate the performance of this algorithm for spike deconvolution on calcium imaging datasets that were recently released as part of the $\texttt{spikefinder}$ challenge (http://spikefinder.codeneuro.org/). The algorithm presented in this article was used in the Allen Institute for Brain Science’s “platform paper” to decode neural activity from the Allen Brain Observatory; this is the main scientific paper in which their data resource is presented. Our $\texttt{C++}$ implementation, along with $\texttt{R}$ and $\texttt{python}$ wrappers, is publicly available. $\texttt{R}$ code is available on $\texttt{CRAN}$ and $\texttt{Github}$, and $\texttt{python}$ wrappers are available on $\texttt{Github}$; see https://github.com/jewellsean/FastLZeroSpikeInference.
Prevalence, Predictors, and Successful Treatment Outcomes of Xpert MTB/RIF–identified Rifampicin-resistant Tuberculosis in Post-conflict Eastern Democratic Republic of the Congo, 2012–2017: A Retrospective Province-Wide Cohort Study
Authors: Bulabula André N H , Nelson Jenna A , Musafiri Eric M , Machekano Rhoderick , Sam-Agudu Nadia A , Diacon Andreas H , Shah Maunank , Creswell Jacob , Theron Grant , Warren Robin M , Jacobson Karen R , Chirambiza Jean-Paul , Kalumuna Dieudonné , Bisimwa Bertin C , Katoto Patrick D M C , Kaswa Michel K , Birembano Freddy M , Kitete Liliane , Grobusch Martin P , Kashongwe Zacharie M , Nachega Jean B 
Published: December 2018

Abstract

Background
Multidrug-resistant tuberculosis (MDR-TB) jeopardizes global TB control. The prevalence and predictors of Rifampicin-resistant (RR) TB, a proxy for MDR-TB, and the treatment outcomes with standard and shortened regimens have not been assessed in post-conflict regions, such as the South Kivu province in the eastern Democratic Republic of the Congo (DRC). We aimed to fill this knowledge gap and to inform the DRC National TB Program.

Methods
of adults and children evaluated for pulmonary TB by sputum smear microscopy and Xpert MTB/RIF (Xpert) from February 2012 to June 2017. Multivariable logistic regression, Kaplan–Meier estimates, and multivariable Cox regression were used to assess independent predictors of RR-TB and treatment failure/death.

Results
Of 1535 patients Xpert-positive for TB, 11% had RR-TB. Independent predictors of RR-TB were a positive sputum smear (adjusted odds ratio [aOR] 2.42, 95% confidence interval [CI] 1.63–3.59), retreatment of TB (aOR 4.92, 95% CI 2.31–10.45), and one or more prior TB episodes (aOR 1.77 per episode, 95% CI 1.01–3.10). Over 45% of RR-TB patients had no prior TB history or treatment. The median time from Xpert diagnosis to RR-TB treatment initiation was 12 days (interquartile range 3–60.2). Cures were achieved in 30/36 (83%) and 84/114 (74%) of patients on 9- vs 20/24-month MDR-TB regimens, respectively (P = .06). Predictors of treatment failure/death were the absence of directly observed therapy (DOT; adjusted hazard ratio [aHR] 2.77, 95% CI 1.2–6.66) and any serious adverse drug event (aHR 4.28, 95% CI 1.88–9.71).

Conclusions
Favorable RR-TB cure rates are achievable in this post-conflict setting with a high RR-TB prevalence. An expanded Xpert scale-up; the prompt initiation of shorter, safer, highly effective MDR-TB regimens; and treatment adherence support are critically needed to optimize outcomes.