bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Kinase D2 Protects against Acute Colitis Induced by Dextran Sulfate Sodium in Mice
Authors: Xiong Jing , Zhou Ming-feng , Wang Ya-dong , Chen Li-ping , Xu Wan-fu , Wang Yao-dong , Deng Fan , Liu Si-de 
Published: September 2016

AbstractInflammatory bowel disease is characterized by dysregulation of the mucosal immune system resulting from impaired intestinal epithelial barrier function. Protein kinase D2 has been implicated in the regulation of immune responses. The present study was to define PKD2 might affect murine colitis. Colitis was induced in wild-type mice (PKD2WT/WT) and PKD2 catalytic activity deficient mice (PKD2SSAA/SSAA) with dextran sulfate sodium. PKD2SSAA-knockin mice displayed catalytic activity deficiency and increased susceptibility to DSS-induced colitis with enhanced weight loss, colonic inflammation compared with PKD2WT/WTmice. Furthermore, crucial inflammatory cytokines mRNA levels in PKD2SSAA-knockin mice were higher than controls accompanied with down-regulation of ZO-1, MUC2 and intestinal barrier dysfunction. However, there were no differences in the proliferation or apoptosis of intestinal epithelial cells in PKD2SSAA-knockin mice compared with wild-type controls. In addition, PKD2 expression was repressed in patients with IBD compared with healthy controls. These studies suggested that activation of PKD2 in the colonic epithelium microenvironment may contribute to protect against DSS-induced colitis through regulation of intestinal mucosal immunity and barrier function.
Genome-wide long non-coding RNA screening, identification and characterization in a model microorganism Chlamydomonas reinhardtii
Authors: Li Hui , Wang Yuting , Chen Meirong , Xiao Peng , Hu Changxing , Zeng Zhiyong , Wang Chaogang , Wang Jiangxin , Hu Zhangli 
Published: September 2016

AbstractMicroalgae are regarded as the most promising biofuel candidates and extensive metabolic engineering were conducted but very few improvements were achieved. Long non-coding RNA (lncRNA) investigation and manipulation may provide new insights for this issue. LncRNAs refer to transcripts that are longer than 200 nucleotides, do not encode proteins but play important roles in eukaryotic gene regulation. However, no information of potential lncRNAs has been reported in eukaryotic alga. Recently, we performed RNA sequencing in Chlamydomonas reinhardtii, and obtained totally 3,574 putative lncRNAs. 1440 were considered as high-confidence lncRNAs, including 936 large intergenic, 310 intronic and 194 anti-sense lncRNAs. The average transcript length, ORF length and numbers of exons for lncRNAs are much less than for genes in this green alga. In contrast with human lncRNAs of which more than 98% are spliced, the percentage in C. reinhardtii is only 48.1%. In addition, we identified 367 lncRNAs responsive to sulfur deprivation, including 36 photosynthesis-related lncRNAs. This is the first time that lncRNAs were explored in the unicellular model organism C. reinhardtii. The lncRNA data could also provide new insights into C. reinhardtii hydrogen production under sulfur deprivation.
The conservative behavior of dissolved organic carbon in surface waters of the southern Chukchi Sea, Arctic Ocean, during early summer
Authors: Tanaka Kazuki , Takesue Nobuyuki , Nishioka Jun , Kondo Yoshiko , Ooki Atsushi , Kuma Kenshi , Hirawake Toru , Yamashita Youhei 
Published: September 2016

AbstractThe spatial distribution of dissolved organic carbon (DOC) concentrations and the optical properties of dissolved organic matter (DOM) determined by ultraviolet-visible absorbance and fluorescence spectroscopy were measured in surface waters of the southern Chukchi Sea, western Arctic Ocean, during the early summer of 2013. Neither the DOC concentration nor the optical parameters of the DOM correlated with salinity. Principal component analysis using the DOM optical parameters clearly separated the DOM sources. A significant linear relationship was evident between the DOC and the principal component score for specific water masses, indicating that a high DOC level was related to a terrigenous source, whereas a low DOC level was related to a marine source. Relationships between the DOC and the principal component scores of the surface waters of the southern Chukchi Sea implied that the major factor controlling the distribution of DOC concentrations was the mixing of plural water masses rather than local production and degradation.
Automated Proposition Density Analysis for Discourse in Aphasia
Authors: Fromm Davida , Greenhouse Joel , Hou Kaiyue , Russell G. Austin , Cai Xizhen , Forbes Margaret , Holland Audrey , MacWhinney Brian 
Published: September 2016

Purpose
This study evaluates how proposition density can differentiate between persons with aphasia (PWA) and individuals in a control group, as well as among subtypes of aphasia, on the basis of procedural discourse and personal narratives collected from large samples of participants.

Method
Participants were 195 PWA and 168 individuals in a control group from the AphasiaBank database. PWA represented 6 aphasia types on the basis of the Western Aphasia Battery–Revised (Kertesz, 2006). Narrative samples were stroke stories for PWA and illness or injury stories for individuals in the control group. Procedural samples were from the peanut-butter-and-jelly-sandwich task. Language samples were transcribed using Codes for the Human Analysis of Transcripts (MacWhinney, 2000) and analyzed using Computerized Language Analysis (MacWhinney, 2000), which automatically computes proposition density (PD) using rules developed for automatic PD measurement by the Computerized Propositional Idea Density Rater program (Brown, Snodgrass, & Covington, 2007; Covington, 2007).

Results
Participants in the control group scored significantly higher than PWA on both tasks. PD scores were significantly different among the aphasia types for both tasks. Pairwise comparisons for both discourse tasks revealed that PD scores for the Broca's group were significantly lower than those for all groups except Transcortical Motor. No significant quadratic or linear association between PD and severity was found.

Conclusion
Proposition density is differentially sensitive to aphasia type and most clearly differentiates individuals with Broca's aphasia from the other groups.
Role of polyamines in abiotic stress responses.
Authors: Merewitz E. 
Published: September 2016

Abstract
Many secondary metabolites in plants are involved in a range of plant physiological processes including abiotic stress tolerance. Major polyamine (PA) compounds including putrescine (Put), spermidine (Spd) and spermine (Spm) have structural, functional and regulatory activities that allow them to play a major role in abiotic stress tolerance. A thorough understanding of PA function in plant stress tolerance is important for improving plant stress responses, breeding, biomarker development and other purposes. In this review, I discuss the role of PA in several types of abiotic stress and the mechanisms associated with dynamic changes in PA content. Major methods to evaluate PA function are discussed including biosynthetic gene expression, exogenous application of PA, use of PA biosynthesis inhibitors, transgenic manipulation and development of gain or loss of function mutants.
Bivariate relationships incorporating method comparison: a review of linear regression methods.
Authors: Dhanoa M. S. , Sanderson R. , López S. , France J. 
Published: September 2016

Abstract

In this review, we describe and illustrate the selection and use of some appropriate regression models for bivariate statistical relationships. The most commonly used method, ordinary least squares (OLS) or type I regression, may be inappropriate when the predictor variable is subject to measurement errors since this violates a fundamental assumption of OLS and as a result estimates of slope are likely to be biased or attenuated. The
y
-axis intercept will be biased too as it is a function of slope estimate and the means of
y
- and
x
-variables. This bias can have some undesirable consequences if OLS regression parameters and/or functions of them are used further with meaningful interpretations. For example, in animal energy balance studies, slope estimate represents efficiency of metabolizable energy utilization for body mass growth or milk production in dairy cows. The
x
-axis intercept, a function of
y
-intercept and slope, gives an estimate of the animal's body mass maintenance energy requirement. The choice of an alternative type II or functional regression model (e.g. maximum likelihood solution, major axis, reduced major axis and others) depends on the availability and ratio of measurement or precision variances of both
y
- and
x
-variables; otherwise non-parametric models (e.g. Theil-Sen non-parametric regression or Bartlett's three-group method) can be used. When the ratio of
y
- and
x
-variable error variances is not constant over the data range then the reiterated weighted functional model as described by Ripley and Thompson in 1987 may be necessary. Application of these models and other tests (e.g. mean-square prediction error, analysis of concordance) in analytical method comparisons is outlined. Data scrutiny and outlier diagnostics are included because outliers affect most of the non-robust statistics.
Comparative analysis of Physics master degree curricula across national and institutional settings: manifestations of student‐centred learning and implications for degree comparability
Authors: Sin Cristina 
Published: September 2016

AbstractThe paper examines comparatively the curricula of six Physics MSc degrees from three countries (England, Portugal and Denmark) in the European policy context driven by the Bologna Process, which advocates degree comparability and student‐centred learning. Degree programme descriptions were analysed and interviews were conducted with students and lecturers from the selected degrees, exploring their teaching and learning practices and experiences. Findings reveal predominantly country‐based differences in degree curriculum regarding students’ freedom to decide their learning path. Curricular flexibility and student input appear high in the English and Danish degrees and low in the Portuguese ones, despite attempts – so far little feasible in practice – to empower students to tailor learning to their interests. In drawing attention to the force of national pedagogic traditions in shaping curricula, the paper has implications for the degree comparability and student mobility advocated by recent European higher education reforms.
The Myth of the ‘Unfinished’ and the Film Das Dreimäderlhaus (1958)
Authors: Lindmayr-Brandl Andrea 
Published: September 2016

Abstract
Schubert’s ‘Unfinished’ Symphony has fascinated the musical world not only by its beauty but also through its rediscovery in the 1860s and the myths that have evolved around its composition. Firstly there is the rumour of a ‘hidden’ symphony—an accusation that goes back to Kreißle von Hellborn, who blamed the Hüttenbrenner brothers of holding back the most precious ‘perls’ of Schubert’s oeuvre. Secondly, there is a mystical relation to Beethoven which recurred in popular literature on Schubert, culminating in a scene of the film Das Dreimäderlhaus (1958) in which we see Schubert abandoning the composition of the symphony at the same time Beethoven was considered definitely to be deaf. Finally, the ‘Unfinished’ retains the nimbus of being a Sterbefragment—a work that was not finished because the composer died while working on it. Collectively, these myths form an important part of its reception history and contributed to its fame.
‘Die Wegweiser’—Signposts on an Accompanist’s Journey to Scholarship
Authors: Johnson Graham 
Published: September 2016

Abstract
This essay explores the relationship that has evolved across my career between musicology and the accompanist’s practice of performing and comprehending Schubert’s songs. It traces the path my own engagement with Schubert’s Lieder has taken, coordinated with the development of Schubert scholarship in this time, from the early impact of Eusebius Mandyczewski and later Otto Erich Deutsch, to the transformative work of Walter Dürr and the Neue Schubert-Ausgabe. I evaluate the ways in which Dürr’s work in particular has changed the way I approach Schubert’s music, pay tribute to the transformation of the Schubertian landscape that the Neue Schubert-Ausgabe has engineered, and offer reflections on the common causes that bind performers and Schubert scholars together.
“He knows the Koran by heart”
Authors: Einboden Jeffrey 
Published: September 2016

Abstract
The final chapter, reaching up to the Civil War and its immediate aftermath, focuses on Ralph Waldo Emerson, mapping the wide expanse between his public image and private practice. Emerson, a celebrated icon of American exceptionalism and philosopher of American Romanticism, is here revealed also as America’s most prolific translator of Islamic verse, rendering more than two thousand lines of Persian poetry through German sources. Scribbled through diaries, letters, even on the backs of envelopes, Emerson’s early appeal to the Qur’ān, and his later translations of Sufi poets—especially Muḥammad Shamsuddīn Ḥāfiẓ—are shown to have shaped Emerson’s own poetic identity, while also promoting his posthumous legacy.
Evolutionary conservation of Ebola virus proteins predicts important functions at residue level
Authors: Arslan Ahmed , van Noort Vera 
Published: September 2016

Abstract

Motivation
The recent outbreak of Ebola virus disease (EVD) resulted in a large number of human deaths. Due to this devastation, the Ebola virus has attracted renewed interest as model for virus evolution. Recent literature on Ebola virus (EBOV) has contributed substantially to our understanding of the underlying genetics and its scope with reference to the 2014 outbreak. But no study yet, has focused on the conservation patterns of EBOV proteins.

Results
We analyzed the evolution of functional regions of EBOV and highlight the function of conserved residues in protein activities. We apply an array of computational tools to dissect the functions of EBOV proteins in detail: (i) protein sequence conservation, (ii) protein–protein interactome analysis, (iii) structural modeling and (iv) kinase prediction. Our results suggest the presence of novel post-translational modifications in EBOV proteins and their role in the modulation of protein functions and protein interactions. Moreover, on the basis of the presence of ATM recognition motifs in all EBOV proteins we postulate a role of DNA damage response pathways and ATM kinase in EVD. The ATM kinase is put forward, for further evaluation, as novel potential therapeutic target.

Availability and Implementation
http://www.biw.kuleuven.be/CSB/EBOV-PTMs

Supplementary information
Supplementary data are available at Bioinformatics online.
3rd European Evidence-based Consensus on the Diagnosis and Management of Crohn’s Disease 2016: Part 2: Surgical Management and Special Situations
Authors: Gionchetti Paolo , Dignass Axel , Danese Silvio , Magro Dias Fernando José , Rogler Gerhard , Lakatos Péter Laszlo , Adamina Michel , Ardizzone Sandro , Buskens Christianne J. , Sebastian Shaji , Laureti Silvio , Sampietro Gianluca M. , Vucelic Boris , van der Woude C. Janneke , Barreiro-de Acosta Manuel , Maaser Christian , Portela Francisco , Vavricka Stephan R. , Gomollón Fernando ,   on behalf of ECCO
Published: September 2016

Abstract
This paper is the second in a series of two publications relating to the European Crohn’s and Colitis Organisation [ECCO] evidence-based consensus on the diagnosis and management of Crohn’s disease [CD] and concerns the surgical management of CD as well as special situations including management of perianal CD and extraintestinal manifestations. Diagnostic approaches and medical management of CD of this ECCO Consensus are covered in the first paper [Gomollon et al. JCC 2016].
No adverse effects detected for simultaneous whole-body exposure to multiple-frequency radiofrequency electromagnetic fields for rats in the intrauterine and pre- and post-weaning periods
Authors: Shirai Tomoyuki , Wang Jianqing , Kawabe Mayumi , Wake Kanako , Watanabe So-ichi , Takahashi Satoru , Fujiwara Osamu 
Published: September 2016

Abstract
In everyday life, people are exposed to radiofrequency (RF) electromagnetic fields (EMFs) with multiple frequencies. To evaluate the possible adverse effects of multifrequency RF EMFs, we performed an experiment in which pregnant rats and their delivered offspring were simultaneously exposed to eight different communication signal EMFs (two of 800 MHz band, two of 2 GHz band, one of 2.4 GHz band, two of 2.5 GHz band and one of 5.2 GHz band). Thirty six pregnant Sprague-Dawley (SD) 10-week-old rats were divided into three groups of 12 rats: one control (sham exposure) group and two experimental (low- and high-level RF EMF exposure) groups. The whole body of the mother rats was exposed to the RF EMFs for 20 h per day from Gestational Day 7 to weaning, and F1 offspring rats (46–48 F1 pups per group) were then exposed up to 6 weeks of age also for 20 h per day. The parameters evaluated included the growth, gestational condition and organ weights of the dams; the survival rates, development, growth, physical and functional development, memory function, and reproductive ability of the F1 offspring; and the embryotoxicity and teratogenicity in the F2 rats. No abnormal findings were observed in the dams or F1 offspring exposed to the RF EMFs or to the F2 offspring for any of the parameters evaluated. Thus, under the conditions of the present experiment, simultaneous whole-body exposure to eight different communication signal EMFs at frequencies between 800 MHz and 5.2 GHz did not show any adverse effects on pregnancy or on the development of rats.
On the surface physics affecting solar oscillation frequencies
Authors: Houdek G. , Trampedach R. , Aarslev M. J. , Christensen-Dalsgaard J. 
Published: September 2016

Abstract
Adiabatic oscillation frequencies of stellar models, computed with the standard mixing-length formulation for convection, increasingly deviate with radial order from observations in solar-like stars. Standard solar models overestimate adiabatic frequencies by as much as ∼ 20 μHz. In this Letter, we address the physical processes of turbulent convection that are predominantly responsible for the frequency differences between standard models and observations, also called ‘surface effects’. We compare measured solar frequencies from the Michelson Doppler Imager instrument on the SOlar and Heliospheric Observatory spacecraft with frequency calculations that include 3D hydrodynamical simulation results in the equilibrium model, non-adiabatic effects, and a consistent treatment of the turbulent pressure in both the equilibrium and stability computations. With the consistent inclusion of the above physics in our model computation, we are able to reproduce the observed solar frequencies to ≲3 μHz without the need of any additional ad hoc functional corrections.
Transvaginal Ultrasound Training for OBGYN Residents: Multi-site Randomized Controlled Trial of Educational DVD
Authors: High Brooke , McCurdy Rebekah , Brest Norman , Schnatz Peter , Baxter Jason , Jiang Xuezhi 
Published: September 2016

BACKGROUND:
Despite ongoing advances in radiologic imaging, ultrasound remains the gold standard for most gynecologic diagnoses. Current practice in OB/GYN requires its frequent use and understanding, yet formal training is typically limited. In fact, while most residencies offer organized training in obstetric ultrasound, the education in gynecologic imaging is frequently inadequate, absent or not standardized. The American Institute of Ultrasound in Medicine developed a video called “Gynecology: Beginners Only” to improve resident knowledge and skills for transvaginal ultrasound. We introduced this DVD to residents with the goal of improving competency in gynecologic ultrasound.

METHODS:
Residents were recruited for a multi-site prospective study using the AIUM DVD, “Gynecology: Beginners Only.” All participants completed a pretest on gynecologic ultrasound images and principles. Subsequently, residents were randomly assigned to a viewing or control group. After watching the DVD, the viewers completed an identical posttest. Over a 6–10-month period, residents were encouraged to log ultrasounds on the ACGME case log system. All residents repeated the test at this time, and results were compared to prior results.

RESULTS:
Fifty-seven residents completed the training with a mean pretest score of 9.7 out of 15. The mean number of ultrasounds performed prior to the intervention was 31.5. The mean posttest score immediately after the intervention was improved at 11.2. However, this improvement did not persist as scores were not significantly improved several months later on a follow-up quiz for either the control or viewing groups. Hospital site, residency year, and experience did not appear to play a role in test scores.

DISCUSSION:
OB/GYN residents receive limited education in gynecologic ultrasound despite its frequent use. While residents would likely benefit from a structured curriculum, more research is needed to identify useful learning methods. Although the use of a DVD such as this is simple to implement and cost effective, it does not have a lasting impact on ultrasound knowledge. Exploration of different teaching modalities is necessary to create a more comprehensive training program and should likely include a hands-on component.
“Who Wants to Be an Ob/Gyne?” The Role of Blended Learning and Gaming for the Obstetrics and Gynecology Student: A Randomized Trial
Authors: Sampson Kimberley , Srinivasan Sunayana , Arynova Bakytbubu , Ahmed Seema 
Published: September 2016

BACKGROUND:
We developed a PowerPoint game based on the TV game show, “Who wants to be a Millionaire.” Looking at gaming and blended learning to teach medical students high yield topics using Pearls of Exxcellence essential to practice obstetrics and gynecology.

METHODS:
A prospective study of 78 first and second year medical students. Cohort A: didactic style learning covering dermatological diseases. Cohort B: independent learning packet followed by team gaming activity “Who wants to an Ob/Gyne.” Assessment: Pre and post-course knowledge and Likert scale surveys. Long term retention: repeat testing at 6 months interval.

RESULTS:
Both groups showed significant improvement in learning (P<.001) on pre- and posttest comparison. Blended learning achieved greater pretest to post-test improvement of high statistical significance (P<.001) compared to didactic learning alone. Students in the group randomized to game format rated it higher in create team comradery and overall enjoyment than students participating in the lecture method (P<.001). In addition, students in the blended learning group responded positively that the format had stimulated their interest, and kept them engaged in class content (P<.001). Six months retest the intervention group had greater retention in clinical knowledge scores (1.2±2.6 versus 3.5±1.8; P=.02).

DISCUSSION:
Blended learning incorporating gaming is an effective and acceptable pedagogical alternative to didactic lectures. Showing both an immediate and 6-month retention benefit.