bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Authors: Farhat Maha R , Shapiro B Jesse , Sheppard Samuel K , Colijn Caroline , Murray Megan 
Published: November 2014

AbstractWhole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little has been published on how and how many pathogen strains should be selected for studies associating phenotype and genotype. There are specific challenges when identifying genetic associations in bacteria which often comprise highly structured populations. Here we consider general methodological questions related to sampling and analysis focusing on clonal to moderately recombining pathogens. We propose that a matched sampling scheme constitutes an efficient study design, and provide a power calculator based on phylogenetic convergence. We demonstrate this approach by applying it to genomic datasets for two microbial pathogens: Mycobacterium tuberculosis and Campylobacter species.
γδ T cells promote inflammation and insulin resistance during high fat diet-induced obesity in mice
Authors: Mehta Pooja , Nuotio-Antar Alli Martina , Smith C Wayne 
Published: November 2014

Abstract
γδ T cells are resident in AT and increase during diet-induced obesity. Their possible contribution to the inflammatory response that accompanies diet-induced obesity was investigated in mice after a 5 to 10 week milk HFD. The HFD resulted in significant increases in CD44hi, CD62Llo, and TNF-α+ γδ T cells in eAT of WT mice. Mice deficient in all γδ T cells (TCRδ−/−) or only Vγ4 and Vγ6 subsets (Vγ4/6−/−) were compared with WT mice with regard to proinflammatory cytokine production and macrophage accumulation in eAT. Obesity among these mouse strains did not differ, but obese TCRδ−/− and Vγ4/6−/− mice had significantly reduced eAT expression of F4/80, a macrophage marker, and inflammatory mediators CCL2 and IL-6 compared with WT mice. Obese TCRδ−/− mice had significantly reduced CD11c+ and TNF-α+ macrophage accumulation in eAT after 5 and 10 weeks on the HFD, and obese Vγ4/6−/− mice had significantly increased CD206+ macrophages in eAT after 5 weeks on the diet and significantly reduced macrophages after 10 weeks. Obese TCRδ−/− mice had significant reductions in systemic insulin resistance and inflammation in liver and skeletal muscle after longer-term HFD feeding (10 and 24 weeks). In vitro studies revealed that isolated γδ T cells directly stimulated RAW264.7 macrophage TNF-α expression but did not stimulate inflammatory mediator expression in 3T3-L1 adipocytes. These findings are consistent with a role for γδ T cells in the proinflammatory response that accompanies diet-induced obesity.
Prediction of general hospital admission in people with dementia: Cohort study
Authors: Russ Tom C. , Parra Mario A. , Lim Alison E. , Law Emma , Connelly Peter J. , Starr John M. 
Published: November 2014

BackgroundPeople with dementia are extremely vulnerable in hospital and unscheduled admissions should be avoided if possible.AimsTo identify any predictors of general hospital admission in people with dementia in a well-characterised national prospective cohort study.MethodA cohort of 730 persons with dementia was drawn from the Scottish Dementia Research Interest Register (47.8% female; mean age 76.3 years, s.d. = 8.2, range 50–94), with a mean follow-up period of 1.2 years.ResultsIn the age- and gender-adjusted multivariable model (n= 681; 251 admitted), Neuropsychiatric Inventory score (hazard ratio per s.d. disadvantage 1.21, 95% CI 1.08–1.36) was identified as an independent predictor of admission to hospital.ConclusionsNeuropsychiatric symptoms in dementia, measured using the Neuropsychiatric Inventory, predict non-psychiatric hospital admission of people with dementia. Further studies are merited to test whether interventions to reduce such symptoms might reduce unscheduled admissions to acute hospitals.
Postpartum change in common mental disorders among rural
Vietnamese women: Incidence, recovery and risk and protective
factors
Authors: Nguyen Trang Thu , Tran Thach Duc , Tran Tuan , La Buoi , Nguyen Hau , Fisher Jane 
Published: November 2014

BackgroundIn low- and middle-income countries little is known about changes in
women's mental health status from the perinatal period to 15 months
postpartum or the factors associated with different trajectories.AimsTo determine the incidence and rates of recovery from common mental
disorders (CMD) among rural Vietnamese women and the risk and protective
factors associated with these outcomes from the perinatal period to 15
months after giving birth.MethodIn a population-based prospective study, a systematically recruited
cohort of women completed baseline assessments in either the last
trimester of pregnancy or 4–6 weeks after giving birth and were followed
up 15 months later. The common mental disorders of major depression,
generalised anxiety and panic disorder were assessed by
psychiatrist-administered Structured Clinical Interview for DSM-IV
Disorders at both baseline and follow-up.ResultsA total of 211 women provided complete data in this study. The incidence
rate of CMD in the first postpartum year was 13% (95% CI 8–19), and 70%
(95% CI 59–80) of women who had perinatal CMD recovered within the first
postpartum year. Incidence was associated with having experienced
childhood maltreatment, experiencing the intimate partner as providing
little care, sensitivity, kindness or affection, and the chronic stress
of household poverty. Recovery was associated with higher quality of a
woman's relationships with her intimate partner and her own mother,
longer period of mandated rest following birth, and sharing of domestic
tasks and infant care.ConclusionsModifiable social factors, in particular the quality of a woman's closest
relationships with her partner and her own mother, and participation by
family members in domestic work and infant care, are closely related to
women's mental health in the first year after giving birth in
resource-constrained settings.
Geographic variation in thermal physiological performance of the intertidal crabPetrolisthes violaceusalong a latitudinal gradient
Authors: Gaitán-Espitia Juan Diego , Bacigalupe Leonardo D. , Opitz Tania , Lagos Nelson A. , Timmermann Tania , Lardies Marco A. 
Published: November 2014

AbstractEnvironmental temperature has profound implications on the biological performance and biogeographical distribution of ectothermic species. Variation of this abiotic factor across geographic gradients is expected to produces physiological differentiation and local adaptation of natural populations depending on their thermal tolerances and physiological sensitivities. Here, we have studied geographic variation in whole-organism thermal physiology of seven populations of the porcelain crab Petrolisthes violaceus across a latitudinal gradient of 3000 km, characterized by a cline of thermal conditions. Our study found that populations of P. violaceus exhibit a lack of differences in the limits of their thermal performance curves and a negative correlation of their optimal temperatures with latitude. Additionally, our findings showed that high latitude populations of P. violaceus exhibited broader thermal tolerances, which is consistent with the Climatic Variability Hypothesis. Interestingly, under a future scenario of warming oceans, the thermal safety margins of P. violaceus indicate that lower latitude populations can physiologically tolerate the ocean warming scenarios projected by the IPCC for the end of the twenty-first century.
The energetic benefits of tendon springs in running: is the reduction of muscle work important?
Authors: Holt Natalie C. , Roberts Thomas J. , Askew Graham N. 
Published: November 2014

AbstractThe distal muscle-tendon units of cursorial species are commonly composed of short muscle fibres and long, compliant tendons. It is assumed that the ability of these tendons to store and return mechanical energy over the course of a stride, thus avoiding the cyclic absorption and regeneration of mechanical energy by active muscle, offers some metabolic energy savings during running. However, this assumption has not been tested directly. We used muscle ergometry and myothermic measurements to determine the cost of force production in muscles acting isometrically, as they could if mechanical energy was stored and returned by tendon, and undergoing active stretch-shorten cycles, as they would if mechanical energy was absorbed and regenerated by muscle. We found no detectable difference in the cost of force production in isometric cycles compared with stretch-shorten cycles. This result suggests that replacing muscle stretch-shorten work with tendon elastic energy storage and recovery does not reduce the cost of force production. This calls into question the assumption that reduction of muscle work drove the evolution of long distal tendons. We proposed that the energetic benefits of tendons are derived primarily from their effect on muscle and limb architecture rather than their ability to reduce cyclic muscle work.
Supervised accelerometry analysis can identify prey capture by penguins at sea
Authors: Carroll Gemma , Slip David , Jonsen Ian , Harcourt Rob 
Published: November 2014

Abstract
Determining where, when and how much animals eat is fundamental to understanding their ecology. We developed a technique to identify a prey capture signature for little penguins from accelerometry, in order to quantify food intake remotely. We categorised behaviour of captive penguins from HD video and matched this to time-series data from back-mounted accelerometers. We then trained a support vector machine (SVM) to classify the penguins’ behaviour at 0.3s intervals as either ‘prey handling’ or ‘swimming’. We applied this model to accelerometer data collected from foraging wild penguins to identify prey capture events. We compared prey capture and non-prey capture dives to test the model predictions against foraging theory. The SVM had an accuracy of 84.95% (S.E. ± 0.26) and a false positive rate of 9.82% (S.E. ± 0.24) when tested on unseen captive data. For wild data, we defined three independent, consecutive prey handling observations as representing true prey capture, with a false positive rate of 0.09%. Dives with prey captures had longer duration and bottom times, were deeper, had faster ascent rates, and had more ‘wiggles’ and ‘dashes’ (proxies for prey encounter used in other studies). The mean number of prey captures per foraging trip was 446.6 (S.E. ± 66.28). By recording the behaviour of captive animals on HD video and using a supervised machine learning approach, we show that accelerometry signatures can classify the behaviour of wild animals at unprecedentedly fine scales.
Bats coordinate sonar and flight behavior as they forage in open and cluttered environments
Authors: Falk Benjamin , Jakobsen Lasse , Surlykke Annemarie , Moss Cynthia F 
Published: November 2014

AbstractEcholocating bats employ active sensing as they emit sounds and listen to the returning echoes to probe their environment for navigation, obstacle avoidance, and pursuit of prey. The sensing behavior of bats includes the planning of 3D spatial trajectory paths, which are guided by echo information. In this study, we examined the relationship between active sonar sampling and flight motor output as bats changed environments from open space to an artificial forest in a laboratory flight room. Using high-speed video and audio recordings, we reconstructed and analyzed 3D flight trajectories, sonar beam aim and acoustic sonar emission patterns as the bats captured prey. We found that big brown bats adjusted their sonar call structure, temporal patterning, and flight speed in response to environmental change. The sonar beam aim of the bats predicted the flight turn rate in both the open room and the forest. However, the relationship between sonar beam aim and turn rate changed in the forest during the final stage of prey pursuit, during which the bat made shallower turns. We found flight stereotypy developed over multiple days in the forest, but did not find evidence for a reduction in active sonar sampling with experience. The temporal patterning of sonar sound groups was related to path planning around obstacles in the forest. Together, these results contribute to our understanding of how bats coordinate echolocation and flight behavior to represent and navigate their environment.
Active learning and decision making: an introduction to the collection
Authors: Gottlieb Jacqueline 
Published: November 2014

The importance of exploratory behaviors by which agents actively sample information has been long appreciated in a range of disciplines. However, because of their complexity and cognitive nature, these behaviors have been difficult to characterize. In recent years, a resurgence of interest in this question has been based on a confluence of ideas from multiple fields, including machine learning, development, perceptual learning and attention and decision making. This collection of articles in F1000Research aims to provide a home for a broad range of studies addressing this topic. We welcome full length research articles, brief communications, single figure studies, and review/opinion articles, and studies using computational, behavioral or neural approaches. Here, we provide an introduction to the collection which we hope will grow and become a valuable resource for the researchers exploring this topic.
Influence of oil and gas emissions on ambient atmospheric non-methane hydrocarbons in residential areas of Northeastern Colorado
Authors: Thompson Chelsea R. , Hueber Jacques , Helmig Detlev 
Published: November 2014

Abstract
The Northern Front Range (NFR) region of Colorado has experienced rapid expansion of oil and gas extraction from shale and tight sands reservoirs in recent years due to advances in hydraulic fracturing technology, with over 25,000 wells currently in operation. This region has also been designated as a federal ozone non-attainment area by the U.S. EPA. High ozone levels are a significant health concern, as are potential health impacts from chronic exposure to primary emissions of non-methane hydrocarbons (NMHC) for residents living near wells. From measurements of ambient atmospheric NMHC present in residential areas located in close proximity to wells in Erie, Colorado, we find that mean mole fractions of the C2–C5 alkanes are enhanced by a factor of 18–77 relative to the regional background, and present at higher levels than typically found in large urban centers. When combined with NMHC observations from downtown Denver and Platteville, it is apparent that these compounds are elevated across the NFR, with highest levels within the Greater Wattenberg Gas Field. This represents a large area source for ozone precursors in the NFR. The BTEX aromatic compounds in Erie were comparable to (e.g., benzene) or lower than (e.g., toluene, ethylbenzene, xylene) in large urban centers, however, benzene was significantly higher in Platteville, and within the range of chronic health-based exposure levels. An initial look at comparisons with data sets from previous years reveal that ambient levels for oil and gas-related NMHC in Erie, as well as further downwind in Boulder, have not decreased, but appear to have been increasing, despite tightening of emissions standards for the oil and gas industries in 2008.
Medicines optimization in the dementias
Authors: Apampa Bugewa , Navti Beryl 
Published: November 2014

Medicines play a key role in the management of persons with dementia by delaying cognitive decline and ameliorating the behavioural and psychological symptoms associated with dementia, when all other interventions have failed. The four guiding principles of medicines optimization: understanding the patient's experience, evidence-based choice of medicines, ensuring safe use of medicines and making medicines optimization part of routine practice, can be systematically incorporated into the routine care of these patients resulting in improved patient outcomes and ultimately reduced cost to the NHS. This article aims to provide an overview of medicines optimization for the health professional.
III-V Multi-junction solar cells and concentrating photovoltaic (CPV) systems
Authors: Philipps Simon P. , Bett Andreas W. 
Published: November 2014

Abstract
It has been proven that the only realistic path to practical ultra-high efficiency solar cells is the monolithic multi-junction approach, i.e., to stack pn-junctions made of different semiconductor materials on top of each other. Each sub pn-junction, i.e., sub solar cell, converts a specific part of the sun’s spectrum. In this way, the energy of the sunlight photons is converted with low thermalization losses. However, large-area multi-junction solar cells are still far too expensive if applied in standard PV modules. A viable solution to solve the cost issue is to use tiny solar cells in combination with optical concentrating technology, in particular, high concentrating photovoltaics (HCPV), in which the light is concentrated over the solar cells more than 500 times. The combination of ultra-high efficient solar cells and optical concentration lead to low cost on system level and eventually to low levelized cost of electricity, today, well below 8 €cent/kWh and, in the near future, below 5 €cent/kWh. A wide variety of approaches exists for III-V multi-junction solar cells and HCPV systems. This article is intended to provide an overview about the different routes being followed.
Dimensional estimates for singular sets in geometric variational problems with free boundaries
Authors: De Philippis Guido , Maggi Francesco 
Published: November 2014

Abstract
We show
that singular sets of free boundaries arising in codimension one anisotropic geometric variational problems are

ℋ

n
-
3

${\mathcal{H}^{n-3}}$

-negligible, where n is the ambient space dimension. In particular our results apply to capillarity type problems, and establish everywhere regularity in the three-dimensional case.
Seed Structure Characteristics of Orobanche cumana Populations
Authors: Krupp Anna , Rücker Erika , Heller Annerose , Spring Otmar 
Published: November 2014

AbstractSunflower broomrape Orobanche cumana Wallr. is a rapidly growing threat to the oil crop production in many countries. Fast adaptation to new environments and increasing host resistance suggests that phenotypically distinctive populations of the weed may have evolved. The classification of the species and the differentiation of such populations on the base of seed micromorphological characters were attempted. Morphometric measurements allowed the distinction of O. cumana from several other Orobanche and Phelipanche species. An irregularly thickened cell wall of the anticlinal testa cells differentiated O. cumana and O. cernua from O. caryophyllacea, O. crenata, O. minor, P. aegyptiaca, P. arenaria and P. ramosa. However, populations of sunflower broomrape from five European countries and China could not be separated from each other on the base of micromorphological seed characters. In contrast, length to width measurements indicated that the Asian samples had a slightly different seed shape which was less elongated than the European samples. However, this seemingly geographic effect may as well be a consequence of sampling which comprised a higher rate of the so-called modern races E-H in the European samples.
Application of Image Processing in Fruit and Vegetable Analysis: A Review
Authors: Dubey Shiv Ram , Jalal Anand Singh 
Published: November 2014

AbstractImages are an important source of data and information in the agricultural sciences. The use of image-processing techniques has outstanding implications for the analysis of agricultural operations. Fruit and vegetable classification is one of the major applications that can be utilized in supermarkets to automatically detect the kinds of fruits or vegetables purchased by customers and to determine the appropriate price for the produce. Training on-site is the underlying prerequisite for this type of arrangement, which is generally caused by the users having little or no expert knowledge. We explored various methods used in addressing fruit and vegetable classification and in recognizing fruit disease problems. We surveyed image-processing approaches used for fruit disease detection, segmentation and classification. We also compared the performance of state-of-the-art methods under two scenarios, i.e., fruit and vegetable classification and fruit disease classification. The methods surveyed in this paper are able to distinguish among different kinds of fruits and their diseases that are very alike in color and texture.
Effects of speech rate, phonetic background and gender on vowel reduction in the speech of nonnative speakers of English
Authors: Brzezicha Bogna , Kul Małgorzata 
Published: November 2014

AbstractThe paper reports the results of a study investigating vowel reduction in the speech of non-native speakers of English. The aim was to unravel the links between reduction and speech rate, phonetic training and gender. We hypothesized that (i) Polish speakers of English reduce vowels; (ii) they speak slower than native speakers; (iii) the higher the rate, the higher the reduction degree; (iv) speakers with phonetic training reduce less than those lacking it; (v) male subjects reduce more than the female ones. In order to realize these aims, an acoustic analysis of vowels was performed on 2 hrs 42 mins of speech produced by 12 Polish speakers of English. The subjects were di-vided into an experimental group consisting of 6 students of English and a control group with 6 speakers who had no phonetic training. The obtained results positively verify that non-native speakers reduce vowels and cast some doubts on whether they speak slower than native speakers. The role of rate and gender could not be established due to statistical and methodological issues. The group with no phonetic training outperformed the group which underwent phonetic training, pointing instead to the role of exposure and perhaps music training in acquiring native-like reduction patterns.
Shame, embarrassment and guilt: Corpus evidence for the cross-cultural structure of social emotions
Authors: Krawczak Karolina 
Published: November 2014

AbstractThis article is a cross-cultural and cross-linguistic comparison of three interrelated emotional categories of shame, embarrassment and guilt in two different cultural settings of individualistic societies, as represented here by Britain and America, and a collectivist society, such as Poland. The conceptual field of SHAME is operationalized through its three near-synonymous adjectival exponents, "ashamed"/"zawstydzony", "embarrassed"/"zażenowany", and "guilty"/"winny". Drawing on relevant research in social and cognitive psychology as well as linguistics, the present study applies advanced quantitative corpus-based methodology to reconstruct the cultural and conceptual profiles of the three emotions.