bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nongenic cancer-risk SNPs affect oncogenes, tumor suppressor genes, and immune function
Authors: Fagny M. , Platig J. , Kuijjer M.L. , Lin X. , Quackenbush J. 
Published: December 2018

AbstractGenome-wide associations studies (GWASes) have identified many germline genetic variants that are associated with an increased risk of developing cancer. However, how these single nucleotide polymorphisms (SNPs) alter biological function in a way that increases cancer risk is still largely unknown. We used a systems biology approach to analyze the regulatory role and functional associations of cancer-risk SNPs in thirteen distinct tissues. Using data from the Genotype-Tissue Expression (GTEx) project, we performed an expression quantitative trait locus (eQTL) analysis, keeping both cis- and trans-eQTLs, and representing those significant associations as edges in tissue-specific eQTL bipartite networks. We find that each network is organized into highly modular communities that group sets of SNPs together with functionally-related collections of genes. We mapped cancer-risk SNPs to each tissue-specific eQTL network. Although we find in each tissue that cancer-risk SNPs are distributed across the network, they are not uniformly distributed. Rather they are significantly over-represented in a small number of communities. This includes communities enriched for immune response processes as well as communities representing tissue-specific functions. Moreover, cancer-risk SNPs are over-represented in the central “cores” of communities, meaning they are more likely to influence the expression of many genes within the same community, thus affecting biological processes. And finally, we find that cancer-risk SNPs preferentially target oncogenes and tumor suppressor genes, suggesting non-genic mutations may still alter the effects of these key cancer-associated genes. This bipartite eQTL network approach provides a new way of understanding genetic effects on cancer risk and provides a biological context for interpreting the results of GWAS cancer studies.
miRsponge: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules
Authors: Zhang Junpeng , Liu Lin , Xu Taosheng , Xie Yong , Zhao Chunwen , Li Jiuyong , Le Thuc Duy 
Published: December 2018

AbstractBackgroundA microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our knowledge of their complex functions remains limited. Moreover, there is still a lack of miRNA sponge research tools that help researchers to quickly compare their proposed methods with other methods, apply existing methods to new datasets, or select appropriate methods for assisting in subsequent experimental design.ResultsTo fill the gap, we present an R/Bioconductor package, miRsponge, for simplifying the procedure of identifying and analyzing miRNA sponge interaction networks and modules. It provides seven popular methods and an integrative method to identify miRNA sponge interactions. Moreover, it supports the validation of miRNA sponge interactions and the identification of miRNA sponge modules, as well as functional enrichment and survival analysis of miRNA sponge modules.ConclusionsThis package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research.
Inductance analytical calculations of brushless surface-mounted permanent-magnet machines based on energy method
Authors: Ebadi Fatemeh , Mardaneh Mohammad , Rahideh Akbar 
Published: December 2018

Purpose
This paper aims to show the proposed energy method for inductance calculation is valid for any number of poles, phases and any winding layout.

Design/methodology/approach
A two-dimensional (2-D) analytical energy-based approach is presented to calculate self-inductances and mutual inductances of brushless surface-mounted permanent-magnet machines.

Findings
The proposed calculation procedure is valid for brushless permanent-magnet machines with slotted or slotless stator structure. Comparisons between energy method and flux linkage method are presented based on simulation and experimental results. It shows that the energy method has an excellent agreement with the result obtained from finite element method (FEM) and experimental study.

Originality/value
This paper compares energy-based method with flux linkage method and FEM for inductance calculations in slotless and slotted permanent-magnet motors. The relations for inductance calculation are presented which are obtained based on 2-D analytical representation of magnetic field.
Modern lessons’ construction based on the taxonomy of pedagogical objectives and the multiple intelligences theory
Authors: Sedov Sergey Alekseevich 
Published: December 2018

Purpose
Currently, teachers meet difficulties when design the modern classes so that they respond to the requirements of new educational standards. Thus, the purpose of this paper is to justify the algorithm for applying the “foundations” for designing modern classes of different types and varied subject areas.

Design/methodology/approach
The author coordinates the “foundations” of constructing modern occupations in various subject areas on the example of lessons for children mastering the basic level of preparation and higher one. As the basis for building classes in modern conditions, the author considers the taxonomy of the pedagogical goals of B. Bloom and G. Gardner’s theory of multiple intelligences (MI).

Findings
The taxonomy of pedagogical goals can be one of the key foundations in the design of modern occupations of various types; the theory of MI – in the construction of classes of different subject areas. As examples for the argumentation, the author used the educational technologies of “problem education” and “project education.”

Practical implications
This study is a modest contribution to didactics (the science of theories and learning technologies). The results of the research actualize the work of B. Bloom and G. Gardner in the context of modern requirements for the results and content of education in general and vocational schools. The main provisions of the paper should supplement a number of such works where the solution of modern problems in education is built on the traditions and innovations balance.

Originality/value
The algorithm of applying the “foundations” in the modern studies’ planning can be used for lessons of various types and different subject areas. Further, research can be built in the context of interpreting the algorithm and testing its effectiveness using examples of other educational technologies.
Elderly suicide in India
Authors: Patel Avanish Bhai 
Published: December 2018

Purpose
The elderly are facing many problems in the phase of life in the contemporary times. The problem of suicide among the elderly is one of them. The purpose of this paper is to focus on the cause of death due to suicide among the elderly in later life. There are two objectives of the present study. The first objective examines the nature and problem of elderly suicide in Indian society. The second objective explores the factors affecting suicidal tendency among the elderly.

Design/methodology/approach
The data have been collected through two newspapers from January 2013 to April 2013. The content of news items has been analysed through content analysis.

Findings
The study finds out that the factors such as family problems, chronic diseases, poverty, lack of social status and bankruptcy give rise to feeling of committing suicide among the elderly.

Originality/value
This is an original paper.
The use of ultrasound‐indicated cerclage or cervical pessary in asymptomatic twin pregnancies with a short cervix at midgestation
Authors: Fichera Anna , Prefumo Federico , Mazzoni Giorgia , Molinaris Valentina , Zanardini Cristina , Fratelli Nicola , Frusca Tiziana , Sartori Enrico 
Published: December 2018

AbstractIntroductionSpontaneous preterm birth in women with a twin pregnancy is one of the main causes of perinatal mortality and morbidity. Our aim was to review the perinatal outcome of asymptomatic twin pregnancies with a sonographic short cervical length during the second trimester treated with an ultrasound‐indicated cerclage or cervical pessary.Material and methodsRetrospective study on asymptomatic twin pregnancies with a short cervix (≤ 25 mm) at transvaginal ultrasound examination during the second trimester treated with a cervical cerclage or pessary (2001‐2017). The rate of preterm birth < 28, 32 and 34 weeks of gestation, neonatal mortality, neonatal morbidity and composite adverse neonatal outcome were compared in the groups of women treated with cerclage or pessary.ResultsSeventy‐four twin pregnancies underwent a cerclage while a cervical pessary was inserted in 34 women with twins at our Department: 36 women with an ultrasound‐indicated cerclage and 20 with a pessary were included in the analysis. Median gestational age at delivery was higher in women treated with cerclage compared with those with pessary placement (P = .02) and the rate of preterm birth before 34 weeks of gestation was lower in the cerclage group (P = .03). Admissions to the Neonatal Intensive Care Unit were more frequent in pregnancies with pessary (P = .01), the length of admission was longer (P = .005) and composite adverse neonatal outcome occurred more often (P = .03) compared with the cerclage group.ConclusionsUltrasound‐indicated cerclage appears to reduce the rate of preterm birth before 34 weeks of gestation in asymptomatic twin pregnancies with a short cervix during the second trimester, and also the composite adverse neonatal outcome compared with pessary.
The joint role of thyroid function and iodine concentration on gestational diabetes risk in a population‐based study
Authors: Bell Griffith A. , Männistö Tuija , Liu Aiyi , Kannan Kurunthachalam , Yeung Edwina H. , Kim Un‐Jung , Suvanto Eila , Surcel Heljä‐Marja , Gissler Mika , Mills James L. 
Published: December 2018

AbstractIntroductionIodine is essential for thyroid function, and iodine deficiency during pregnancy is common in Europe and the USA. However, no published studies have examined the role of iodine deficiency in the relation between thyroid function and gestational diabetes mellitus (GDM).Material and methodsWe conducted a population‐based, nested case‐control study within the Finnish Maternity Cohort using pregnancy and perinatal outcome data from the Finnish Maternal Birth Register. We randomly selected 224 GDM cases with singleton pregnancies and 224 controls without GDM from all singleton births occurring in Finland during 2012‐2013. Blood was drawn at 10‐14 weeks’ gestation and analyzed for serum iodide, thyroglobulin, and thyroid‐stimulating hormone (TSH) concentrations. Logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CI) of GDM.ResultsVery high thyroglobulin concentration (>95% percentile; >83 μg/L) was not associated with significantly altered odds of GDM compared to those with normal levels (OR 0.41; 95% CI: 0.12, 1.38). High concentrations of TSH were also not associated with increased odds of GDM compared to normal levels of TSH (OR 0.45; 95% CI: 0.06, 3.18). Women in the lowest 5th percentile (<1.58 ng/mL) of iodine did not have increased odds of GDM compared to those with iodide in the highest quartile (OR 0.39; 95% CI: 0.11, 1.35).ConclusionsLow levels of iodide and thyroid function in early pregnancy are not associated with increased risk of GDM in this mildly iodine‐deficient population.
The effects of acupuncture on the secondary outcomes of anxiety and quality of life for women undergoing IVF: A randomized controlled trial
Authors: Smith Caroline A. , de Lacey Sheryl , Chapman Michael , Ratcliffe Julie , Norman Robert J. , Johnson Neil P. , Fahey Paul 
Published: December 2018

AbstractIntroductionStudies have shown in vitro fertilization (IVF) treatment to have a significant impact on women's quality of life. In addition, anxiety is experienced during IVF treatment and prior to knowing the outcome from a treatment cycle. Although support services are available at many IVF clinics, the uptake of these opportunities may not be high. Acupuncture is used by women undertaking IVF treatment in the belief that it improves their reproductive outcomes, and some studies suggest that it may reduce anxiety. The objective of this study was to examine the effects of acupuncture compared with sham acupuncture on quality of life and anxiety for women undergoing an IVF cycle.Material and methodsA multicenter randomized controlled trial was conducted in Australia and New Zealand. Women were eligible if they were aged 18‐42 years, undergoing a fresh IVF cycle and not using acupuncture. Recruitment occurred between June 2011 and October 2015. Women were randomized to acupuncture or a sham acupuncture control group and three treatments were administered, the first treatment between day 6 and 8 of ovarian stimulation, and two treatments were given on the day of embryo transfer. The primary outcome was livebirth. Secondary outcomes included quality of life and anxiety, and were assessed at baseline, on the day of embryo transfer and 14 weeks from trial entry.ResultsIn all, 848 women were randomized to the trial, 608 women underwent an embryo transfer, of which 526 (86%) received all three treatments. Adjusted analysis found that women receiving acupuncture reported reduced anxiety following embryo transfer (mean difference [MD] −1.1, 95% CI −2.2 to −0.1, P = 0.03). Unadjusted analysis of quality of life did not differ between groups following embryo transfer. Adjusted analyses by per protocol found a significant positive change for the acupuncture group for the general health MOS Short Form 36 (SF36) domain (MD 2.6, 95% CI 0.5‐4.7, P = 0.01) following embryo transfer. The benefit was not sustained at 14 weeks (MD 0.1, 95% CI −2.7 to 2.9).ConclusionsAcupuncture may reduce anxiety at embryo transfer. Quality of life did not differ between the groups. Women experience reduced emotional well‐being 3 months following the IVF cycle, highlighting ongoing unmet psycho‐social needs.
Review shows paediatric protracted bacterial bronchitis needs an accurate diagnosis and strictly targeted extended antibiotics
Authors: Korppi Matti 
Published: December 2018

AbstractAimIn 2017, the European Respiratory Society task force stated that protracted bacterial bronchitis (PBB) was a distinct clinical entity and outlined the diagnostic criteria and principles for treatment. However, this guidance was based on data from Australia and the USA. This mini review evaluated the data and addressed the lack of research‐based data from Europe.MethodsWe supplemented the 2017 report by conducting a nonsystematic review of the literature on prolonged wet or productive cough and on PBB in children up to September 2018.ResultsOur review confirmed the lack of European data on PBB. Based on the available literature, and the 2017 European guidance, PBB is a wet or productive cough that lasts for four or more weeks, with no signs or symptoms, known as specific cough pointers, which suggest an underlying illness. PBB usually recovers with appropriate antibiotics for two weeks. Failing that radiological investigations or lung function measurements are needed. If PBB occurs three times over 12 months, then computerised tomography can diagnose bronchiectasis and determine other permanent changes.ConclusionMore data are needed on PBB, especially in Europe. The implementation of PBB may help clinicians to prescribe antibiotics more effectively and reduce their inappropriate use.
The peer relations of pupils with special educational needs in mainstream primary schools: The importance of meaningful contact and interaction with peers
Authors: Pinto Cynthia , Baines Ed , Bakopoulou Ioanna 
Published: December 2018

Background and aimsChildren with special educational needs (SEN) are generally less accepted by peers in school and have fewer friendships than those without SEN. However, little research has examined peer relations across multiple dimensions, relative to severity of need and in relation to classroom experiences and individual behavioural characteristics. This unique study aimed to extend understanding of the peer relations of pupils with differing levels of SEN support relative to children of differing attainment levels without a formally recognized SEN and in relation to levels of social contact in class and teacher ratings of behaviour.SampleThree hundred and seventy‐five 9‐ to 11‐year‐old children recruited from 13 classes in four mainstream primary schools in the south of England. Fifty‐nine pupils had been identified as having a SEN, of which 17 had a statement of SEN.MethodPupil sociometric questionnaires provided a range of peer relations measures and the extent of meaningful contact with peers. Pupil behaviour was rated by teachers using the Pupil Behaviour Rating scales. Analyses examined differences in peer relations measures, pupil behaviour, and meaningful contact across different levels of educational need.ResultsCompared to pupils without SEN, pupils with a statement of SEN had lower levels of peer acceptance, fewer reciprocated friendships, and were less integrated into peer groups. While internalizing behaviours, such as social anxiousness and anxiety, and externalizing behaviours, such as aggression and hyperactivity, were related to peer relations measures, frequency of meaningful contact with peers was more predictive of peer relations measures than either SEN status or behaviour.ConclusionFindings point to the crucial role of meaningful social contact in the classroom for children's relationships with peers. The study advances understanding by highlighting that greater opportunity for meaningful social contact may improve social involvement of, as well as enhance academic outcomes for, pupils with SEN educated in mainstream schools.
Mid Campanian‐Lower Maastrichtian magnetostratigraphy of the James Ross Basin, Antarctica: Chronostratigraphical implications
Authors: Milanese Florencia N. , Olivero Eduardo B. , Raffi María E. , Franceschinis Pablo R. , Gallo Leandro C. , Skinner Steven M. , Mitchell Ross N. , Kirschvink Joseph L. , Rapalini Augusto E. 
Published: December 2018

AbstractThe James Ross Basin, in the northern Antarctic Peninsula, exposes which is probably the world thickest and most complete Late Cretaceous sedimentary succession of southern high latitudes. Despite its very good exposures and varied and abundant fossil fauna, precise chronological determination of its infill is still lacking. We report results from a magnetostratigraphic study on shelfal sedimentary rocks of the Marambio Group, southeastern James Ross Basin, Antarctica. The succession studied covers a ~1,200 m‐thick stratigraphic interval within the Hamilton Point, Sanctuary Cliffs and Karlsen Cliffs Members of the Snow Hill Island Formation, the Haslum Crag Formation, and the lower López de Bertodano Formation. The basic chronological reference framework is given by ammonite assemblages, which indicate a Late Campanian – Early Maastrichtian age for the studied units. Magnetostratigraphic samples were obtained from five partial sections located on James Ross and Snow Hill islands, the results from which agree partially with this previous biostratigraphical framework. Seven geomagnetic polarity reversals are identified in this work, allowing to identify the Chron C32/C33 boundary in Ammonite Assemblage 8‐1, confirming the Late Campanian age of the Hamilton Point Member. However, the identification of the Chron C32/C31 boundary in Ammonite Assemblage 8‐2 assigns the base of the Sanctuary Cliffs Member to the early Maastrichtian, which differs from the Late Campanian age previously assigned by ammonite biostratigraphy. This magnetostratigraphy spans ~14 Ma of sedimentary succession and together with previous partial magnetostratigraphies on Early‐Mid Campanian and Middle Maastrichtian to Danian columns permits a complete and continuous record of the Late Cretaceous distal deposits of the James Ross Basin. This provides the required chronological resolution to solve the intra‐basin and global correlation problems of the Late Cretaceous in the Southern Hemisphere in general and in the Weddellian province in particular, given by endemism and diachronic extinctions on invertebrate fossils, including ammonites. The new chronostratigraphic scheme allowed us to calculate sediment accumulation rates for almost the entire Late Cretaceous infill of the distal James Ross Basin (the Marambio Group), showing a monotonous accumulation for more than 8 Myr during the upper Campanian and a dramatic increase during the early Maastrichtian, controlled by tectonic and/or eustatic causes.
Discrete element modelling of extensional, growth, fault‐propagation folds
Authors: Hardy Stuart 
Published: December 2018

AbstractExtensional fault‐propagation folds are now recognised as being an important part of basin structure and development. They have a very distinctive expression, often presenting an upward‐widening monocline, which is subsequently breached by an underlying, propagating fault. Growth strata, if present, are thought to provide a crucial insight into the manner in which such structures grow in space and time. However, interpreting their stratigraphic signal is neither straightforward nor unique. Both analogue and numerical models can provide some insight into fold growth. In particular, the trishear kinematic model has been widely adopted to explain many aspects of the evolution and geometry of such fault‐propagation folds. However, in some cases the materials/rheologies used to represent the cover do not reproduce the key geometric/stratigraphic features of such folds seen in nature. This appears to arise from such studies not addressing adequately the very heterogenous mechanical stratigraphy seen in many sedimentary covers. In particular, flexural slip between beds/layers is often not explicitly modelled but, paradoxically, it appears to be an important deformation mechanism operative in such settings. Here, I present a 2D discrete element model of extensional fault‐propagation folding which explicitly includes flexural slip between predefined sedimentary units or layers in the cover. The model also includes growth strata and shows how they may reflect the various evolutionary stages of fold and fault growth. When flexural slip is included in the modelling scheme, the resultant breached monoclines and their growth strata are strikingly similar to some of those seen in nature. Results are also compared with those obtained using simple, homogeneous, frictional‐cohesive and elastic cover materials. Both un‐lithified and lithified growth strata are considered and clearly show that, rather than just being passive recorders of structural evolution, growth strata can themselves have an important effect on fault‐related fold growth. Implications for the evolution of and strain within, the resultant growth structures are discussed. A final focus of this study is the relationship that trishear might have with the upward‐widening zone of flexural slip activation away from a fault tip singularity.