bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells
Authors: Semrau Stefan , Goldmann Johanna , Soumillon Magali , Mikkelsen Tarjei S. , Jaenisch Rudolf , Oudenaarden Alexander van 
Published: August 2016

ABSTRACTGene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measured the gene expression dynamics of retinoic acid driven mESC differentiation using an unbiased single-cell transcriptomics approach. We found that the exit from pluripotency marks the start of a lineage bifurcation as well as a transient phase of susceptibility to lineage specifying signals. Our study revealed several transcriptional signatures of this phase, including a sharp increase of gene expression variability. Importantly, we observed a handover between two classes of transcription factors. The early-expressed class has potential roles in lineage biasing, the late-expressed class in lineage commitment. In summary, we provide a comprehensive analysis of lineage commitment at the single cell level, a potential stepping stone to improved lineage control through timing of differentiation cues.
Capturing the student user experience (UX) in York and Loughborough University Library buildings
Authors: Burn Katie , Cunningham Matthew , Waller Liz , Walton Emma , Walton Graham 
Published: August 2016

Purpose
– In higher education libraries, the concept of the user experience has increased in profile and importance. The concept of the “student as customer” has generated much debate but there is general agreement that universities need to be more successful in meeting student expectations. A key strategic area for university libraries has been to adapt and improve their physical spaces to ensure that they are still relevant for today’s students. York and Loughborough University Libraries have both undergone building refurbishments and both are committed to monitoring and reviewing services and spaces. The paper aims to discuss these issues.

Design/methodology/approach
– There were various constraints which very much influenced the methodology. These included: avoiding survey overload no resource allocation an acknowledgement that the methodology employed needed to combine rigour and validity with a pragmatic approach to data collection. A joint project team was established of representatives from each university. A questionnaire created on Google Forms was administered by staff with individuals in the library and entering the data onto a iPad.

Findings
– Findings provide evidence of use across a range of users along with valuable information on who is using our library spaces and for what purpose.

Originality/value
– This research is a rich contribution to the evidence based around student’s learning in universities. It benefits from the expertise and knowledge of two university libraries. As university’s continue to develop learning spaces, this work will enable further investigation around what makes a successful learning space and what makes the library a destination of choice.
The remaining core: a fresh look at religiosity trends in Great Britain
Authors: Wilkins‐Laflamme Sarah 
Published: August 2016

AbstractIn recent years, there has been a growing argument that the end product of secularization may not be a disappearance of all things religious, but rather a polarization between a larger secular group in society and smaller religiously fervent and active communities. Yet, there has been little empirical testing of this theory in contexts of advanced secularization. The aim of this paper is to fill this gap by studying individual belief and religiosity trends over the past four decades in Great Britain, searching specifically for evidence of the population splitting more and more between religious ‘nones’ removed from all forms of religion, and actively religious individuals characterized by strong beliefs and favourable to the public involvement of religion. Analysing descriptive statistics from the 1983–2012 BSAs as well as more detailed models from the 1991, 1998 and 2008 BSAs, we find growing differences in levels of beliefs and attitudes towards public religion between the increasing proportions of unaffiliated and, in recent years and among younger cohorts, more stable proportions of religiously committed individuals. The remaining religiously committed generally have stronger beliefs and more favourable views towards religious leaders influencing politics in 2008 compared with 1991, and the unaffiliated, less favourable views towards public religion.
Age‐Related Differences of Organism‐Specific Peritonitis Rates: A Single‐Center Experience
Authors: Kotera Nagaaki , Tanaka Mototsugu , Aoe Mari , Chikamori Masatomo , Honda Tomoko , Ikenouchi Ayako , Miura Rika , Sugahara Mai , Furuse Satoshi , Saito Katsunori , Mise Naobumi 
Published: August 2016

AbstractPeritonitis remains an important cause of morbidity and mortality in peritoneal dialysis (PD) patients, but its incidence and the distribution of causative organisms vary widely between institutions and age groups. This study was performed to investigate the recent status and risk factors of PD‐related peritonitis and to clarify differences between age groups. We retrospectively reviewed the medical records of 119 PD patients treated at our department between January 2002 and January 2013. We calculated both overall and organism‐specific peritonitis rates and also analyzed risk factors. Sixty‐three episodes of peritonitis occurred during 261.5 patient‐years for an incident rate of 0.24 episodes/patient‐year. Multivariate analysis showed that older age (≥65 years) and hypoalbuminemia (<3.0 g/dL) were associated with an increased risk of peritonitis (P = 0.035 and P = 0.029, respectively). In elderly patients (≥65 years old), the rate of peritonitis due to Gram‐positive and Gram‐negative bacteria was 0.17 and 0.08 episodes/patient‐year, respectively, and Gram‐positive peritonitis was markedly more frequent than in younger patients (<65 years old). In particular, there was a high frequency of Staphylococcus aureus peritonitis in elderly patients (0.09 episodes/patient‐year) and it had a poor outcome. At our department, the risk of peritonitis was increased in older patients and patients with hypoalbuminemia. The distribution of causative organisms was markedly different between age groups and analysis of organism‐specific peritonitis rates helped to identify current problems with our PD program.
Habitat suitability models for the sand lizard Liolaemus wiegmannii based on landscape characteristics in temperate coastal dunes in Argentina
Authors: Block Carolina , Pedrana Julieta , Stellatelli Oscar Aníbal , Vega Laura Estela , Isacch Juan Pablo 
Published: August 2016

AbstractThe knowledge of environmental variables associated with the species occurrence allows the recognition of sites which fulfil ecological requirements eventually used for conservation of species. The coastal dunes of Argentina are inhabited by sand lizards. Anthropic activities have severely degraded this ecosystem, affecting the habitat structure at a large scale. In this context, the effects of landscape characteristics on the sand lizard's (Liolaemus wiegmannii, Liolaemidae) presence were analysed to build habitat suitability maps along the coastal dunes of Argentina. A thematic map of study area was obtained from supervised classification of satellite images to identify landscape characteristics. Surveys were conducted during the lizard activity season, and landscape variables were measured in two spatial units. All information collected was compiled into a Geographic Information System. The relationship between the presence of lizards and landscape variables was evaluated by Generalized Linear Models. The predictions of these models were transferred by using Geographic Information System to habitat suitability maps. Almost all individuals (80%) were observed in semi‐fixed dunes. The analysis of landscape metrics in the two spatial extents showed complementary results. The habitat suitability models suggest that: (i) heterogeneous landscapes composed by disaggregated patches of semi‐fixed dunes and low or null percentages of active dunes distant from the coastline are the preferred environments, and (ii) human modifications such as urbanizations and forestation of dunes, have a negative impact on species occurrence. Suitable habitats were almost absent in those sectors of coastal dunes with highest level of urbanization, whereas they were distributed almost continuously in those areas without human disturbances.
Anxiety and quality of life after first‐trimester termination of pregnancy: a prospective study
Authors: Toffol Elena , Pohjoranta Elina , Suhonen Satu , Hurskainen Ritva , Partonen Timo , Mentula Maarit , Heikinheimo Oskari 
Published: August 2016

AbstractIntroductionPossible effects of termination of pregnancy (TOP) on mental health are a matter of debate.Material and methodsWe assessed anxiety and quality of life during a one‐year follow up after first‐trimester TOP using the State‐Trait Anxiety Inventory (STAI) Scale and EuroQoL Quality of Life Questionnaire (EQ‐5D, EQ‐VAS) in 742 women participating in a randomized controlled trial on early provision of intrauterine contraception. The measurements were performed before TOP, at 3 months and 1 year after TOP. Inclusion criteria were age ≥18 years, residence in Helsinki, duration of gestation <12 weeks, non‐medical indication for TOP, and approval of intrauterine contraception. The trial was registered with Clinical Trials [NCT01223521].ResultsWhen compared with baseline, the overall anxiety level was significantly lower and quality of life higher at 3 months and at 1 year. Reduction of anxiety and improvement of quality of life was especially evident (p < 0.001) in the 58% of women reporting clinically relevant anxiety at baseline. High levels of anxiety at baseline, history of psychiatric morbidity and smoking predicted significantly greater risk of poorer quality of life and elevated level of anxiety during the follow up.ConclusionsTOP is associated with a significant overall reduction of anxiety and an improvement of quality of life among women undergoing it for non‐medical indications. High baseline anxiety, history of psychiatric morbidity and smoking are risk factors of persistently high levels of anxiety and poor quality of life after an induced abortion. These data are important when designing and providing post‐abortion care.
Interpretation of a gas chimney in the Polish Carpathian Foredeep based on integrated seismic and geochemical data
Authors: Marzec Paweł , Sechman Henryk , Kasperska Monika , Cichostępski Kamil , Guzy Piotr , Pietsch Kaja , Porębski Szczepan J. 
Published: August 2016

AbstractGas chimneys are common in offshore petroliferous basins, but little known on land where seismic columnar anomalies are often attributed as poor data quality or processing artefacts. This study utilizes high‐quality 3D seismic data to document a seismic columnar anomaly penetrating through the Miocene heterolithic submarine fan‐deltaic infill of the Carpathian Foredeep. The interpreted gas chimney exhibits vertically clustered velocity push‐down features throughout the attenuated amplitude column accompanied by gas shows in well tests, has its root in gas‐bearing Palaeozoic interval and culminates in an anomalous geochemical gas record at soil level. The chimney system, ca 2 km in height and 500‐m wide, begins above the flank of a rotational bedrock fault‐block and extends vertically along a fault‐controlled conduit. At shallower levels, it passes upwards into amplitude wipeout zones that spread laterally around and partly across thin, gas‐charged reservoirs showing bright spots associated with an AVO response. At shallow levels, gas pathways through muddy slope and deltaic clinoforms are not imaged in low‐fold regions of the seismic volume. The surface geochemical anomalies, in contrast to the microbial methane signature of the Miocene succession, show significant enrichment in higher alkanes and alkenes with C2H6/C3H8 ratios indicative of a deep‐sourced, thermogenic gas or gas condensate. These anomalies form a semi‐enclosed halo around the chimney. Despite the juxtaposition of biogenic and thermogenic methane, the chimney structure imaged on seismic data supports a causal link of gases derived from Palaeozoic source rocks ascending to the surface.
Evaluation of dynamic fracture toughness parameters of locomotive axle steel by instrumented Charpy impact test
Authors: Sorochak A. P. , Maruschak P. O. , Yasniy O. P. , Vuherer T. , Panin S. V. 
Published: August 2016

AbstractThe analysis of the energy of fracture of specimens from steel OSL, which is widely used for the manufacture of railway axles under shock loading, is performed. The nature and quantitative parameters of the typical stages of the processes of plastic and brittle fracture, depending on the test temperature and stiffness of the stress state at the tip of the crack‐like defect, are established. It is shown that impact loading at 20 °C leads to the formation of the local zone of plasticity and ductile–brittle fracture of the material. An increased stiffness of the stress state at the tip of the defect at −40 °C causes brittle fracture. An approach is developed, which is based on using the size of shear lips as a quantitative parameter of fracture under normal and low temperatures, similar in its physical essence to deformation approaches of nonlinear fracture mechanics. Based on this approach and the quantitative analysis of specimen fracture zones, the physical and mechanical scheme of specimen fracture is proposed in the presence of localized plasticity and in its absence near the tip of the concentrator.
Mechanistic variables can enhance predictive models of endotherm distributions: the American pika under current, past, and future climates
Authors: Mathewson Paul D. , Moyer‐Horner Lucas , Beever Erik A. , Briscoe Natalie J. , Kearney Michael , Yahn Jeremiah M. , Porter Warren P. 
Published: August 2016

AbstractHow climate constrains species’ distributions through time and space is an important question in the context of conservation planning for climate change. Despite increasing awareness of the need to incorporate mechanism into species distribution models (SDMs), mechanistic modeling of endotherm distributions remains limited in this literature. Using the American pika (Ochotona princeps) as an example, we present a framework whereby mechanism can be incorporated into endotherm SDMs. Pika distribution has repeatedly been found to be constrained by warm temperatures, so we used Niche Mapper, a mechanistic heat‐balance model, to convert macroclimate data to pika‐specific surface activity time in summer across the western United States. We then explored the difference between using a macroclimate predictor (summer temperature) and using a mechanistic predictor (predicted surface activity time) in SDMs. Both approaches accurately predicted pika presences in current and past climate regimes. However, the activity models predicted 8–19% less habitat loss in response to annual temperature increases of ~3–5 °C predicted in the region by 2070, suggesting that pikas may be able to buffer some climate change effects through behavioral thermoregulation that can be captured by mechanistic modeling. Incorporating mechanism added value to the modeling by providing increased confidence in areas where different modeling approaches agreed and providing a range of outcomes in areas of disagreement. It also provided a more proximate variable relating animal distribution to climate, allowing investigations into how unique habitat characteristics and intraspecific phenotypic variation may allow pikas to exist in areas outside those predicted by generic SDMs. Only a small number of easily obtainable data are required to parameterize this mechanistic model for any endotherm, and its use can improve SDM predictions by explicitly modeling a widely applicable direct physiological effect: climate‐imposed restrictions on activity. This more complete understanding is necessary to inform climate adaptation actions, management strategies, and conservation plans.
Origin of dolomites in the Cambrian (upper 3rd‐Furongian) formation, south‐eastern Sichuan Basin, China
Authors: Hou M. C. , Jiang W. J. , Xing F. C. , Xu S. L. , Liu X. C. , Xiao C. 
Published: August 2016

AbstractThe origin of large‐scale ancient dolomite is one of the most hotly debated topics in sedimentology. The Loushanguan group of the upper 3rd‐Furongian Cambrian series on the south‐eastern margin of the Sichuan Basin consists of numerous dolomites, and the origins of these dolomites have never been reported previously although they are probably good hydrocarbon reservoirs. Based on a systematic analysis of petrology, fluid inclusions, carbon and oxygen isotopes, trace elements and rare earth elements (REEs), this study provides some unique insights into the origins of the dolomites. Four dolomite types have been identified in the study area: dolomicrite, fabric‐retentive oolitic dolomite, fabric‐obliterative dolomite and saddle dolomite cement. In the dolomicrite and fabric‐retentive oolitic dolomite, high Sr contents (with respect to the fabric‐obliterative dolomite) and the lack of two‐phase aqueous inclusions suggest that they formed at shallow‐to‐intermediate burial depths at low temperatures (<50–60°C). Carbon and oxygen isotopes and seawater‐like REE+Y characteristics of the dolomicrite and fabric‐retentive oolitic dolomite indicate that the dolomitizing fluids were evaporated seawater or slightly modified seawater. The obliteration of the original sedimentary fabric and relatively low δ18O and Sr values compared to the fabric‐retentive dolomite indicate that fabric‐obliterative dolomite formed at intermediate‐to‐deep burial diagenesis. The chemical composition approaches pure dolomite and the REE+Y characteristics are similar to those of the fabric‐retentive dolomite, indicating that the fabric‐obliterative dolomite was formed due to the recrystallization of the previously formed fabric‐retentive dolomite at elevated burial depths and temperatures. High fluid inclusion homogenization temperatures (115–150°C), low δ18O values, nonplanar‐a crystals and seawater‐like REE+Y characteristics suggest that saddle dolomite cement formed by reprecipitation of dolomite that related to seawater‐driven and deep burial fluid. In the study area, dolomicrite and fabric‐retentive oolitic dolomite may have been formed by penecontemporaneous or seepage‐reflux dolomitization during early‐stage diagenesis. Subsequently, during progressive burial, most of the fabric‐retentive dolomite was converted into fabric‐obliterative dolomite by recrystallization. This study confirms that fabric‐obliterative dolomite was the main dolomite type, and although deeply buried, these Cambrian dolomites most likely have preserved coeval seawater geochemical signals.
Energy‐aware scheduling mandatory/optional tasks in multicore real‐time systems
Authors: Méndez‐Díaz Isabel , Orozco Javier , Santos Rodrigo , Zabala Paula 
Published: August 2016

AbstractReward‐based scheduling of real‐time systems of periodic, preemptable, and independent tasks with mandatory and optional parts in homogeneous multiprocessors with energy considerations is a problem that has not been analyzed before. The problem is NP‐hard. In this paper, a restricted migration schedule is adopted in which different jobs of the same task may execute in different processors and at different power modes but no migration is allowed after the job has started its execution. An objective function to maximize the performance of the system considering the execution of optional parts, the benefits of slowing down the processor, and a penalty for changing the operation frequency is introduced together with a set of constraints that guarantee the real‐time performance of the system. Different algorithms are proposed to find a feasible schedule maximizing the objective function and are compared using synthetic systems of tasks generated following guidelines proposed in previous papers.
Processes underpinning fish species composition patterns in estuarine ecosystems worldwide
Authors: Henriques Sofia , Cardoso Pedro , Cardoso Inês , Laborde Marina , Cabral Henrique N. , Vasconcelos Rita P. 
Published: August 2016

AbstractAimWe present the first global biogeographical regionalization of estuaries, assessing how dispersal limitation and/or environmental filtering mechanisms drive the patterns of fish assemblage composition among and within biogeographical regions.LocationEstuaries worldwide.MethodsA bootstrapped hierarchical cluster analysis was applied to define biogeographical regions based on pairwise beta diversity (βsim) of fish assemblages among 393 estuaries worldwide. Variables representing dispersal limitation and environmental features were used to disentangle the possible effects of assembly processes acting among and within biogeographical regions, through hierarchical partitioning of variation. Finally, we assessed the contribution of species to beta diversity through a method newly developed in this article.ResultsEstuaries were grouped into seven major biogeographical regions explained by geographical dispersal variables. Dissimilarity in species composition within each biogeographical region was mainly determined by ecosystem‐connectivity dispersal variables, with a minor influence of environmental variables (chiefly sea surface temperature). Marine species contributed highly to beta diversity between estuaries but less than expected by chance, whilst freshwater species had low contributions yet also less than expected. Estuarine (i.e. brackish) and diadromous species had low contributions to beta diversity but higher than expected by chance.Main conclusionsFish assemblage composition in estuaries seems to be driven by dispersal limitation processes both among and within biogeographical regions, with only a minor role of environmental filtering evident within biogeographical regions. These findings contrast with the acknowledged importance of environmental variables as drivers of species richness patterns. Irrespective of biogeographical region, the ecosystem affinity of a species determined its contribution to beta diversity between estuaries. The new method presented here offers new opportunities for assessing the effects of taxonomic and functional aspects on beta diversity (βsim) across taxa and ecosystems, and thus contributes to improving knowledge of assembly processes.