bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physicochemical characteristics and toxicity of surface-modified zinc oxide nanoparticles to freshwater and marine microalgae
Authors: Yung Mana M. N. , Fougères Paul-Antoine , Leung Yu Hang , Liu Fangzhou , Djurišić Aleksandra B. , Giesy John P. , Leung Kenneth M. Y. 
Published: November 2017

AbstractBecause of wide applications of surface-modified zinc oxide nanoparticles (ZnO-NPs) in commercial sunscreens and their easiness of being released into water, concerns have been raised over their potential effects on aquatic organisms. This study compared physicochemical properties of silane-coated and uncoated ZnO-NPs to elucidate their toxic potencies toward three freshwater and three marine microalgae. Surfaces of ZnO-NPs (20 nm) were modified by coating with 3-aminopropyltrimethoxysilane (A-ZnO-NPs) that provides the particles with a more hydrophilic surface, or dodecyltrichlorosilane (D-ZnO-NPs) that turns the particles to hydrophobic. Uncoated ZnO-NPs formed larger aggregates and released more Zn2+ than did either of the two coated ZnO-NPs. The three nanoparticles formed larger aggregates but released less Zn2+ at pH 8 than at pH 7. Although sensitivities varied among algal species, A-ZnO-NPs and uncoated ZnO-NPs were more potent at inhibiting growth of algal cells than were D-ZnO-NPs after 96-h exposure to ZnO, uncoated ZnO-NPs, each of the coated ZnO-NPs or ZnSO4 at 10 concentrations ranging from 0.1 to 100 mg/L. The marine diatom Thalassiosira pseudonana exposed to ZnO-NPs, A-ZnO-NPs or D-ZnO-NPs resulted in differential expressions of genes, suggesting that each of the coatings resulted in ZnO-NPs acting through different mechanisms of toxic action.
Encoding of menstrual pain experience with theta oscillations in women with primary dysmenorrhea
Authors: Lee Pin-Shiuan , Low Intan , Chen Yong-Sheng , Tu Cheng-Hao , Chao Hsiang-Tai , Hsieh Jen-Chuen , Chen Li-Fen 
Published: November 2017

AbstractTheta oscillation (4–7 Hz) is well documented for its association with neural processes of memory. Pronounced increase of theta activity is commonly observed in patients with chronic neurogenic pain. However, its association with encoding of pain experience in patients with chronic pain is still unclear. The goal of the present study is to investigate the theta encoding of sensory and emotional information of long-term menstrual pain in women with primary dysmenorrhea (PDM). Forty-six young women with PDM and 46 age-matched control subjects underwent resting-state magnetoencephalography study during menstrual and periovulatory phases. Our results revealed increased theta activity in brain regions of pain processing in women with PDM, including the right parahippocampal gyrus, right posterior insula, and left anterior/middle cingulate gyrus during the menstrual phase and the left anterior insula and the left middle/inferior temporal gyrus during the periovulatory phase. The correlations between theta activity and the psychological measures pertaining to pain experience (depression, state anxiety, and pain rating index) implicate the role of theta oscillations in emotional and sensory processing of pain. The present study provides evidence for the role of theta oscillations in encoding the immediate and sustained effects of pain experience in young women with PDM.
Via mucosa incision EUS-guided sampling for the diagnosis of conventional endoscopic biopsy-negative gastric wall thickening
Authors: Shan Hongbo , Gao Xiaoyan , Luo Guangyu , Xiang Jieqing , Zhong Bilv , Qiu Xiaofang , Lin Shiyong , Li Shuhong , Li Yin , Xu Guoliang , Zhang Rong 
Published: November 2017

AbstractAbnormal thickened lesions of the gastric wall are usually covered with normal mucosa. Conventional endoscopic biopsies often do not yield sufficient positive histological results for clinical treatment. To increase the rate of diagnosis of conventional endoscopic biopsy-negative gastric wall thickening, we used an endoscopic submucosal dissection (ESD)-like sampling method under endoscopic ultrasound (EUS) guidance to obtain tissue of gastric wall-thickening lesions. Between 2012 and 2016, patients with gastric wall thickening (as identified by computed tomography (CT), EUS or other imaging methods that showed no positive findings in repeating conventional endoscopic biopsy) underwent via mucosa incision EUS-guided sampling. Final diagnosis was determined after surgical or biopsy pathology. A total of 10 patients with gastric wall thickening were included in this study. Eight cases received definite results, whereas in two cases the biopsy results were ambiguous and in these two patients poorly differentiated adenocarcinoma was determined by postoperative pathology. The results of the cases presented in this study demonstrated that via mucosa incision EUS-guided sampling provided a complementary option for the diagnosis of conventional endoscopic biopsy-negative gastric wall thickening.
Overexpression of suppressive microRNAs, miR-30a and miR-200c are associated with improved survival of breast cancer patients
Authors: Kawaguchi Tsutomu , Yan Li , Qi Qianya , Peng Xuan , Gabriel Emmanuel M. , Young Jessica , Liu Song , Takabe Kazuaki 
Published: November 2017

AbstractSome microRNAs (miRNAs) are known to suppress breast cancer. However, whether the expressions of these tumor suppressive miRNAs translate to patient survival were not investigated in large cohort. Nine miRNAs (miR-30a, miR-30c, miR-31, miR-126, miR-140, miR-146b, miR-200c, miR-206, and miR-335) known to be tumor suppressive miRNAs in breast cancer were investigated in Genomic Data Common data portal miRNA-Seq dataset and The Cancer Genome Atlas (TCGA) (n = 1052). Of the 9 miRNAs, miR-30a, miR-30c, miR-126, miR-140, miR-206, and miR-335 were found to have significantly lower expression in breast cancer tissues compared to paired normal breast tissue. High expression of miR-30a or miR-200c was associated with significantly better overall survival (OS). Gene Set Enrichment Analysis (GSEA) demonstrated that low expression levels of miR-30a had the tendency to associate with gene enrichment of EMT, while miR-200c did not, in TCGA cohort, and our findings support the need of validation using large cohort to use miRNA as prognostic biomarker for patients with breast cancer.
The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: genome-wide characterization and expression analyses during developmental processes and stress responses
Authors: Grimplet Jérôme , Pimentel Diana , Agudelo-Romero Patricia , Martinez-Zapater Jose Miguel , Fortes Ana Margarida 
Published: November 2017

AbstractLATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies.
Identification of microRNAs as potential cellular monocytic biomarkers in the early phase of myocardial infarction: a pilot study
Authors: Parahuleva Mariana S. , Euler Gerhild , Mardini Amar , Parviz Behnoush , Schieffer Bernhard , Schulz Rainer , Aslam Muhammad 
Published: November 2017

AbstractMicroRNA has been increasingly suggested to be involved in vascular inflammation. The aim of this study was to assess the expression profile of miRs as possible novel cellular biomarkers in circulating monocytes in patients with ST-segment elevation myocardial infarction (STEMI). Microarray techniques and TaqMan polymerase chain reaction were used to analyse the global expression of 352 miRNAs in peripheral blood monocytes from healthy donors (n = 20) and patients (n = 24) with acute STEMI. The expression level of miR-143 in monocytes from STEMI patients compared to healthy controls was increased, whereas the expression of miR-1, -92a, -99a, and -223 was reduced significantly. During 3.5 ± 1.5 months of follow-up miR-1 and -223 were back to baseline, whereas miR-92a and -99a return to normal levels over 3 months, but remained lower than healthy controls. Furthermore, monocytic expression of miR-143 was positively correlated with hs-CRP (R2 = 0.338; P < 0.031), but not with cTnT. Importantly, treatment of monocytes isolated from healthy individuals with INFγ, but not LPS or TNFα caused an upregulation of miR-143 and downregulation of miR-1. Our findings identify circulating monocytes as putative biomarkers and as novel carriers for the cell-specific transfer of miRs in the early phase of myocardial infarction.
Wind speed optimisation method of numerical prediction for wind farm based on Kalman filter method
Authors: Hua Shenbing , Wang Shu , Jin Shuanglong , Feng Shuanglei , Wang Bo 
Published: November 2017

In recent years, with the rapid increase of wind turbine install, the volatility and randomness of wind speed restrict the development of wind power industry. The uncertainty of wind speed forecast has the mainly impact on wind power prediction. The subject of this manuscript is to study the impact of wind speed prediction on wind power prediction. Firstly, The authors compare the observed wind speed in one wind farm with the forecasted wind speed using the 3 km × 3 km Weather Research and Forecast (WRF) model. Then the revised is conducted based on Kalman filter theory. In the revised process, the special and temporal impact of observed wind speed on target wind farm is considered and the reasonable predictive factor matrix is built to lower the systematic and random error. The wind speed data at heights of 10, 30, 50, and 70 m are processed using this revised approach, respectively. It turns out that the correlation coefficient between the wind speed forecast and observation has been raised from 0.48 and 0.47 (no revision) to 0.88 and 0.89 (after revision). The RMSE of wind speed has been decreasing from 3.98 and 4.20 to 1.72 and 1.60 m/s. The accuracy of wind speed forecast has been improved.
Variability of extragalactic sources: its contribution to the link between ICRF and the futureGaiaCelestial Reference Frame
Authors: Taris F. , Damljanovic G. , Andrei A. , Souchay J. , Klotz A. , Vachier F. 
Published: November 2017

Context.The first release of theGaiacatalog is available since 14 September 2016. It is a first step in the realization of the futureGaiareference frame. This reference frame will be materialized by the optical positions of the sources and will be compared with and linked to the International Celestial Reference Frame, materialized by the radio position of extragalactic sources.Aim.As in the radio domain, it can be reasonably postulated that quasar optical flux variations can alert us to potential changes in the source structure. These changes could have important implications for the position of the target photocenters (together with the evolution in time of these centers) and in parallel have consequences for the link of the reference systems.Methods.A set of nine optical telescopes was used to monitor the magnitude variations, often at the same time asGaia, thanks to theGaiaObservation Forecast Tool. The Allan variances, which are statistical tools widely used in the atomic time and frequency community, are introduced.Results.This work describes the magnitude variations of 47 targets that are suitable for the link between reference systems. We also report on some implications for theGaiacatalog. For 95% of the observed targets, new information about their variability is reported. In the case of some targets that are well observed by the TAROT telescopes, the Allan time variance shows that the longest averaging period of the magnitudes is in the range 20−70 d. The observation period byGaiafor a single target largely exceeds these values, which might be a problem when the magnitude variations exhibit flicker or random walk noises. Preliminary computations show that if the coordinates of the targets studied in this paper were affected by a white-phase noise with a formal uncertainty of about 1 mas (due to astrophysical processes that are put in evidence by the magnitude variations of the sources), it would affect the precision of the link at the level of 50μas.
Bedeutung der Abdomen-Sonografie zur Infektfokussuche in der Notaufnahme
Authors: Werkmeister Barbara , Langgartner Julia , Schacherer Doris , Mohr Arno 
Published: November 2017

Zusammenfassung
Einleitung Ein sehr großer Anteil von Patienten, die sich in zentralen Notaufnahmen vorstellen, haben einen unklaren Infekt bzw. Fieber. Sofern eine apparative Diagnostik notwendig ist, bietet sich die Sonografie an. Ob die Sonografie, gerade auch mit Rücksicht auf die in den letzten Jahren deutlich verbesserte Technik, Anamnese und klinischer Untersuchung überlegen ist und damit auch bei fehlender abdomineller Symptomatik, insbesondere bei Patienten mit nicht-offensichtlichem Fokus zur Identifikation desselbigen heranzuziehen ist, kann durch Literaturrecherche alleine nicht beantwortet werden.Ziel dieser Untersuchung war es, die Bedeutung der Sonografie zur abdominellen Infektfokussuche zu evaluieren und zu untersuchen, ob auf eine Sonografie des Abdomens zur Infektfokussuche, bei fehlendem Hinweis auf abdominellen Fokus aus Anamnese und klinischer Untersuchung, verzichtet werden kann.
Methode Es erfolgt eine retrospektive Auswertung aller Patienten, die sich von 4/2013 – 7/2013 in der Zentralen Notaufnahme der Universitätsklinik Regensburg vorgestellt haben und eine Sonografie erhalten haben. In 500 Fällen bezog sich die Fragestellung der Ultraschallanforderung auf eine abdominelle Infektfokussuche. Diese Fälle wurden herausgegriffen und bezüglich eines Hinweises auf einen abdominellen Fokus in der Anamnese und der klinischen Untersuchung evaluiert. Weiter wurden der sonografische Befund selbst, die letztlich gestellte Diagnose, so wie klinische Parameter wie z. B. Infektionszeichen (Laborwerte, Fieber) der Patienten anhand der Patientenakte und des Arztbriefes retrospektiv ausgewertet.
Ergebnis Bei 208 (41,6 %) der 500 untersuchten Fälle fand sich nach Angaben des Arztbriefes ein abdomineller Infektfokus. Bei wiederum 122 (59,0 %) dieser Patienten konnte mittels abdominellem Ultraschall der Infektfokus korrekt nachgewiesen werden. Bei 206 (99,0 %) Patienten konnte bereits in der Anamnese und bei 152 (73,1 %) Patienten konnte in der klinischen Untersuchung ein Hinweis auf einen abdominellen Fokus erhoben werden. In der Subgruppenanalyse von 38 immunsupprimierten Patienten konnte bei 25 Patienten (65,8 %) ein abdomineller Fokus mittels Ultraschall ermittelt werden. Bei Patienten mit negativer Anamnese und gleichzeitig unauffälliger klinischer Untersuchung ergab sich in keinem einzigen Fall (23 Untersuchungen) ein abdomineller Infektfokus in der Sonografie des Abdomens.
Diskussion Bei Patienten, die weder anamnestisch (d. h. vollständige Anamnese möglich) noch klinisch (Klinik beurteilbar, d. h. v. a. keine Immunsuppression) Anhaltspunkte für einen abdominellen Fokus aufweisen, kann auf eine notfallmäßige Sonografie des Abdomens zur Infektfokussuche verzichtet werden.
Medizinischer Pluralismus – was wir aus der Geschichte lernen können
Authors: Jütte Robert 
Published: November 2017

ZusammenfassungWenn jemand vor dem Beginn des Zeitalters der modernen Medizin krank wurde, konnte er unter einem großen Angebot unterschiedlichster Therapeuten wählen. Zu jener Zeit dominierten die approbierten Heiler noch nicht den medizinischen Markt, wenngleich es schon eine Tendenz zur Monopolisierung, die vom Staat begünstigt wurde, gab. Als am Ende des 18. Jahrhunderts Samuel Hahnemann seine neue Heilkunst, die er spä­ter Homöopathie nannte, propagierte, führte das zu einem Bruch in der Ärzteschaft, der noch heute zu spüren ist. Die Homöopathie und nicht eine andere CAM-Therapie bildet nämlich den Lackmustest für den medizinischen Pluralismus.
Tertiärprävention nach Krebs
Authors: Schilling Georgia 
Published: November 2017

ZusammenfassungModerne multimodale Therapieverfahren ermöglichen heute vielen Krebspatienten auch in der metastasierten Situation ein Langzeitüberleben, d.
h. ein Überleben 5 Jahre nach Diagnosestellung. In dieser Zeit nach der Erkrankung können die Patienten durch Lebensstilveränderungen viel
selbst dazu beitragen, dass Zweitkrebserkrankungen oder andere Komorbiditäten, Rezidive oder Langzeitnebenwirkungen verringert bzw.
verhindert werden. Leider hat sich aber am Gesundheitsverhalten der ehemaligen Krebspatienten im Sinne von Tertiärprävention (gesundes
Essen, Gewichtsreduktion, Nikotinabstinenz, körperliche Aktivität) in den letzten Jahren kaum etwas verändert. Es muss also unsere Aufgabe
sein, die Patienten nachhaltig und niederschwellig mit entsprechenden Programmen über die stationären Rehabilitationsmaßnahmen hinaus zu
unterstützen und sie zu einem entsprechenden Gesundheitsverhalten immer wieder aufs Neue zu motivieren.
On translatability from the perspective of Wittgensteinian prototype: translations of “Dao” as exemplars
Authors: Yang Bingjun 
Published: November 2017

ABSTRACTTranslatingDaodejingis quite intricate and prompts much thinking in translation studies. In order to inquire whether translatability is possible and how we should judge what might be a good translation, we explore the issue of translatability from the perspective of Wittgensteinian prototype. Within this perspective, translatability is seen as a category bearing four features: abstractness, integrability, priority, and expansibility. These features not only posit translatability onto a different stage, but also help adequately explain such phenomena as “Dao” in translation. The abstractness suggests that translatability as a category is more than possible. By integrability, it means the translation of a text usually integrates characteristic elements of possible interpretations and understandings. An exemplar which bears many shared features is usually perceived with priority by readers as the good translation. The degree of translatability can be expanded when new translations join in.
Reception and Recomposition in the Polyphonic Conductus cum caudis: The Metz Fragment
Authors: Everist Mark 
Published: November 2017

AbstractA membrane fragment in the Bibliothèque da la Ville de Metz (réserve précieux, MS 732bis/20) contains parts of four works (Premii dilatio, Ego reus confiteor, Sursum corda and one as yet unidentified composition), of which three are known from the Florence manuscript (Biblioteca Medicea-Laurenziana, MS Pluteo 29.1). The notation, decoration and handwriting of the fragment suggest that the manuscript from which they were taken dates from c.1300. The notation of the fragment clearly distinguishes between longae and breves in passages cum littera; in sine littera sections, the graphic presentation of ligatures reveals attempts to reflect changing concepts of notational precision from the last quarter of the thirteenth century. The Metz fragment is therefore analogous with other late thirteenth-century redactions of conducti. Although all four compositions in the Metz fragment are in three parts, concordances for two of the works from earlier thirteenth-century sources are in two parts only. While normal practice in the late thirteenth-century transmission of the conductus was to strip away voices, the versions of Ego reus confiteor and Sursum corda in the Metz fragment added a new third part to a two-part original. Such a practice was more typical of the motet repertory, and in this as well as its use of mensural notation the Metz fragment shows how the conductus was beginning to approach the compositional priorities of the motet c.1300.
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches
Authors: Liu Bin 
Published: November 2017

AbstractWith the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typically, predictors based on machine learning techniques contain three main steps: feature extraction, predictor construction and performance evaluation. Although several Web servers and stand-alone tools have been developed to facilitate the biological sequence analysis, they only focus on individual step. In this regard, in this study a powerful Web server called BioSeq-Analysis (http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/) has been proposed to automatically complete the three main steps for constructing a predictor. The user only needs to upload the benchmark data set. BioSeq-Analysis can generate the optimized predictor based on the benchmark data set, and the performance measures can be reported as well. Furthermore, to maximize user’s convenience, its stand-alone program was also released, which can be downloaded from http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/download/, and can be directly run on Windows, Linux and UNIX. Applied to three sequence analysis tasks, experimental results showed that the predictors generated by BioSeq-Analysis even outperformed some state-of-the-art methods. It is anticipated that BioSeq-Analysis will become a useful tool for biological sequence analysis.
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks
Authors: Avsec Žiga , Barekatain Mohammadamin , Cheng Jun , Gagneur Julien 
Published: November 2017

Abstract

Motivation
Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed.

Results
Here we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances. Modeling distances to various genomic landmarks with spline transformations significantly increased state-of-the-art prediction accuracy of in vivo RNA-binding protein binding sites for 120 out of 123 proteins. We also developed a deep neural network for human splice branchpoint based on spline transformations that outperformed the current best, already distance-based, machine learning model. Compared to piecewise linear transformation, as obtained by composition of rectified linear units, spline transformation yields higher prediction accuracy as well as faster and more robust training. As spline transformation can be applied to further quantities beyond distances, such as methylation or conservation, we foresee it as a versatile component in the genomics deep learning toolbox.

Availability and implementation
Spline transformation is implemented as a Keras layer in the CONCISE python package: https://github.com/gagneurlab/concise. Analysis code is available at https://github.com/gagneurlab/Manuscript_Avsec_Bioinformatics_2017.

Supplementary information
Supplementary data are available at Bioinformatics online.