bluuebunny/crossref_metadata_2025 huggingface dataset:
Teaching CLIL?
Authors: Gierlinger Erwin Maria
Published: July 2017

CLIL (content and language integrated learning) is an educational approach where a classroom subject is taught through a second language. However, its core features are ambiguously interpreted. Research on CLIL teaching has consistently shown that teachers focus their methodological efforts on the teaching of subject matter concepts and take any language related aspects mostly as by-products of such an approach. This has led to only sparsely planned methodological efforts when it comes to the teaching of language. Contrary to this, it is argued in this hermeneutical study that thinking and language acquisition are inextricably intertwined and CLIL teachers are therefore by definition also language teachers. Following this, the author reports on a pedagogical CLIL model, named SALT, that was devised for and successfully implemented in CLIL training courses to support subject teachers on their way to becoming language-aware CLIL teachers. Pedagogical procedures of the model's principles and concepts are also presented.
A sociocognitive model of interventions for writing instruction
Authors: Le Bouthillier Josée
Published: July 2017

This summary reports on an ethnographic study conducted in French immersion concerning the writing development of at-risk and typically developing writers. Eight Grade 7 writers – four at-risk and four typically developing – were observed closely during classroom observations and participated in think-aloud protocols at the beginning and at the end of the school year 2012–2013 as well as in formal and informal interviews. In addition, the context in which those eight writers were learning to write was taken into consideration, therefore a total of 20 students participated in this study. Four teachers, the resource teacher, the counselor, and the two administrators were informants. Adopting a sociocognitive lense, the data reported here provide a detailed description of how the socioaffective, affective, and academic domains affected writing development, especially for at-risk writers. In order to respond to the affective and social needs of the writers of this study, a Sociocognitive Model of Interventions for Writing Instruction is proposed.
How subject animacy constrains motion event descriptions
Authors: Berthaud Sarah , Antonijević Stanislava
Published: July 2017

Research has indicated that during sentence processing, French native speakers predominantly rely upon lexico-semantic cues (i.e., animacy) while native speakers of English rely upon syntactic cues (i.e., word order). The present study examined sentence production in L1 French/L2 English and L1 English/L2 French sequential bilinguals. Participants used animate and inanimate entities as sentence subjects while describing motion events represented by static pictures. To test a gradual change in animacy cue weighting in second-language sequential bilinguals with different proficiency levels were included. Sentence production of sequential bilinguals was compared against that of simultaneous bilinguals. The results indicated an overall preference for the use of animate subjects for both languages at all proficiency levels. The effect of animacy was stronger for English L2 than French L2 while it did not differ between languages in simultaneous bilinguals. Evidence for potential change in the animacy-cue weighting was only observed for English L2.
Obstetric complications
Authors: Doumouchtsis Stergios K. , Arulkumaran S. , Chandraharan Edwin , Coroyannakis Christina , Ghai Vishalli , Hordern Claire , Morris Edward , Mukhopadhyay Sambit , Shehata Hassan , Shehata Mishkat , Tamizian Onnig
Published: July 2017

This chapter explores obstetric complications during pregnancy, including leakage of fluid, bleeding in late pregnancy, leg pain and swelling, fainting episodes, pyrexia, painful uterine contractions, abnormal vaginal discharge, frequency of micturition, and acute retention of urine.
Complications associated with complex psychosocial needs
Authors: Doumouchtsis Stergios K. , Arulkumaran S. , Doumouchtsi Joanna Bécares , Dominguez-Hernandez Jonathan , Osbourne Astrid
Published: July 2017

This chapter presents information and management options for complications in pregnancy associated with complex psychological needs. These include alcohol and substance misuse, detection of violence against women and children, and safeguarding children.
Abnormal menses and bleeding
Authors: Doumouchtsis Stergios K. , Arulkumaran S. , Mahmood Tahir
Published: July 2017

This chapter discusses abnormal menses and bleeding. It explores the physiological basis of menstrual bleeding, and the causes, investigations, and management of abnormal uterine bleeding, heavy menstrual bleeding (HMB), and dysmenorrhoea (period pains).
Phylogenetic inferences on the systematics of squaliform sharks based on elasmobranch scapular morphology (Chondrichthyes: Elasmobranchii)
Authors: Da Silva João Paulo C B , Vaz Diego F B , de Carvalho Marcelo R
Published: July 2017

The scapulae of elasmobranchs project dorsolaterally from their fusion with the coracoid bar of the pectoral girdle, serving as anchoring points for the cucullaris, trunk and appendicular muscles and as articular points for the pectoral-fin skeleton. The scapulae of many elasmobranch taxa are described, with an emphasis on variations in the posterior margin, in an effort to reveal characters of phylogenetic relevance. In particular, phylogenetic information from the scapula was found for some squaliform sharks. Representatives of Dalatiidae, Somniosidae, Oxynotidae and Etmopteridae have a process on the ventral third of the posterior margin of the scapula, providing an additional surface for anchoring the origin of the appendicular muscle: the levator pectoralis. The ventral scapular process in Dalatiidae, Somniosus and Etmopterus is remarkably developed. This contrasts with an absent or weakly developed ventral triangular process observed in remaining squaliforms and other shark taxa. A single dorsal projection of the scapulae is restricted for Carcharhinidae and Centrophorus and provides an additional anchoring point for the m. epaxialis. Most representatives of Somniosidae (except Somniosus), Trigonognathus and some genera of Scyliorhinidae, Proscylliidae and Triakidae have both dorsal and ventral triangular processes. These structures are described and discussed in the context of previous morphological and molecular phylogenies of elasmobranchs.
Physical Activity Interventions for Children with Social, Emotional, and Behavioral Disabilities—A Systematic Review
Authors: Ash Tayla , Bowling April , Davison Kirsten , Garcia Jeanette
Published: July 2017

Objective:

Perform a systematic review of the available literature regarding the effectiveness of exercise interventions on children with any type of social, emotional, or behavioral disability (SEBD), with attention to a range of physiological, behavioral, and mood outcomes.

Methods:

Six databases were searched using a systematic methodology. References of included studies, as well as relevant reviews, were also examined. The review was limited to studies published since 2000 reporting a quantitative analysis of the effects of a physical activity (PA) intervention on at least 1 behavioral, psychological, or cognitive outcome in children aged 21 and under, diagnosed with a SEBD. Only studies with a control group were included.

Results:

We identified 24 eligible studies. Studies varied in design, participant characteristics, and intervention characteristics (single-bout vs repeated exposure, duration, intensity level, mode of exercise). Of the 20 behavioral outcome assessments, there was 1 negative finding, 12 null findings, 5 positive findings, and 2 mixed findings. For the 25 executive functioning outcome assessments, there were 5 null findings, 18 positive findings, and 2 mixed findings. For the remaining outcome domains, 1 of 2 studies looking at academic performance, 3 of 6 studies looking at objective neurological measures, and 1 of 3 studies looking at affect outcomes found positive results. All other results were null or mixed.

Conclusion:

Although additional research is warranted to further understand the mechanisms by which PA affects behavioral and cognitive outcome measures in children with SEBDs, PA offers a safe and alternative form of treatment for this population.
Associations Between Maternal Mental Health and Well-being and Physical Activity and Sedentary Behavior in Children
Authors: Maher Jaclyn P. , Ra Chaelin , O'Connor Sydney G. , Belcher Britni R. , Leventhal Adam , Margolin Gayla , Dunton Genevieve F.
Published: July 2017

Objective:

This study assessed whether aspects of maternal mental health and well-being were associated with objective monitor-based measures of child's physical activity (PA) and sedentary behavior (SB) and the extent to which household structure (i.e., single- vs multigenerational/dual-parent) and maternal employment (i.e., full-time vs not full-time) moderated those associations.

Methods:

Dyads (N = 191) of mothers and their 8- to 12-year-old children participated in the baseline wave of the Mother's and Their Children's Health study. Mothers (Mage= 40.9 yr [SD = 6.1]; 49% Hispanic) completed a battery of questionnaires to assess maternal mental health and well-being (i.e., self-esteem, life satisfaction, depressive symptoms, anxiety, perceived stress, parenting stress, financial stress, and life events stress). Children (Mage= 9.6 yr [SD = 0.9]; 54% Hispanic; 51% girls) wore an accelerometer across 1 week during waking hours to objectively measure moderate-to-vigorous PA (MVPA) and SB.

Results:

In single-parent families (n = 47), but not multigenerational/dual-parent families, mothers' parenting stress was negatively associated with child's MVPA (β = −.34,p= .02). In corrected analyses, all other aspects of maternal mental health and well-being were not related to children's activity patterns.

Conclusion:

Parenting stress was the only maternal mental health variable associated with objective monitor-based measures of child's PA after adjusting for multiple comparisons. Results indicated weaker associations between maternal mental health and well-being and child's MVPA and SB than previously identified using subjective measures of behavior. Study findings support the need to use objective measurements of child's activity patterns to minimize potential confounding because of maternal report in evaluating child's PA and SB.
Validation of the English Version of the HeartQoL Health-Related Quality of Life Questionnaire in Patients With Coronary Heart Disease
Authors: Oldridge Neil , Cho Chris , Thomas Randal , Low Murray , Höfer Stefan
Published: July 2017

Purpose:

The aim of this study was to validate the English version of the HeartQoL health-related quality of life questionnaire for use in patients with angina or myocardial infarction.

Methods:

Patients living in the United States and referred, either for percutaneous coronary intervention or to cardiac rehabilitation, completed the HeartQoL, the Short Form-36 Health Survey, and the Hospital Anxiety and Depression Scale at baseline and 3-months later. The data were analyzed for validity, reliability, and responsiveness.

Results:

Patients (n = 313 with angina and n = 97 with myocardial infarction) who were referred either for percutaneous coronary intervention (n = 164) or to cardiac rehabilitation (n = 246) completed baseline questionnaires. Patients with angina had significantly lower HeartQoL scores (poorer health-related quality of life) compared with patients with myocardial infarction. Exploratory factor analysis largely supported the 2-factor structure of the HeartQoL in both diagnoses, but further investigation is warranted. Internal consistency reliability was adequate, convergent validity correlations were significant, and discriminative validity was fully confirmed in patients with angina and largely confirmed in patients with myocardial infarction. Responsiveness was largely confirmed in patients who underwent percutaneous coronary intervention (n = 67) and those referred to cardiac rehabilitation (n = 167) with conventional statistical tests and clinically with the effect size, a standardized measure of change.

Conclusions:

The English HeartQoL health-related quality of life questionnaire is valid, reliable, and responsive in patients with angina and myocardial infarction allowing (1) assessment of baseline, (2) between-diagnosis comparisons, and (3) evaluation of change over time.
Associations of Exercise Tolerance With Hemodynamic Parameters for Pulmonary Arterial Hypertension and for Chronic Thromboembolic Pulmonary Hypertension
Authors: Tsuboi Yasunori , Tanaka Hidekazu , Nishio Ryo , Sawa Takuma , Terashita Daisuke , Nakayama Kazuhiko , Satomi-Kobayashi Seimi , Sakai Yoshitada , Emoto Noriaki , Hirata Ken-ichi
Published: July 2017

Purpose:

Pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTEPH) are the main subgroups of pulmonary hypertension (PH). Despite differences in their etiologies, both diseases are characterized by vascular remodeling, resulting in progressive right heart failure. Noninvasive periodic evaluation of exercise tolerance has become increasingly important. Cardiopulmonary exercise testing (CPET) and a 6-minute walk test (6MWT) are now both recommended for evaluating exercise tolerance, but there is insufficient knowledge about possible differences in the associations of exercise tolerance with right heart catheterization (RHC) data for patients with PAH and CTEPH.

Methods:

A retrospective study was performed with 57 patients with PH (24 with PAH and 33 with CTEPH) all of whom underwent echocardiography, CPET, 6MWT, and RHC.

Results:

For both patients with PAH and CTEPH, peak heart rate during CPET was significantly higher than that from 6MWT, whereas minimum peripheral oxygen saturation during CPET and 6MWT was similar. For patients with PAH, significant correlations were observed between peak

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2 and cardiac index (CI) (r = 0.59; P = .002) and between

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2 slopes and CI (r =−0.46, P = .02), as well as a nonsignificant correlation tendency for peak

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2 and pulmonary vascular resistance (PVR) and for

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2 and PVR (r =−0.39; P = .05; and r = 0.39; P = .06, respectively). For patients with CTEPH, however, a significant correlation was observed only between

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2 slopes and CI (r =−0.38; P = .02).

Conclusion:

PH etiology should be considered when assessing exercise tolerance, whereas CPET can be effective in addition to hemodynamic assessment by means of RHC for periodic evaluation during followup.
Outdoor Reproducibility of a 1-km Treadmill Walking Test to Predict Peak Oxygen Uptake in Cardiac Patients
Authors: Grazzi Giovanni , Chiaranda Giorgio , Myers Jonathan , Pasanisi Giovanni , Lordi Rosario , Conconi Francesco , Mazzoni Gianni
Published: July 2017

Introduction:

The aim of this study was to determine whether the 1-km treadmill walking test, previously developed to predict peak oxygen uptake (

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2peak) in stable cardiac outpatients, could be reproduced outdoors.

Methods:

Fifty male cardiac outpatients performed the 1-km walking test on a treadmill and on a flat track within 1 week.

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2peak was estimated for both testing conditions considering age, height, weight, walking speed, and heart rate.

Results:

Average walking speed was slightly higher during outdoor conditions (5.73 ± 0.77 km/h vs 5.55 ± 0.84 km/h), whereas mean heart rates were similar for both testing conditions (102 ± 18 beats/min vs 103 ± 16 beats/min).

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2peak values for treadmill and outdoor tests were not significantly different (26.4 ± 4.1 mL/kg/min vs 26.8 ± 4.5 mL/kg/min) and were strongly correlated (r = 0.93, P < .0001). The slope and the intercept of the

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2peak values were not different from the line of identity.

Conclusions:

This moderate and perceptually regulated 1-km walking test administered outdoors gives similar results compared with a similar test performed on a treadmill. Therefore,

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2peak can be reasonably estimated using both testing modalities. This suggests that the outdoor 1-km test can be applied for indirect estimations of cardiorespiratory fitness in an outpatient setting.
EVALUATION OF MACULAR ISCHEMIA IN EYES WITH CENTRAL RETINAL VEIN OCCLUSION
Authors: Ghashut Rima , Muraoka Yuki , Ooto Sotaro , Iida Yuto , Miwa Yuko , Suzuma Kiyoshi , Murakami Tomoaki , Kadomoto Shin , Tsujikawa Akitaka , Yoshimura Nagahisa
Published: July 2017

Purpose:

To quantitatively assess macular perfusion status using optical coherence tomography angiography in eyes with aflibercept-treated central retinal vein occlusion and resolved macular edema and to investigate the impact of macular morphology and perfusion status on visual function.

Methods:

This prospective consecutive case series included 23 patients with central retinal vein occlusion. All patients received intravitreal aflibercept injections before analysis. Visual acuity, macular sensitivity, and the macular nonperfusion area (NPA) were evaluated in eyes without macular edema. The macular NPA was evaluated by optical coherence tomography angiography using 3 mm × 3 mm images of the macula. Foveal ellipsoid zone disruption was also analyzed.

Results:

The superficial macular NPA measured 4.15 mm2 ± 0.71 mm2 (95% confidence interval 3.85–4.46), and the deep macular NPA measured 4.23 mm2 ± 0.97 mm2 (95% confidence interval 3.82–4.56). The logarithm of the minimum angle of resolution visual acuity was significantly associated with foveal ellipsoid zone disruption (P = 0.001), the superficial macular NPA (P = 0.015), and the deep macular NPA (P = 0.018). Macular sensitivity correlated negatively with logarithm of the minimum angle of resolution visual acuity (P = 0.007), the superficial macular NPA (P = 0.029), and the deep macular NPA (P = 0.040), but not with the foveal ellipsoid zone disruption (P = 0.435).

Conclusion:

Optical coherence tomography angiography is a novel technique that enables segmented evaluation of the macular perfusion status in eyes with central retinal vein occlusion and provides visual prognostic information. Enlargement of the macular NPA in the superficial and deep layers was significantly correlated with impaired visual acuity and with decreased macular sensitivity in patients with aflibercept-treated central retinal vein occlusion and resolved macular edema.
sNucDrop-Seq: Dissecting cell-type composition and neuronal activity state in mammalian brains by massively parallel single-nucleus RNA-Seq
Authors: Hu Peng , Fabyanic Emily , Zhou Zhaolan , Wu Hao
Published: July 2017

Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues, such as adult mammalian brains, is challenging. Here, we integrate sucrose-gradient assisted nuclear purification with droplet microfluidics to develop a highly scalable single-nucleus RNA-Seq approach (sNucDrop-Seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ~11,000 nuclei isolated from adult mouse cerebral cortex, we demonstrate that sNucDrop-Seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity, but also enables analysis of long non-coding RNAs and transient states such as neuronal activity-dependent transcription at single-cell resolutionin vivo.
Patchwork of contrasting medication cultures across the USA
Authors: Melamed Rachel D. , Rzhetsky Andrey
Published: July 2017

Health care in the United States is markedly heterogeneous, with large disparities in treatment choices and health spending. Drug prescription is one major component of health care—reflecting the accuracy of diagnosis, the adherence to evidence-based guidelines, susceptibility to drug marketing, and regulatory factors. Using medical claims data covering nearly half of the USA population, we have developed a framework to compare prescription rates of 600 popular drugs in 2,334 counties. Our approach uncovers geographically separated sub-Americas, where patients receive treatment for different diseases, and where physicians choose different drugs for the same disease. The geographical variation suggests influences of racial composition, state-level health care laws, and wealth. Some regions consistently prefer more expensive drugs, even when they have not been proven more efficacious than cheaper alternatives. Our study underlines the benefit of aggregating massive information on medical practice into a summarized and actionable form. We hope that our methodology and conclusions will guide policy measures for aligning prescriptions with best-practice guidelines.
Evolution of an enzyme from a solute-binding protein
Authors: Clifton Ben E. , Kaczmarski Joe A. , Carr Paul D. , Gerth Monica L. , Tokuriki Nobuhiko , Jackson Colin J.
Published: July 2017

Much of the functional diversity observed in modern enzyme superfamilies originates from molecular tinkering with existing enzymes1. New enzymes frequently evolve from enzymes with latent, promiscuous activities2, and often inherit key features of the ancestral enzyme, retaining conserved catalytic groups and stabilizing analogous intermediates or transition states3. While experimental evolutionary biochemistry has yielded considerable insight into the evolution of new enzymes from existing enzymes4, the emergence of catalytic activityde novoremains poorly understood. Although certain enzymes are thought to have evolved from non-catalytic proteins5–7, the mechanisms underlying these complete evolutionary transitions have not been described. Here we show how the enzyme cyclohexadienyl dehydratase (CDT) evolved from a cationic amino acid-binding protein belonging to the solute-binding protein (SBP) superfamily. Analysis of the evolutionary trajectory between reconstructed ancestors and extant proteins showed that the emergence and optimization of catalytic activity involved several distinct processes. The emergence of CDT activity was potentiated by the incorporation of a desolvated general acid into the ancestral binding site, which provided an intrinsically reactive catalytic motif, and reshaping of the ancestral binding site, which facilitated enzyme-substrate complementarity. Catalytic activity was subsequently gainedviathe introduction of hydrogen-bonding networks that positioned the catalytic residue precisely and contributed to transition state stabilization. Finally, catalytic activity was enhanced by remote substitutions that refined the active site structure and reduced sampling of non-catalytic states. Our work shows that the evolutionary processes that underlie the emergence of enzymes by natural selection in the wild are mirrored by recent examples of computational design and directed evolution of enzymes in the laboratory.
The control of epistemic curiosity in the human brain
Authors: Ligneul Romain , Mermillod Martial , Morisseau Tiffany
Published: July 2017

Epistemic curiosity (EC) is a cornerstone of human cognition that contributes to the actualization of our cognitive potential by stimulating a myriad of information-seeking behaviours. Yet, its fundamental relationship with uncertainty remains poorly understood, which limits our ability to predict within- and between-individual variability in the willingness to acquire knowledge. Here, a two-step stochastic trivia quiz designed to induce curiosity and manipulate answer uncertainty provided behavioural and neural evidence for an integrative model of EC inspired from predictive coding. More precisely, our behavioural data indicated an inverse relationship between average surprise and EC levels, which depended upon hemodynamic activity in the rostrolateral prefrontal cortex from one trial to another and from one individual to another. Complementary, the elicitation of epistemic surprise and the relief of acute curiosity states were respectively related to ventromedial prefrontal cortex and ventral striatum activity. Taken together, our results account for the temporal evolution of EC over time, as well as for the interplay of EC, prior knowledge and surprise in controlling memory gain.
Parent-progeny imputation from pooled samples for cost-efficient genotyping in plant breeding
Authors: Technow Frank , Gerke Justin
Published: July 2017

The increased usage of whole-genome selection (WGS) and other molecular evaluation methods in plant breeding relies on the ability to genotype a very large number of untested individuals in each breeding cycle. Many plant breeding programs evaluate large biparental populations of homozygous individuals derived from homozygous parent inbred lines. This structure lends itself to parent-progeny imputation, which transfers the genotype scores of the parents to progeny individuals that are genotyped for a much smaller number of loci. Here we introduce a parent-progeny imputation method that infers individual genotypes from index-free pooled samples of DNA of multiple individuals using a Hidden Markov Model (HMM). We demonstrated the method for pools of simulated maize double haploids (DH) from biparental populations, genotyped using a genotyping by sequencing (GBS) approach for 3,000 loci at 0.125xto 4xcoverage. We observed high concordance between true and imputed marker scores and the HMM produced well-calibrated genotype probabilities that correctly reflected the uncertainty of the imputed scores. Genomic estimated breeding values (GEBV) calculated from the imputed scores closely matched GEBV calculated from the true marker scores. The within-population correlation between these sets of GEBV approached 0.95 at 1xand 4xcoverage when pooling two or four individuals, respectively. Our approach can reduce the genotyping cost per individual by a factor up to the number of pooled individuals in GBS applications without the need for extra sequencing coverage, thereby enabling cost-effective large scale genotyping for applications such as WGS in plant breeding.
Physiological factors of importance for load carriage
Authors: Godhe Manne , Helge Torbjoern , Mattsson C. Mikael , Ekblom Oerjan , Ekblom Bjoern
Published: July 2017

The energy expenditure during carrying no load, 20, 35 and 50 kg at two walking speeds, 3 and 5 km/h, was studied in 36 healthy participants, 19 men (30 ± 6 yrs, 82.5 ± 7.0 kg) and 17 women (29 ± 6 yrs, 66.1 ± 8.9 kg). Anthropometric data, leg muscle strength as well as trunk muscle endurance and muscle fibre distribution of the thigh were also obtained. To load the participant a standard backpack filled with extra weight according to the carrying weight tested was used. Extra Load Index (ELI), the oxygen uptake (VO2) during total load over no-load-exercise, was used as a proxy for load carrying ability. In addition to analyzing factors of importance for the ELI values, we also conducted mediator analyzes using sex and long term carrying experience as causal variables for ELI as the outcome value. For the lowest load (20 kg), ELI20, was correlated with body mass but no other factors. Walking at 5 km/h body mass, body height, leg muscle strength and absolute VO2max were correlated to ELI35 and ELI50, but relative VO2max, trunk muscle endurance and leg muscle fibre distribution were not. Sex as causal factor was evaluated in a mediator analyses with ELI50 as outcome. ELI50 at 5 km/h differed between the sexes. The limit for acceptable body load, 40% of VO2max (according to Astrand, 1967), was nearly reached for women carrying 35 kg (39%) and surpassed at 50 kg at 3 km/h, and for men carrying 50 kg at 5 km/h. This difference was only mediated by difference in body mass. Neither muscle fibre distribution, leg muscle strength, trunk muscle endurance and body height nor did absolute or relative VO2max explain the difference. Participants with long term experience of heavy load carrying had significant lower ELI20 and ELI50 values than those with minor or non-experience, but none of the above studied factors could explain this difference. The study showed that body mass and experience of carrying heavy loads are important factors for the ability to carry heavy loads.
zingeR: unlocking RNA-seq tools for zero-inflation and single cell applications
Authors: Van den Berge Koen , Soneson Charlotte , Love Michael I. , Robinson Mark D. , Clement Lieven
Published: July 2017

Dropout in single cell RNA-seq (scRNA-seq) applications causes many transcripts to go undetected. It induces excess zero counts, which leads to power issues in differential expression (DE) analysis and has triggered the development of bespoke scRNA-seq DE tools that cope with zero-inflation. Recent evaluations, however, have shown that dedicated scRNA-seq tools provide no advantage compared to traditional bulk RNA-seq tools. We introduce zingeR, a zero-inflated negative binomial model that identifies excess zero counts and generates observation weights to unlock bulk RNA-seq pipelines for zero-inflation, boosting performance in scRNA-seq differential expression analysis.
Sensitivity to sequential regularities in risky decision making
Authors: Kóbor Andrea , Takács Ádám , Janacsek Karolina , Kardos Zsófia , Csépe Valéria , Nemeth Dezso
Published: July 2017

Probabilistic sequence learning involves a set of robust mechanisms that enable the extraction of statistical patterns embedded in the environment. It contributes to different perceptual and cognitive processes as well as to effective behavior adaptation, which is a crucial aspect of decision making. Although previous research attempted to model reinforcement learning and reward sensitivity in different risky decision-making paradigms, the basic mechanism of the sensitivity to statistical regularities has not been anchored to external tasks. Therefore, the present study aimed to investigate the statistical learning mechanism underlying individual differences in risky decision making. To reach this goal, we tested whether implicit probabilistic sequence learning and risky decision making share common variance. To have a more complex characterization of individual differences in risky decision making, hierarchical cluster analysis was conducted on performance data obtained in the Balloon Analogue Risk Task (BART) in a large sample of healthy young adults. Implicit probabilistic sequence learning was measured by the Alternating Serial Reaction Time (ASRT) task. According to the results, a four-cluster structure was identified involving average risk-taking, slowly responding, risk-taker, and risk-averse groups of participants, respectively. While the entire sample showed significant learning on the ASRT task, we found greater sensitivity to statistical regularities in the risk-taker and risk-averse groups than in participants with average risk-taking. These findings revealed common mechanisms in risky decision making and implicit probabilistic sequence learning and an adaptive aspect of higher risk taking on the BART. Our results could help to clarify the neurocognitive complexity of decision making and its individual differences.
Transient telomerase inhibition alters cell cycle kinetics
Authors: Thompson Connor AH , Gu Alice , Yang Sunny , Mathew Veena , Fleisig Helen B , Wong Judy MY
Published: July 2017

Telomerase is the ribonucleoprotein reverse transcriptase that catalyzes the synthesis of telomeres at the ends of linear human chromosomes and contributes to proper telomere-loop (T-loop) formation. Formation of the T-loop, an obligate step before cell division can proceed, requires the generation of a 3’-overhang on the G-rich strand of telomeric DNA via telomerase or C-strand specific nucleases. Here, we discover telomerase activity is critical for efficient cell cycle progression using transient chemical inhibition by the telomerase inhibitor imetelstat. Telomerase inhibition caused changes in cell cycle kinetics and increased the proportion of cells in G2 phase, suggesting delayed clearance through this checkpoint. Investigating the possible contribution of unstructured telomere ends to these cell cycle distribution changes, we observed that imetelstat treatment induced γH2AX DNA damage foci in a subset of telomerase-positive cells but not telomerase-negative primary human fibroblasts. Chromatin-immunoprecipitation with γH2AX antibodies demonstrated imetelstat treatment-dependent enrichment of this DNA damage marker at telomeres. Notably, the effects of telomerase inhibition on cell cycle profile alterations were abrogated by pharmacological inhibition of the DNA-damage-repair transducer ATM.

Additionally, imetelstat potentiation of etoposide, a DNA-damaging drug that acts preferentially during S/G2 phases of the cell cycle, also depended on functional ATM signaling. Our results suggest that telomerase inhibition delays the removal of ATM-dependent DNA damage signals from telomeres in telomerase-positive cancer cells. This demonstrates for the first time that telomerase activity directly facilitates the progression of the cell cycle through modulation of transient telomere dysfunction signals.
Double insertion of transposable elements provides a substrate for the evolution of satellite DNA
Authors: McGurk Michael P. , Barbash Daniel A.
Published: July 2017

Eukaryotic genomes are replete with repeated sequences, in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequence. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites. The best available population resources, short-read DNA sequences, are often considered to be of limited utility for analyzing repetitive DNA due to the challenge of mapping individual repeats to unique genomic locations. Here we develop a new pipeline called ConTExt which demonstrates that paired-end Illumina data can be successfully leveraged to identify a wide range of structural variation within repetitive sequence, including tandem elements. Analyzing 85 genomes from five populations ofDrosophila melanogasterwe discover that TEs commonly form tandem dimers. Our results further suggest that insertion site preference is the major mechanism by which dimers arise and that, consequently, dimers form rapidly during periods of active transposition. This abundance of TE dimers has the potential to provide source material for future expansion into satellite arrays, and we discover one such copy number expansion of the DNA transposonHoboto ~16 tandem copies in a single line. The very process that defines TEs —transposition— thus regularly generates sequences from which new satellites can arise.
Genome-wide association mapping and genomic prediction unravels CBSD resistance in aManihot esculentabreeding population
Authors: Kayondo Siraj Ismail , Pino Del Carpio Dunia , Lozano Roberto , Ozimati Alfred , Wolfe Marnin , Baguma Yona , Gracen Vernon , Samuel Offei , Ferguson Morag , Kawuki Robert , Jannink Jean-Luc
Published: July 2017

Cassava(Manihot esculentaCrantz), a key carbohydrate dietary source for millions of people in Africa, faces severe yield loses due to two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD). The completion of the cassava genome sequence and the whole genome marker profiling of clones from African breeding programs (www.nextgencassava.org) provides cassava breeders the opportunity to deploy additional breeding strategies and develop superior varieties with both farmer and industry preferred traits. Here the identification of genomic segments associated with resistance to CBSD foliar symptoms and root necrosis as measured in two breeding panels at different growth stages and locations is reported. Using genome-wide association mapping and genomic prediction models we describe the genetic architecture for CBSD severity and identify loci strongly associated on chromosomes 4 and 11. Moreover, the significantly associated region on chromosome 4 colocalises with aManihot glazioviiintrogression segment and the significant SNP markers on chromosome 11 are situated within a cluster of nucleotide-binding site leucine-rich repeat (NBS-LRR) genes previously described in cassava. Overall, predictive accuracy values found in this study varied between CBSD severity traits and across GS models with Random Forest and RKHS showing the highest predictive accuracies for foliar and root CBSD severity scores.
The plant circadian clock influences rhizosphere community structure and function
Authors: Hubbard Charley J. , Brock Marcus T. , van Diepen Linda T.A. , Maignien Loïs , Ewers Brent E. , Weinig Cynthia
Published: July 2017

Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S rRNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs. clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison to clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.
Transfer Learning from Markov models leads to efficient sampling of related systems
Authors: Sultan Mohammad M. , Pande Vijay S.
Published: July 2017

We recently showed that the time-structure based independent component analysis method from Markov state model literature provided a set of variationally optimal slow collective variables for Metadynamics (tICA-Metadynamics). In this paper, we extend the methodology towards efficient sampling of related mutants by borrowing ideas from transfer learning methods in machine learning. Our method explicitly assumes that a similar set of slow modes and metastable states are found in both the wild type (base line) and its mutants. Under this assumption, we describe a few simple techniques using sequence mapping for transferring the slow modes and structural information contained in the wild type simulation to a mutant model for performing enhanced sampling. The resulting simulations can then be reweighted onto the full-phase space using Multi-state Bennett Acceptance Ratio, allowing for thermodynamic comparison against the wild type. We first benchmark our methodology by re-capturing alanine dipeptide dynamics across a range of different atomistic force fields, including the polarizable Amoeba force field, after learning a set of slow modes using Amber ff99sb-ILDN. We next extend the method by including structural data from the wild type simulation and apply the technique to recapturing the affects of the GTT mutation on the FIP35 WW domain.
Relationship between budget allocation and growth of resources at the university libraries of Northern India – a study
Authors: Singh Har , Mahajan Preeti
Published: July 2017

Purpose

The purpose of the study is to find out the budgetary allocation for books and journals (Print and Electronic) and growth of resources during 2003-2004 to 2012-2013. The study also explored the significant/non-significant relationship for budget allocated for books and journals (Print and Electronic) as well as growth of resources across the libraries. This will help the librarians of such universities to build their collection accordingly.

Design/methodology/approach

The data were collected with the help of a structured questionnaire. Moreover, information was obtained from the primary library records such as annual reports, budget estimates, ledgers and also the staff involved in the acquisition section. The hypotheses were tested using chi-square test. The relationship between budgetary allocation and growth of resources amongst the five university libraries during 2003-2004 to 2012-2013 were analysed and discussed.

Findings

Maharishi Dayanand University library had the highest budget for purchase of books (Rs.125 lakh), whereas Panjab University library had the highest budget (Rs.208 lakh) for purchase of journals (Print and Electronic) during 2012-2013. Panjab University library allocated Rs.18 lakh for purchase of books and Rs.208 lakh for purchase of journals (Print and Electronic) during 2012-2013. Punjabi University library allocated 16 lakh for purchase of books and 45 lakh for purchase of journals (Print and Electronic) during 2012-2013. Guru Nanak Dev University library allocated Rs.16.80 lakh as the budget for purchase of books and Rs.8.30 lakh for purchase of journals (Print and Electronic) from 2007-2008 to 2012-2013. Kurukshetra University library allocated Rs.9 lakh for purchase of books during 2010-2011 and 2011-2012, whereas it had allocated Rs.79.20 lakh for purchase of journals (Print and Electronic) during 2008-2009. Maharishi Dayanand University library allocated Rs.125 lakh for purchase of books during 2011-2012 and 2012-2013, whereas it allocated Rs.125 lakh for purchase of journals (Print and Electronic) during 2012-2013.

Research limitations/implications

The study was limited to five universities of Northern India, which comprised Panjab University, Chandigarh (PU); Punjabi University, Patiala (PbiU); Guru Nanak Dev University, Amritsar (GNDU); Kurukshetra University, Kurukshetra (KU); and Maharishi Dayanand University, Rohtak (MDU). The data related to budgetary allocation for resources and growth and cumulative growth of books and journals (print and electronic) during 2003-2004 to 2012-2013 were collected and analysed.

Originality/value

This is the first of its kind of study in these universities, which provides an overview of how much budget was allocated for collection development in these university libraries. The relation between budget allocation and growth of resources were compared, and their significant/non-significant relationship in five university libraries in North India was found.
Self-initiated international career transition: a qualitative case study of Pakistani immigrants to Canada
Authors: Malik Amina Raza , Manroop Laxmikant , Singh Parbudyal
Published: July 2017

Purpose

The purpose of this study is to examine the career transition experiences of three immigrants from Pakistan in Canadian organisations using Nicholson’s four-phase transition cycle.

Design/methodology/approach

A case study approach was used, and data were collected through three in-depth, semi-structured interviews to determine how immigrants experience career transitions in Canadian organisations.

Findings

The findings show that all three participants had almost the same level of expectations before coming to Canada; however, there were significant differences in their career transition experiences. These findings demonstrate that immigrants’ career experiences can be understood and examined through the lens of Nicholson’s transition framework; their expectations and experiences at one stage subsequently affected their experiences at later stages.

Research limitations/implications

A longitudinal research design would be an excellent approach to explore immigrants’ career transition over time.

Practical implications

Organisations hiring skilled immigrants need to be more supportive of their efforts in reducing immigrants’ feeling of underemployment and discrimination.

Originality/value

The study contributes to the immigrant literature by presenting a new way of looking at immigrants’ experiences in Canadian organisations. It also contributes to the career literature by extending the application of Nicholson transition cycle to an underrepresented population (i.e. immigrants) in careers research.
Positioning health professional identity: on-campus training and work-based learning
Authors: Christensen Mette Krogh , Henriksen Jette , Thomsen Kristian Raun , Lund Ole , Mørcke Anne Mette
Published: July 2017

Purpose

Drawing on positioning theory, the purpose of this paper is to characterize the activities and positions of students and supervisors at workplaces and on-campus skills training sites across the higher health professional educations of medicine, sports science, and nursing. Furthermore, the study explored the impact of work-based learning (WBL) and skills training on students’ personal professional identity development.

Design/methodology/approach

A qualitative case study was conducted across six workplace sites and three on-campus skills training sites with 20 days of observation and 21 in-depth interviews. The data were inductively analyzed resulting in the identification of 12 characteristic narratives. This was followed by abductive analysis using Harré’s concept of positioning as the theoretical framework.

Findings

Across the three higher health professional educations, work-based and on-campus skills training sites were characterized by two learning spaces with distinct positions, rights, and duties. The WBL sites gave the students rich opportunities to position themselves, act independently, and behave as professionals seriously striving for mastery. On the on-campus sites, the students behaved less seriously, and were conscious of their rights to try out things, get support, and have fun.

Research limitations/implications

The authors recommend that future studies explore aspects of professional identity formation due to its consequences for curriculum design, including the distribution of simulated spaces and professional spaces in students’ learning environments.

Originality/value

This study adds to the empirical evidence and conceptual frameworks of personal and shared professional identity development in the field of skills and WBL, and it underlines the ongoing value of Harré’s positioning theory in educational research.