bluuebunny/crossref_metadata_2025_split huggingface dataset:
LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines
Authors: Seyres Denis , Darbo Elodie , Perrin Laurent , Herrmann Carl , González Aitor 
Published: December 2015

Abstract
Summary: Supervised classification based on support vector machines (SVMs) has successfully been used for the prediction of cis-regulatory modules (CRMs). However, no integrated tool using such heterogeneous data as position-specific scoring matrices, ChIP-seq data or conservation scores is currently available. Here, we present LedPred, a flexible SVM workflow that predicts new regulatory sequences based on the annotation of known CRMs, which are associated to a large variety of feature types. LedPred is provided as an R/Bioconductor package connected to an online server to avoid installation of non-R software. Due to the heterogeneous CRM feature integration, LedPred excels at the prediction of regulatory sequences in Drosophila and mouse datasets compared with similar SVM-based software.
Availability and implementation: LedPred is available on GitHub: https://github.com/aitgon/LedPred and Bioconductor: http://bioconductor.org/packages/release/bioc/html/LedPred.html under the MIT license.
Contact: aitor.gonzalez@univ-amu.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Assessing the Unseen Bacterial Diversity in Microbial Communities
Authors: Caro-Quintero Alejandro , Ochman Howard 
Published: November 2015

Abstract
For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs —that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations.
Dietary Opportunities and Constraints on Islands
Authors: Allen Melinda S. 
Published: December 2015

Abstract
This chapter considers the advantages of islands as analytical units and the benefits of multi-proxy approaches to diet reconstructions. An overview of some common historical trends in Pacific Island diets is provided, followed by more detailed examination of two southern Cook Island sequences (Mangaia and Aitutaki Islands) in Polynesia, localities which were settled by closely related peoples but offered different dietary opportunities given their contrastive geographies. Archaeofaunal, archaeobotanical, and stable isotope records are used to explore dietary variability on these two islands over an approximately 750-year period. The analysis emphasizes the relationships between different dietary components (terrestrial foraging, marine exploitation, and evolving agroeconomies) and the dynamic feedback relationships that can shape dietary change.
Out-of-hospital cardiopulmonary resuscitation strategies using one-handed chest compression technique for children suffering a cardiac arrest
Authors: Jung Gun Hee , Oh Je Hyeok , Kim Chan Woong , Kim Sung Eun , Lee Dong Hoon 
Published: December 2015

Objective
We evaluated the decrease in chest compression depth during 30 : 2 compression-to-ventilation ratio one-handed chest compression (OHCC) in an out-of-hospital pediatric arrest setting, and whether switching hands every other cycle could maintain compression depth.

Methods
A 5-year-old child-sized manikin was used, and 50 medical students participated in the present study. First, the participants performed 5 min OHCC with a 30 : 2 compression-to-ventilation ratio on the floor (baseline test). Second, the compression technique was changed from the OHCC to the two-handed chest compression when they became subjectively fatigued (test 1). Third, the compression hand was alternated every other cycle (test 2). Average compression depth (ACD) data were recorded using an accelerometer device.

Results
ACD changed significantly during the baseline test (0–1 min: 44.5±5.3 mm, 1–2 min: 43.7±6.1 mm, 2–3 min: 43.4±6.5 mm, 3–4 min: 43.2±6.5 mm, and 4–5 min: 42.3±6.5 mm, P=0.012). However, no significant differences were observed during test 1 or test 2. The baseline ACD value for the 4–5-min interval [95% confidence interval (CI), 40.5–44.2 mm] was significantly lower than those in test 1 (95% CI, 43.0–45.9 mm, P=0.004) and test 2 (95% CI, 42.4–45.9 mm, P=0.004). No differences in the ACDs at any interval were observed between test 1 and test 2.

Conclusion
Compression depth decreased significantly after 4 min during 30 : 2 ratio OHCC. However, it was maintained by changing from the OHCC to the two-handed chest compression or by alternating compression hands every other cycle.
Mesoscopic oscillations in a single-gene circuit without delay
Authors: Guisoni N. , Monteoliva D. , Diambra L. 
Published: December 2015

AbstractIt is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of thecis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture plays a key role for oscillatory behavior of gene expression.PACS numbers: 82.40.Bj,87.10.Mn,87.16.-b,87.16.Yc,87.18.Tt,87.18.Vf
Inferring past effective population size from distributions of coalescent-times
Authors: Gattepaille Lucie , Jakobsson Mattias 
Published: December 2015

AbstractInferring and understanding changes in effective population size over time is a major challenge for population genetics. Here we investigate some theoretical properties of random mating populations with varying size over time. In particular, we present an exact method to compute the population size as a function of time using the distributions of coalescent-times of samples of any size. This result reduces the problem of population size inference to a problem of estimating coalescent-time distributions. Using tree inference algorithms and genetic data, we can investigate the effects of a range of conditions associated with real data, for instance finite number of loci, sample size, mutation rate and presence of cryptic recombination. We show that our method requires at least a modest number of loci (10,000 or more) and that increasing the sample size from 2 to 10 greatly improves the inference whereas further increase in sample size only results in a modest improvement, even under as scenario of exponential growth. We also show that small amounts of recombination can lead to biased population size reconstruction when unaccounted for. The approach can handle large sample sizes and the computations are fast. We apply our method on human genomes from 4 populations and reconstruct population size profiles that are coherent with previous knowledge, including the Out-of-Africa bottleneck. Additionally, a potential difference in population size between African and non-African populations as early as 400 thousand years ago is uncovered.
iCOBRA: open, reproducible, standardized and live method benchmarking
Authors: Soneson Charlotte , Robinson Mark D. 
Published: December 2015

AbstractWe present iCOBRA, a flexible general-purpose web-based application and accompanying R package to evaluate, compare and visualize the performance of methods for estimation or classification when ground truth is available. iCOBRA is interactive, can be run locally or remotely and generates customizable, publication-ready graphics. To facilitate open, reproducible and standardized method comparisons, expanding as new innovations are made, we encourage the community to provide benchmark results in a standard format.
Carbon constrains fungal endophyte assemblages along the timberline
Authors: Yang Teng , Weisenhorn Pamela , Gilbert Jack A. , Ni Yingying , Sun Ruibo , Shi Yu , Chu Haiyan 
Published: December 2015

SummaryThe alpha diversity of foliar fungal endophytes (FEs) in leaves of Betula ermanii in a subalpine timberline ecotone on Changbai Mountain, China increased with elevation. There were also significant differences in beta diversity along the elevation gradient. Among the environmental variables analysed, leaf carbon significantly increased with elevation, and was the most significant environmental factor that constrained the alpha and beta diversity in the FE communities. Tree height and the cellulose, lignin, and carbon/nitrogen ratio of the leaves also affected the FE assemblages. When controlled for the effects of elevation, leaf carbon was still the main driver of changes in evenness, Shannon diversity and FE community composition. The results offered clues of the carbon acquisition strategy of the foliar FEs across this cold terrain. There was strong multicollinearity between both annual precipitation and temperature, with elevation (|Pearson r| > 0.986), so the effects of these climatic variables were impossible to separate; however, they may play key roles, and the direct effects of both warrant further investigation. As pioneer decomposers of leaf litter, variations in diversity and community composition of FE measured here may feedback and influence carbon cycling and dynamics in these forest ecosystems.
Impact of OmpR on the membrane proteome of Yersinia enterocolitica in different environments: repression of major adhesin YadA and heme receptor HemR
Authors: Nieckarz Marta , Raczkowska Adrianna , Dębski Janusz , Kistowski Michał , Dadlez Michał , Heesemann Jürgen , Rossier Ombeline , Brzostek Katarzyna 
Published: December 2015

SummaryEnteropathogenic Yersinia enterocolitica is able to grow within or outside the mammalian host. Previous transcriptomic studies have indicated that the regulator OmpR plays a role in the expression of hundreds of genes in enterobacteria. Here, we have examined the impact of OmpR on the production of Y. enterocolitica membrane proteins upon changes in temperature, osmolarity and pH. Proteomic analysis indicated that the loss of OmpR affects the production of 120 proteins, a third of which are involved in uptake/transport, including several that participate in iron or heme acquisition. A set of proteins associated with virulence was also affected. The influence of OmpR on the abundance of adhesin YadA and heme receptor HemR was examined in more detail. OmpR was found to repress YadA production and bind to the yadA promoter, suggesting a direct regulatory effect. In contrast, the repression of hemR expression by OmpR appears to be indirect. These findings provide new insights into the role of OmpR in remodelling the cell surface and the adaptation of Y. enterocolitica to different environmental niches, including the host.
Using Data Envelopment Analysis to Address the Challenges of Comparing Health System Efficiency
Authors: Cylus Jonathan , Papanicolas Irene , Smith Peter C. 
Published: December 2015

AbstractEfficiency is one of the most potent measures of health system performance and is of particular interest to policy makers because it seeks to assess the valued outcomes of a health system in relation to the resources that are sacrificed to achieve those outcomes. However, the production process of the health care system is a complex sequence, and most indicators are only able to capture part of that process; these indicators offer limited scope for analysis. While researchers have previously constructed composite indicators which combine partial measures into a single number, the weights used for aggregating data can be contentious and may not be universally applicable across systems. Data envelopment analysis (DEA) is most often used to compare the productivity of different producing entities, including health systems. In this article, we instead propose a method that relies on DEA to construct composite health system efficiency indicators from several partial efficiency measures. Among other noted benefits, this enables the construction of composite indicators where different weights are attached to partial indicators for each country, allowing countries to be viewed according to the weights that cast each in the best light. Our application of this method suggests that there is reasonable consistency among the countries that are found to be efficient.
Extended nicotine self‐administration increases sensitivity to nicotine, motivation to seek nicotine and the reinforcing properties of nicotine‐paired cues.
Authors: Clemens Kelly J. , Lay Belinda P. P. , Holmes Nathan M. 
Published: December 2015

AbstractAn array of pharmacological and environmental factors influence the development and maintenance of tobacco addiction. The nature of these influences likely changes across the course of an extended smoking history, during which time drug seeking can become involuntary and uncontrolled. The present study used an animal model to examine the factors that drive nicotine‐seeking behavior after either brief (10 days) or extended (40 days) self‐administration training. In Experiment 1, extended training increased rats' sensitivity to nicotine, indicated by a leftward shift in the dose–response curve, and their motivation to work for nicotine, indicated by an increase in the break point achieved under a progressive ratio schedule. In Experiment 2, extended training imbued the nicotine‐paired cue with the capacity to maintain responding to the same high level as nicotine itself. However, Experiment 3 showed that the mechanisms involved in responding for nicotine or a nicotine‐paired cue are dissociable, as treatment with the partial nicotine receptor agonist, varenicline, suppressed responding for nicotine but potentiated responding for the nicotine‐paired cue. Hence, across extended nicotine self‐administration, pharmacological and environmental influences over nicotine seeking increase such that nicotine seeking is controlled by multiple sources, and therefore highly resistant to change.
“Never Wholly Respectable:” Divination, Death, and Humanism in Contemporary Anthropology
Authors: Landry Timothy R. 
Published: December 2015

SummaryIn 1993, Bruce Grindal wrote that “Humanistic anthropology must never become wholly respectable.” Implying that humanism is anthropology's important gadfly or jester, designed to “challenge and occasionally outrage the priestly purveyors” of science, his influence perpetuates the continued salience and current engagement of interpretative and humanistic anthropology. In this article, I compare Grindal's work with Sisala notions of death in northern Ghana with my own work among Yorùbá peoples in Bénin, West Africa. Exploring anthropology's reflective turn, I use our combined ethnography to explore the ways in which humanistic approaches to anthropology are well positioned to engage with those subtle, complex, and sometimes “messy” layers of meaning that almost define the “human experience.” Struggling with similar themes, in 1983, Grindal wrote, in his prescient style, that he had with “intuitive certainty … witnessed the raising of the dead.” He described the experience as a “real” occurrence that “wounded and sickened” his “soul.” Here, I argue that this reaction is precisely the goal of humanistic anthropology. To be effective, humanistic anthropology, like life itself, while potentially uplifting and unifying, must also be painful and sickening. It is in this way that humanism facilitates an understanding—a type of divinatory “knowing—among disparate people who live in worlds that are at once vastly different and startlingly similar.
Management of multiple sclerosis in daily practice for general neurologist and healthcare professionals
Authors: Yokoyama Kazumasa , Hattori Nobutaka 
Published: December 2015

AbstractWhen we consider neuroimmunological disorders, the most common disease is multiple sclerosis (MS). MS is an intractable disease, affecting younger generations with an increasing prevalence all over the world, including Japan. The main goal of treatment is to decrease the frequency of relapses, manage symptoms, improve function and delay disease progression for better quality of life. However, halting the neurodegenerative process of axonal damage is difficult, and that is why there is no cure for MS. In the present article, we summarize the current disease‐modifying therapies and the meaning of no evidence of disease activity. Even though the ability to initiate disease‐modifying therapies in the earlier stage of MS and the window of opportunity exists, patients need to stay on therapy for a long period of time. In this regard, there is no set algorithm to treat all of the complications of MS. Individual medicines are required to manage the specific symptoms to maintain the quality of life of the patient. In this review article, we concentrate on how healthcare professionals can manage the clinical symptoms of patients with MS.
Characterization of products of the early stages of pedogenesis in ornithogenic soil from Maritime Antarctica
Authors: Poggere G. C. , Melo V. F. , Francelino M. R. , Schaefer C. E. , Simas F. N. 
Published: December 2015

SummaryLimited pedogenesis on the Antarctic continent results in unusual, but important, short‐range order inorganic phases and organo‐mineral complexes (both with broad peaks from X‐ray diffraction) in the clay fraction, which can be studied by sequential chemical extractions. We aimed to develop a better sequential extraction procedure to obtain more detailed discrimination of the short‐range order phases (SROP) of the clay fraction of soil from Maritime Antarctica. Selected chemical properties of the soil and clay fraction were related to different phases of these products. The total amount of SROP and organo‐mineral complexes in the clay fraction ranged from 15.1 to 43.9%, with greater occurrence in ornithogenic soil. The continuous incorporation of guano from penguins into the soil profile has contributed to increasing amounts of organo‐mineral complexes. Short‐range order phases have an important effect on soil chemical properties, such as an increase in non‐exchangeable acidity, quantity of hydroxyl groups on the surface of the colloidal fraction, the buffering capacity of Al3+ from non‐exchangeable and structural forms of the element, and a decrease in soil CEC. The greater number of sequential extraction steps enabled the separation of SROP and organo‐mineral complexes into two phases of stability, with a clear predominance of the more soluble forms.
Technology, offshoring and the task content of occupations in the United Kingdom
Authors: AKÇOMAK Semih , KOK Suzanne , ROJAS‐ROMAGOSA Hugo 
Published: December 2015

AbstractThe authors analyse change in employment levels and in the task content of occupations, both within occupations (i.e. at the intensive margin) and between occupations (i.e. at the extensive margin) in the United Kingdom over the period 1997–2006 using data from the national Skills Survey, which has comparable within‐occupation task data for three waves: 1997, 2001 and 2006. They find that within‐occupation task content changed significantly, and that the magnitude of change was similar to that found at the extensive margin. Their econometric results suggest that these intensive‐margin shifts can be explained by technological improvements but not by offshoring.
Evaluation of Implementation of the Kentucky Court Rules of Procedure and Practice: An Approach to Assessing the Impact of Court Reform Efforts
Authors: Boes Corey , Collins‐Camargo Crystal , Thomas Tammi Alvey 
Published: December 2015

AbstractThis article describes a Supreme Court of Kentucky court improvement initiative designed to promote uniformity and improved court practice with an ultimate goal of the improvement of outcomes for children and families through implementation of Family Court Rules of Procedure and Practice. Twelve jurisdictions were purposely selected to exhibit a range of family and non‐family court jurisdictions, rural and middle‐sized locations. This article focuses on the results of court case file review related to indicators of due process and timeliness. Implications for court evaluation and reform activities are discussed.
Characterization and Sensory Evaluation of a Novel Grapefruit Beverage Made with Lactose‐Free Demineralized Milk Permeate
Authors: Rahimi Monireh , Kalbasi‐Ashtari Ahmad , Labbafi Mohsen , Longnecker Michael , Khodayian Fereidoon 
Published: December 2015

AbstractA variety of fruit beverage formulations using demineralized milk permeates hydrolyzed with β‐galactosidase and mixed with concentrated grapefruit juice, sugar and pectin were evaluated for sensory criteria (appearance, aroma, mouthfeel, taste and after taste) and measured physiochemical (PC) parameters. The total sensory scores (TSS) and PC parameters of accepted beverages were comparable for most grapefruit drinks. The newly formulated beverages had very low lactose and sodium (<1%) without any astringency and salty taste. A regression model relating the TSS of the beverages and six effective PC parameters (Brix, lightness, color value of a, viscosity, sedimentation and pH) was formulated. The resulting regression model provides consistent predictions of TSS for the new beverages without having to impanel a new set of tasters to reassess the TSS properties of the new formulations. The model of TSS had an R2 value of 94% and provided the trend in TSS for the increases in the formulation parameters.Practical ApplicationsMilk permeate (a low‐cost by‐product of the ultrafiltration) is a rich source of growth factors such as essential amino acids. Demineralized and dried milk permeate (DDMP) is a salt‐free additive with numerous nutrients and a long shelf life. Varying amounts of DDMP (hydrolyzed with β‐galactosidase), concentrated grapefruit juice (full of antioxidants, vitamins and minerals), sugar and high methoxyl pectin were mixed to determine appealing physiochemical (PC) parameters and to evaluate sensory criteria (appearance, odor, mouthfeel, taste and aftertaste) after refining and pasteurization. The optimal combinations of raw materials resulted in pleasant beverages (free of lactose) that had total sensory scores (TSS) and PC parameters completely comparable with the scores and parameters of fresh grapefruit drink. A regression model relating TSS to important PC parameters yielded predicted TSS of the beverage with a high degree of accuracy. This model has a potential to predict TSS of a formulated beverage without performing the tedious and time‐consuming taste panel process.