bluuebunny/crossref_metadata_2025_split huggingface dataset:
A first-principles self-consistent model of plasma turbulence and kinetic neutral dynamics in the tokamak scrape-off layer
Authors: Wersal C. , Ricci P. 
Published: November 2015

Abstract
A first-principles self-consistent model that couples plasma and neutral physics suitable for the simulation of turbulent plasma behavior in the tokamak SOL is presented. While the plasma is modeled by the drift-reduced two fluid Braginskii equations, a kinetic model for the neutrals is developed, valid in short and in long mean free path scenarios. The model includes ionization, charge-exchange, recombination, and elastic collisional processes. The solution of the neutral kinetic equation is implemented within the GBS plasma turbulence code (Ricci et al 2012 Plasma Phys. Control. Fusion
54 124047) and it is performed by using the method of characteristics. The details of the numerical implementation are discussed. Finally, we show initial results of the first self-consistent simulations of plasma turbulence and neutral dynamics.
Fast, fully Bayesian spatiotemporal inference for fMRI data
Authors: Musgrove Donald R. , Hughes John , Eberly Lynn E. 
Published: November 2015

AbstractWe propose a spatial Bayesian variable selection method for detecting blood oxygenation level dependent activation in functional magnetic resonance imaging (fMRI) data. Typical fMRI experiments generate large datasets that exhibit complex spatial and temporal dependence. Fitting a full statistical model to such data can be so computationally burdensome that many practitioners resort to fitting oversimplified models, which can lead to lower quality inference. We develop a full statistical model that permits efficient computation. Our approach eases the computational burden in two ways. We partition the brain into 3D parcels, and fit our model to the parcels in parallel. Voxel-level activation within each parcel is modeled as regressions located on a lattice. Regressors represent the magnitude of change in blood oxygenation in response to a stimulus, while a latent indicator for each regressor represents whether the change is zero or non-zero. A sparse spatial generalized linear mixed model captures the spatial dependence among indicator variables within a parcel and for a given stimulus. The sparse SGLMM permits considerably more efficient computation than does the spatial model typically employed in fMRI. Through simulation we show that our parcellation scheme performs well in various realistic scenarios. Importantly, indicator variables on the boundary between parcels do not exhibit edge effects. We conclude by applying our methodology to data from a task-based fMRI experiment.
Using Cox cluster processes to model latent pulse location patterns in hormone concentration data
Authors: Carlson Nichole E. , Grunwald Gary K. , Johnson Timothy D. 
Published: November 2015

AbstractMany hormones, including stress hormones, are intermittently secreted as pulses. The pulsatile location process, describing times when pulses occur, is a regulator of the entire stress system. Characterizing the pulse location process is particularly difficult because the pulse locations are latent; only hormone concentration at sampled times is observed. In addition, for stress hormones the process may change both over the day and relative to common external stimuli. This potentially results in clustering in pulse locations across subjects. Current approaches to characterizing the pulse location process do not capture subject-to-subject clustering in locations. Here we show how a Bayesian Cox cluster process may be adapted as a model of the pulse location process. We show that this novel model of pulse locations is capable of detecting circadian rhythms in pulse locations, clustering of pulse locations between subjects, and identifying exogenous controllers of pulse events. We integrate our pulse location process into a model of hormone concentration, the observed data. A spatial birth-and-death Markov chain Monte Carlo algorithm is used for estimation. We exhibit the strengths of this model on simulated data and adrenocorticotropic and cortisol data collected to study the stress axis in depressed and non-depressed women.
Modeling Long-term Vaccination Strategies With MenAfriVac in the African Meningitis Belt
Authors: Karachaliou Andromachi , Conlan Andrew J. K. , Preziosi Marie-Pierre , Trotter Caroline L. 
Published: November 2015

Abstract
Background.  The introduction of MenAfriVac in campaigns targeting people aged 1–29 years across the African meningitis belt has successfully reduced meningitis incidence and carriage due to Neisseria meningitidis group A (MenA). It is important to consider how best to sustain population protection in the long term.
Methods.  We created a mathematical model of MenA transmission and disease to investigate the potential impact of a range of immunization strategies. The model is age structured; includes classes of susceptible, carrier, ill, and immune people (who may be vaccinated or unvaccinated); and incorporates seasonal transmission and a stochastic forcing term that models between year variation in rates of transmission. Model parameters were primarily derived from African sources. The model can describe the typical annual incidence of meningitis in the prevaccine era, with irregular epidemics of varying size. Parameter and structural uncertainty were explored in sensitivity analyses.
Results.  Following MenAfriVac introduction at high uptake, the model predicts excellent short-term disease control. With no subsequent immunization, strong resurgences in disease incidence were predicted after approximately 15 years (assuming 10 years’ average vaccine protection). Routine immunization at 9 months of age resulted in lower average annual incidence than regular mass campaigns of 1- to 4-year-olds, provided coverage was above approximately 60%. The strategy with the lowest overall average annual incidence and longest time to resurgence was achieved using a combination strategy of introduction into the Expanded Programme on Immunization at 9 months, 5 years after the initial mass campaigns, with a catch-up targeting unvaccinated 1- to 4-year-olds.
Conclusions.  These results can be used to inform policy recommendations for long-term vaccination strategies with MenAfriVac.
Energetics of tent roosting in bats: the case of
Ectophylla alba
and
Uroderma bilobatum
(Chiroptera: Phyllostomidae).
Authors: Rodríguez-Herrera Bernal , Víquez-R Luis , Cordero-Schmidt Eugenia , Sandoval Jean M. , Rodríguez-Durán Armando 
Published: November 2015

Abstract
Roost selection in mammals is an important selective pressure, and many animals find shelter in previously existing structures. Furthermore, the microclimate of roosts is a crucial element for bat survival, and modified leaves are used for roosting (“tents”) by 22 species of bats. Our objective was to determine whether the inverted boat tents used by Ectophylla alba and pinnate tents used by Uroderma bilobatum provide energetic benefits. We measured the ambient temperature under modified and unmodified leaves (UMLs) of Heliconia imbricata and Cocos nucifera . We also measured temperature with (simulated bat presence) and without a heat source, and finally we measured bat energy expenditure at different temperatures. Our results show that when a heat source is present tents conserve heat better than a UML. The energy expenditure of E. alba and U. bilobatum increased up to 55% and 48%, respectively, with a decrease of temperature from 25°C to 20°C. We concluded that since the temperature at our study site drops below 25°C every night and remains that way until mid-morning, using a “tent” that maintains a temperature higher than ambient temperature, or close to 25°C degrees, provides an energetic advantage.
La selección del refugio en los mamíferos es una presión selectiva importante y muchos animales encuentran refugio en estructuras ya existentes. El microclima del refugio es un elemento crucial para la sobrevivencia de los murciélagos. Las hojas modificadas (tiendas) son utilizadas por 22 especies de murciélagos. Nuestro objetivo era determinar si la tienda de bote invertido utilizada por Ectophylla alba y tiendas pinnadas utilizadas por Uroderma bilobatum brindan un beneficio energético a los murciélagos. Se midió la temperatura bajo hojas modificadas y no modificadas de Heliconia imbricata y Cocos nucifera . Además se midió la temperatura con fuente (simulando la presencia de murciélagos) y sin fuente de calor, finalmente se midió el gasto energético de los murciélagos a diferentes temperaturas. Los resultados muestran que cuando hay una fuente de calor presente, la tienda conserva el calor mejor que una hoja no modificada. El gasto energético de E. alba y U. bilobatum puede incrementarse hasta 55% y 48%, respectivamente, cuando la temperatura decrece entre 25°C y 20°C. Concluimos que como la temperatura en este sitio de estudio baja de los 25°C cada noche y hasta media mañana, utilizar una tienda que mantiene la temperatura arriba o cerca de los 25°C, provee una ventaja energética.
Survival of fishers in the southern Sierra Nevada region of California
Authors: Sweitzer Richard A. , Thompson Craig M. , Green Rebecca E. , Barrett Reginald H. , Purcell Kathryn L. 
Published: November 2015

Abstract
Fishers in the western United States were recently proposed for listing under the U.S. Endangered Species Act because of concerns for loss of suitable habitat and evidence of a diversity of mortality risks that reduce survival. One of 2 remnant populations of fishers in California is in the southern Sierra Nevada region, where we studied them at 2 research sites in the Sierra National Forest. Our objectives were to evaluate whether survival was lower for male fishers and dispersal-aged individuals or if survival varied seasonally. We captured and monitored 232 radiocollared fishers from March 2007 to March 2014 and used model analyses to identify important predictors of survival. Fifty-two percent ( n = 120) of the radiocollared fishers died, and survival varied by sex and season, but not by age or between study sites. There was no evidence that dispersal-aged fishers experienced lower survival than older fishers. Annual survival trended lower for male (0.62 [95% CI 0.54–0.70]) compared to female fishers (0.72 [95% CI 0.67–0.78]), was lowest in the spring to mid-summer season (0.83 [95% CI 0.78–0.87]), and highest in late fall and winter (0.92 [95% CI 0.89–0.94]). Lower survival among male fishers appeared linked to males moving over large areas to locate mates, while lower survival for females was potentially related to high energetic cost of reproduction. It was possible but unknown if lower survival among all fishers in spring was linked to secondary exposure to toxicants dispersed around illicit marijuana grow sites. Six-month survival of juvenile fishers was 0.85 for females and 0.79 for males, but lower at 0.62 for females and 0.57 for males when adjusted for deaths before late September. Annual survival among adult female fishers was 20% lower than 0.90, a value that prior modeling suggested was required for population expansion in the overall southern Sierra Nevada. Survival data from our study imply a greater challenge for maintaining self-sustaining fisher populations in the southern Sierra Nevada region, and resource managers are working to mitigate several of the human-associated factors that limit population growth.
A sky-high view of the Third Pole: an interview with Tandong Yao and Weiming Fan
Authors: Qiu Jane 
Published: November 2015

Abstract
The Tibetan Plateau and surrounding mountain regions covers 5 million square kilometres—nearly half the China's landmass—with an average elevation of over 4000 metres. It's often regarded as the Third Pole because it has the largest stock of ice outside the Arctic and the Antarctic. Tibetan Plateau research is one of China's Strategic Pioneering Programmes that was launched in 2012 with a budget of 300 million yuan (US $47 million) over 5 years and is led by Chinese Academy of Sciences (CAS)’ Institute of Tibetan Plateau Research (ITP) in Beijing. In January 2014, CAS set up the Centre for Excellence in Tibetan Plateau Earth Sciences, headquartered in ITP, aiming at providing long-term support for this area of research and raising academic standards. NSR recently talked to glaciologist Tandong Yao and geologist Weiming Fan—ITP's director and deputy director, respectively—about why Tibetan Plateau research is important, what it is like to work there, how the region is faring in face of climate change and why international collaboration is important.
Comparison of Continuous Noninvasive Blood Pressure Monitoring by TL-300 With Standard Invasive Blood Pressure Measurement in Patients Undergoing Elective Neurosurgery
Authors: Lin Wen-Qian , Wu Huang-Hui , Su Chang-Sheng , Yang Jian-Teng , Xiao Jin-Rong , Cai Yu-Ping , Wu Xiao-Zhi , Chen Guo-Zhong 
Published: November 2015

Background:
Intraoperative blood pressure (BP) is one of the basic vital signs monitoring. Compared with standard invasive BP measurement, TL-300 allows for a continuous and beat-to-beat noninvasive intraoperative BP monitoring. The current retrospective study compared the accuracy and precision of this noninvasive technique for continuous BP monitoring with that of standard invasive BP measurement in patients undergoing elective neurosurgery.

Materials and Methods:
BP records of 23 patients undergoing elective neurosurgery, measured by both noninvasive TL-300 and invasive radial arterial catheter method, were retrospectively analyzed. Variability in BP data was analyzed by using linear regressions and Bland-Altman analysis.

Results:
Four thousand three hundred eighty-one pairs of BP measurements from a total of 23 patients were included. The coefficient of determination of systolic, diastolic, and mean BP were 0.908, 0.803, and 0.922, respectively. And their bias was found to be 1.3±5.87 mm Hg (95% limits of agreement: −10.2 to +12.8 mm Hg), 2.8±6.40 mm Hg (95% limits of agreement: −9.8 to +15.3 mm Hg), and 1.8±4.20 mm Hg (95% limits of agreement: −6.4 to +10.1 mm Hg), respectively.

Conclusions:
TL-300 system is a promising noninvasive alternative to the invasive arterial catheter method for intraoperative BP monitoring, with a high accuracy and precision. With the limitation of the current retrospective study, further prospective method comparison studies are needed.
Simultaneous Acquired Self-limited Hemophagocytic Lymphohistiocytosis and Kikuchi Necrotizing Lymphadenitis in a 16-Year-Old Teenage Girl
Authors: Sykes Joseph A. , Badizadegan Kamran , Gordon Paul , Sokol Dawn , Escoto Marcella , Ten Irina , Vyas Shayan , Torres Adalberto , Levine Ann-Marie 
Published: November 2015

Objectives
The aim of this study was to increase education and awareness among pediatric practitioners of possibility of simultaneous hemophagocytic lymphohistiocytosis and Kikuchi-Fujimoto disease/Kikuchi disease occurring in the pediatric population and the diagnostic dilemma it can present. We describe a case presentation of acquired and self-limited simultaneous hemophagocytic lymphohistiocytosis and Kikuchi-Fujimoto disease in a 16-year-old in the United States who presented with fevers, night sweats, and joint pain, along with tiredness and decreased appetite along with pancytopenia and elevated lactate dehydrogenase. To the best of our knowledge, simultaneous hemophagocytic lymphohistiocytosis and Kikuchi-Fujimoto in the pediatric population has not been described in North America but remains fairly common in Asia. The literature on both diseases and their simultaneous occurrence is comprehensively reviewed.

Methods
This was a case report and review of the literature.

Results
The patient was diagnosed with both hemophagocytic lymphohistiocytosis and Kikuchi-Fujimoto disease based on bone marrow aspiration/biopsy and axillary node biopsy, respectively. Both illnesses resolved completely.

Conclusions
Benign causes of pancytopenia and elevated lactate dehydrogenase exist, but they may not be always straightforward diagnostically. Bone marrow aspiration and lymph node biopsy may be helpful in ascertaining the diagnosis. Hemophagocytic lymphohistiocytosis and Kikuchi-Fujimoto disease may represent a continuum of illness.
Antibiotic Prescribing Patterns Across the Continuum of Care for Children Hospitalized With Community-Acquired Pneumonia
Authors: Milner Tiffany L. , McCulloh Russell , Koster Michael , Biondi Eric , Hill Vanessa , Ralston Shawn 
Published: November 2015

Objectives
The aim of this study was to describe the variation in antibiotic prescribing practices for uncomplicated community-acquired pneumonia across the continuum of care for hospitalized pediatric patients to better inform future efforts at standardizing antibiotic therapy throughout a single hospitalization.

Methods
This is a retrospective cohort study involving 4 hospitals caring for children aged 3 months to 18 years, hospitalized between January 1, 2011, and December 31, 2012, with diagnosis of uncomplicated pneumonia and without complex chronic medical conditions.
Data collected include antibiotics prescribed before hospitalization, at the emergency department (ED) encounter, during hospitalization, and at hospital discharge.

Results
Six hundred nine children met inclusion criteria, with a mean age of 5.3 years and median length of stay of 2 days. Emergency department providers prescribed narrow-spectrum therapy 27% of the time, whereas discharging providers prescribed narrow-spectrum therapy 56% of the time. Third- and fourth-generation cephalosporins were less often prescribed in the preadmission setting and at discharge but were more often prescribed in the ED and inpatient setting. There was an association between inpatient prescription of broad-spectrum antibiotics when a blood culture was obtained, when broad-spectrum antibiotics were prescribed in the ED, and with increasing length of stay.

Conclusion
Broad-spectrum antibiotic therapy for community-acquired pneumonia, especially third- and fourth-generation cephalosporins, often originates in the ED. When initiated in this setting, it is likely to be continued in the inpatient setting.
Electronic Health Record–Related Events in Medical Malpractice Claims
Authors: Graber Mark L. , Siegal Dana , Riah Heather , Johnston Doug , Kenyon Kathy 
Published: November 2015

Background
There is widespread agreement that the full potential of health information technology (health IT) has not yet been realized and of particular concern are the examples of unintended consequences of health IT that detract from the safety of health care or from the use of health IT itself. The goal of this project was to obtain additional information on these health IT–related problems, using a mixed methods (qualitative and quantitative) analysis of electronic health record–related harm in cases submitted to a large database of malpractice suits and claims.

Methods
Cases submitted to the CRICO claims database and coded during 2012 and 2013 were analyzed. A total of 248 cases (<1%) involving health IT were identified and coded using a proprietary taxonomy that identifies user- and system-related sociotechnical factors. Ambulatory care accounted for most of the cases (146 cases). Cases were most typically filed as a result of an error involving medications (31%), diagnosis (28%), or a complication of treatment (31%). More than 80% of cases involved moderate or severe harm, although lethal cases were less likely in cases from ambulatory settings. Etiologic factors spanned all of the sociotechnical dimensions, and many recurring patterns of error were identified.

Conclusions
Adverse events associated with health IT vulnerabilities can cause extensive harm and are encountered across the continuum of health care settings and sociotechnical factors. The recurring patterns provide valuable lessons that both practicing clinicians and health IT developers could use to reduce the risk of harm in the future. The likelihood of harm seems to relate more to a patient's particular situation than to any one class of error.
Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?
Authors: Fernández Rosa , Edgecombe Gregory D. , Giribet Gonzalo 
Published: November 2015

AbstractMyriapods are one of the dominant terrestrial arthropod groups including the diverse and familiar centipedes and millipedes. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes in many species) or on maximizing matrix occupancy (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed forty Illumina transcriptomes representing three myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Eight supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at three levels of mean gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but two nodes remained in conflict in the different analyses despite dense taxon sampling at the family level, situating the order Scolopendromorpha as sister group to a morphologically-anomalous grouping of Lithobiomorpha + Geophilomorpha in a subset of analyses. Interestingly, this anomalous result was obtained for all analyses conducted with the most complete matrix (90% of occupancy), being at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) or with the matrices optimizing phylogenegic informativeness and the most conserved genes, but also with previous hypotheses based on morphology, development or other molecular data sets. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies. [Chilopoda; Diplopoda; Symphyla: gene tree; species tree; node calibration; missing data.]
Haplotag: software for haplotype-based genotyping-by-sequencing analysis
Authors: Tinker Nicholas A , Bekele Wubishet A , Hattori Jiro 
Published: November 2015

AbstractGenotyping-by-sequencing (GBS) and related methods are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of SNPs within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analysing large data sets, applications of GBS may require substantial time, expertise and computational resources. Haplotag, the novel GBS software described here, is freely available and operates with minimal user-investment on widely-available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; (6) provides an intuitive visual “passport” for each inferred locus. Haplotag is optimized for use in a self-pollinating plant species.