bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of Home-Time After Acute Ischemic Stroke in Medicare Beneficiaries
Authors: Fonarow Gregg C. , Liang Li , Thomas Laine , Xian Ying , Saver Jeffrey L. , Smith Eric E. , Schwamm Lee H. , Peterson Eric D. , Hernandez Adrian F. , Duncan Pamela W. , O’Brien Emily C. , Bushnell Cheryl , Prvu Bettger Janet
Published: February 2016

Background and Purpose—

Stroke survivors have identified home-time as a meaningful outcome. We evaluated home-time as a patient-centered outcome in Medicare beneficiaries with ischemic stroke in comparison with modified Rankin Scale (mRS) score at 90 days and at 1 year post event.

Methods—

Patients enrolled in Get With The Guidelines-Stroke (GWTG-Stroke) and Adherence Evaluation After Ischemic Stroke-Longitudinal (AVAIL) registries were linked to Medicare claims to ascertain home-time, defined as time spent alive and out of a hospital, inpatient rehabilitation, or skilled nursing facilities, at 90 days and at 1 year after admission. The correlation of home-time with mRS at 90 days and at 1 year was evaluated by Pearson correlation coefficients, and the ability of home-time to discriminate mRS (0–2) was assessed by
c
-index.

Results—

There were 815 patients with ischemic stroke (age median, 76 years [interquartile range {IQR}, 70–82]; 46% women; National Institutes of Health Stroke Scale median, 4 [IQR, 2–7]) from 88 hospitals. The 90-day and 1-year median home-times were 79 (IQR, 52–86) days and 349 (IQR, 303–360) days and median mRS were 2 (IQR, 1–4) and 2 (IQR, 1–4). Greater home-time within 90 days was significantly correlated with lower 90-day mRS (Pearson correlation coefficient, −0.731;
P
<0.0001) and showed strong ability to discriminate functional independence with mRS 0 to 2 (
c
-index, 0.837). Similar findings were observed at 1 year.

Conclusions—

In a population of older patients with ischemic stroke, home-time was readily available from administrative data and associated with mRS at 90 days and 1 year. Home-time represents a novel, easily measured, patient-centered, outcome measure for an episode of stroke care.
Beating the Daf and Darbuka: Testing the Boundaries of Ethnicity, Evoking a National Imaginary, and Dancing a Contemporary Iraqi Identity
Authors: Leffler Elliot
Published: February 2016

In the heat of a spontaneous dance party at an international summer camp, an ethnically and religiously diverse group of young Iraqis stretched their national imaginary through an exuberant, embodied engagement. In a moment when the strict universality discourses of their camp programs did not seem to apply, the adolescents—Sunni and Shia, Kurdish and Arab—explored the potential synapses and interrelationships of their ethnic identities on their own terms.
The Structure of Plasticity: Resistance and Accommodation in Russian New Drama
Authors: Weygandt Susanna
Published: February 2016

The history of the Russian stage traces the importance of objects in storytelling back to an earlier art: plastika, a stylized acting technique that “speaks” spatially with objects. In Russian New Drama, objects enter the stage as supplements to the hero, who survives the disintegration of the Soviet Union as a shell-of-the-self. As extensions of the hero, the hitherto lifeless things begin “to act” and tell their own story.
Choreographing Violence: Arkadi Zaides’s Archive
Authors: Abeliovich Ruthie
Published: February 2016

Israeli choreographer Arkadi Zaides’s solo dance Archive investigates the choreography of transgressions performed by Israeli fundamentalist settlers against Palestinians in the West Bank. Screening fragments from a video archive documenting human rights violations in the occupied territories, this work invites Israeli spectators to sense the somatic impact of such actions and to consider the corporal resonance of the ongoing violence.
Online Pairwise Learning Algorithms
Authors: Ying Yiming , Zhou Ding-Xuan
Published: February 2016

Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.
Causal Inference on Discrete Data via Estimating Distance Correlations
Authors: Liu Furui , Chan Laiwan
Published: February 2016

In this article, we deal with the problem of inferring causal directions when the data are on discrete domain. By considering the distribution of the cause [Formula: see text] and the conditional distribution mapping cause to effect [Formula: see text] as independent random variables, we propose to infer the causal direction by comparing the distance correlation between [Formula: see text] and [Formula: see text] with the distance correlation between [Formula: see text] and [Formula: see text]. We infer that X causes Y if the dependence coefficient between [Formula: see text] and [Formula: see text] is smaller. Experiments are performed to show the performance of the proposed method.
Recurrent Neural Network for Computing Outer Inverse
Authors: Živković Ivan S. , Stanimirović Predrag S. , Wei Yimin
Published: February 2016

Two linear recurrent neural networks for generating outer inverses with prescribed range and null space are defined. Each of the proposed recurrent neural networks is based on the matrix-valued differential equation, a generalization of dynamic equations proposed earlier for the nonsingular matrix inversion, the Moore-Penrose inversion, as well as the Drazin inversion, under the condition of zero initial state. The application of the first approach is conditioned by the properties of the spectrum of a certain matrix; the second approach eliminates this drawback, though at the cost of increasing the number of matrix operations. The cases corresponding to the most common generalized inverses are defined. The conditions that ensure stability of the proposed neural network are presented. Illustrative examples present the results of numerical simulations.
Characterization of 17 novel microsatellite loci in the Nile monitor (Varanus niloticus) via 454 pyrosequencing
Authors: Wood Jared P. , Campbell Todd S. , Page Robert B.
Published: February 2016

We used 454 pyrosequencing to characterize 17 novel microsatellite loci from the Nile monitor (Varanus niloticus), using samples from an invasive population in the US state of Florida. These markers were screened for variation in 40 individuals from the City of Cape Coral. Observed heterozygosity ranged from 0.18 to 0.73 (mean ± SE = 0.46 ± 0.06) and the number of alleles per locus ranged from 1 to 4 (mean ± SE = 2.5 ± 0.2). Preliminary genotyping of samples from populations in West Palm Beach and Homestead revealed two loci (Mon6andMon15) that are monomorphic in Cape Coral, but polymorphic in these other two populations. We found no statistical departures from Hardy-Weinberg equilibrium or evidence of null alleles. However, there was statistical evidence for genotypic disequilibrium betweenMon1-Mon14andMon3-Mon8. BLASTn searches of NCBI’s nr/nt database identified four microsatellites containing 454 fragments that exhibit substantial sequence similarity to loci in other reptilian genomes, suggesting these markers should be prioritized by researchers interested in cross-amplification in other varanids. The resources we have developed will enable investigations of the population genetic dynamics of invasive Nile monitors in Florida and may facilitate studies within this species native range.
Species distribution modelling leads to the discovery of new populations of one of the least known European snakes, Vipera ursinii graeca, in Albania
Authors: Mizsei Edvárd , Üveges Bálint , Vági Balázs , Szabolcs Márton , Lengyel Szabolcs , Pfliegler Walter P. , Nagy Zoltán T. , Tóth János P.
Published: February 2016

Vipera ursinii graeca is a restricted-range, endemic snake of the Pindos mountain range in the southwestern Balkans. The subspecies was previously reported from eight localities in Greece and one locality in southern Albania. We used species distribution modelling based on climate data from known localities in Greece to estimate the potential distribution of the subspecies. The model predicted suitable areas for eleven mountains in southern Albania, which we visited in ten field expeditions in four years. Based on 78 live individuals and 33 shed skins, we validated the presence of the snake on eight of the eleven mountains. Six populations (Dhëmbel, Llofiz, Griba, Shendelli, Tomorr and Trebeshinë Mountains) are reported here for the first time. Morphological characters undoubtedly supported that all individuals found at these new localities belong to V. u. graeca. Genetic analysis of mitochondrial DNA sequences also confirmed the identity of the snakes as V. u. graeca and a low number of identified haplotypes suggested low genetic variability among populations despite significant spatial isolation. All localities were subalpine-alpine calcareous meadows above 1600 m. These high montane habitats are separated by deep valleys and are threatened by overgrazing, soil erosion, and a potential increase in the elevation of the tree line due to climate change. Our surveys increased the number of known populations by 60% and the known geographical range of the subspecies by approximately 30%. Our study serves as a baseline for further ecological research and for conservation measures for one of the least known European viperid snakes.
The conservation status of the Galápagos marine iguanas, Amblyrhynchus cristatus: a molecular perspective
Authors: MacLeod Amy , Steinfartz Sebastian
Published: February 2016

Traditionally, conservation management focuses efforts on taxonomic units. However, when the taxa used do not reflect biologically meaningful units, such methods should be reconsidered to avoid the loss of irreplaceable biodiversity. The Galápagos marine iguana (Amblyrhynchus cristatus) is listed as Vulnerable on the IUCN Red List of Threatened Species and is facing growing anthropogenic threats. Currently, management is based on a taxonomy which is questionable in the light of recent molecular data. As such, there is a danger that evolutionarily significant populations may be left vulnerable to extirpation. Herein, we apply molecular data to elucidate the population structure of this species across the Galápagos archipelago, and thus advise conservation management in the absence of a revised taxonomy. Applying a wealth of molecular data including 12 microsatellite loci and 1181 bp of the mitochondrial control region in over 1200 individuals, we delineate distinct populations and prioritize their management. Bayesian population structure analysis revealed 10 distinct population clusters, which we propose as management units (MUs). All MUs are significantly differentiated, with one unit on San Cristóbal Island being particularly distinct in terms of both microsatellite loci and mitochondrial data. Based on estimates of the genetic effective population size (Ne), we find the MUs comprised of populations occurring on Floreana, Española, Marchena, and San Cristóbal to be alarmingly small. In consideration of both Neand anthropogenic threats, we recommend that conservation practitioners focus efforts on Floreana and San Cristóbal islands, and argue that better census size estimates of populations are urgently needed.
An Evaluation of the Effect of Auditory Emotional Stimuli on Interval Timing
Authors: Halbertsma Hinke N. , Van Rijn Hedderik
Published: February 2016

Emotions modulate cognitive processes, including those involved in the perception of time. A number of studies have demonstrated that the emotional modulation of interval timing can be described in terms of an attentional or an arousal-based mechanism, depending on the exact task setup. In this paper, two temporal generalization experiments with auditory emotional stimuli as distractors are presented. These experiments are modeled after the work by Lui et al. (PLoS One, 2011,6, e218292011) who, using visual distractors, provided evidence for an attentional account of emotion-regulated modulation of the perception of time. Experiment 1 replicates the findings of Lui et al., and thus generalizes their work to auditory stimuli. However, Experiment 2, in setup highly similar to Experiment 1, failed to find any effects of emotional modulation on interval timing. These results indicate that emotional effects on interval timing, although often reported, might not be as ubiquitous as earlier research has (implicitly) suggested.
Salience in Metonymy-motivated Constructional Abbreviated Form with Particular Attention to English Clippings
Authors: Barcelona Antonio
Published: February 2016

I have claimed in some of my earlier publications that abbreviated constructional forms (at any level from lexemes upwards) are motivated by a part-for-whole metonymy (salient part of form for whole form). But what exactly is meant by “salient part of form”? In this paper I report on unpublished research on the topic, with particular attention to clipped lexical forms. In that research, I propose a salience factor grid determining the saliency of a “natural” segment in a lexical form and showing that salience is relative, scalar, and multi-factorial.

The paper illustrates how the application of the factor grid to two clippings (gas for gasoline and prof for professor) and other non-conventional segments of the same words (e.g. -line, -soline, and -essor) explains the motivated nature of the conventional clippings. Five tables sum up the application of the grid to these and other examples.
Molecular data shows Didymella aptrootii is a new genus in Bambusicolaceae
Authors: ZHANG HUANG , DONG WEI , HYDE KEVIN D. , BAHKALI ALI H. , LIU JIAN-KUI , ZHOU DE-QUN , ZHANG DI
Published: February 2016

Longipedicellata gen. nov. is introduced to accommodate the common freshwater ascomycete Didymella aptrootii which occurs on bamboo in freshwater. It is characterized by lenticular ascomata, immersed beneath a blackened pseudoclypeus, with relatively large ostioles, sparse pseudoparaphyses, bitunicate, broadly clavate asci, with a long pedicel and 1-septate, hyaline ascospores, surrounded by large irregular mucilaginous sheath. Illustrated accounts of the type and fresh collections of Longipedicellata aptrootii are provided and morphological differences between Longipedicellata and some related taxa are noted. We place Longipedicellata in Bambusicolaceae, based on analysis of LSU, SSU, RPB2 and TEF sequence comparisons.
Intraseasonal-to-Interannual Variability of the Indian Monsoon Identified with the Large-Scale Index for the Indian Monsoon System (LIMS)
Authors: Carvalho Leila M. V. , Jones Charles , Cannon Forest , Norris Jesse
Published: February 2016

The Indian monsoon system (IMS) is among the most complex and important climatic features on land. This study proposes a simple and robust method to investigate large-scale variations and changes in the IMS that accounts for fluctuations in amplitude, onset, and duration of the summer monsoon, including active and break phases, and the postmonsoon season. This study uses 35 years (1979–2013) of daily data from the National Centers for Environmental Prediction (NCEP) Climate Forecast System Reanalysis (CFSR) at 1° resolution and indicates great potential for application to other reanalyses and climate model datasets. The method is based on combined EOF (CEOF) analysis of variables associated with the IMS’s seasonal cycle (precipitation, circulation at 10 m, and temperature and specific humidity at 2 m). The first CEOF (CEOF-1) explains ~40% of the total variance and represents the continental-scale Asian monsoon. The second CEOF (CEOF-2) explains 11% of the variance and characterizes the Indian monsoon variability, including increased precipitation over western, central, and northern parts of India and the monsoon onset and demise over those regions. Thus, CEOF-2 is referred to as the large-scale index for the Indian monsoon system (LIMS). It is shown that LIMS’s amplitude is strongly correlated with the total June–September precipitation over India. LIMS is continuous in time and can be used to evaluate significant postmonsoon rainfall events that often affect the Indian subcontinent. Moreover, LIMS exhibits spectral variance on intraseasonal time scales that are associated with active and break phases of the monsoon during summer and enhanced rainfall in the postmonsoon period.
Reproducibility of Summer Precipitation over Northern Eurasia in CMIP5 Multiclimate Models
Authors: Hirota Nagio , Takayabu Yukari N. , Hamada Atsushi
Published: February 2016

Reproducibility of summer precipitation over northern Eurasia in climate models from phase 5 of the Coupled Model Intercomparison Project (CMIP5) is evaluated in comparison with several observational and reanalysis datasets. All CMIP5 models under- and overestimate precipitation over western and eastern Eurasia, respectively, and the reproducibility measured using the Taylor skill score is largely determined by the severity of these west–east precipitation biases. The following are the two possible causes for the precipitation biases: very little cloud cover and very strong local evaporation–precipitation coupling. The models underestimate cloud cover over Eurasia, allowing too much sunshine and leading to a warm bias at the surface. The associated cyclonic circulation biases in the lower troposphere weaken the modeled moisture transport from the Atlantic to western Eurasia and enhance the northward moisture flux along the eastern coast. Once the dry west and wet east biases appear in the models, they become amplified because of stronger evaporation–precipitation coupling. The CMIP5 models reproduce precipitation events well over a time scale of several days, including the associated low pressure systems and local convection. However, the modeled precipitation events are relatively weaker over western Eurasia and stronger over eastern Eurasia compared to the observations, and these are consistent with the biases found in the seasonal average fields.
Salt Dynamics in Well-Mixed Estuaries: Importance of Advection by Tides
Authors: Wei Xiaoyan , Schramkowski George P. , Schuttelaars Henk M.
Published: February 2016

Understanding salt dynamics is important to adequately model salt intrusion, baroclinic forcing, and sediment transport. In this paper, the importance of the residual salt transport due to tidal advection in well-mixed tidal estuaries is studied. The water motion is resolved in a consistent way with a width-averaged analytical model, coupled to an advection–diffusion equation describing the salt dynamics. The residual salt balance obtained from the coupled model shows that the seaward salt transport driven by river discharge is balanced by the landward salt transport due to tidal advection and horizontal diffusion. It is found that the tidal advection behaves as a diffusion process, and this contribution is named tidal advective diffusion. The horizontal diffusion parameterizes processes not explicitly resolved in the model and is called the prescribed diffusion. The tidal advective diffusion results from the correlation between the tidal velocity and salinity and can be explicitly calculated with the dominant semidiurnal water motion. The sensitivity analysis shows that tidal advective diffusivity increases with increasing bed roughness and decreasing vertical eddy viscosity. Furthermore, tidal advective diffusivity reaches its maximum for moderate water depth and moderate convergence length. The relative importance of tidal advective diffusion is investigated using the residual salt balance, with the prescribed diffusion coefficient obtained from the measured salinity field. The tidal advective diffusion dominates the residual salt transport in the Scheldt estuary, and other processes significantly contribute to the residual salt transport in the Delaware estuary and the Columbia estuary.
Numerical Simulation of Global-Scale Atmospheric Chemical Transport with High-Order Wavelet-Based Adaptive Mesh Refinement Algorithm
Authors: Semakin A. N. , Rastigejev Y.
Published: February 2016

High computational cost associated with numerical modeling of multiscale global atmospheric chemical transport (ACT) imposes severe limitations on the spatial resolution of fixed nonadaptive grids. Recently it has been shown that the interaction of numerical diffusion caused by the crude resolution with complex velocity field of atmospheric flows leads to large numerical errors. To address the described difficulties, the authors have developed a wavelet-based adaptive mesh refinement (WAMR) method for numerical simulation of two-dimensional multiscale ACT problems. The WAMR is an adaptive method that minimizes the number of grid points by introducing a fine grid only in the locations where fine spatial scales occur and uses high-order spatial discretization throughout the computational domain. The algorithm has been tested for several challenging ACT problems. Particularly, it is shown that the method correctly simulates dynamics of a pollution plume traveling on a global scale, producing less than 1% error with a relatively low number (~105) of grid points. To achieve such accuracy, conventional nonadaptive techniques would require more than three orders of magnitude more computational resources. The method possesses good mass conservation properties; it is shown that an error in the total pollutant mass does not exceed 0.02% for this number of points. The obtained results demonstrate the WAMR’s ability to achieve high numerical accuracy for challenging ACT problems at a relatively low computational cost.
Regulating California’s Prison Population
Authors: Austin James
Published: February 2016

While many scholars and social commentators bemoan the rise of “mass incarceration” in the United States, few states have succeeded in significantly reducing prison populations. Fueled by systemic changes in penal codes, sentencing practices, and federal funding all designed to increase the use of imprisonment, most states have been unable to reverse the massive increase that has transpired over the past four decades. More alarming, there are few indications that mass incarceration will be reduced any time soon. There are a few exceptions, with California being one. Since 2007, California’s prison population has dropped by over 43,000 prisoners. Reductions have also been achieved in the state parole (82,000) and probation (15,000) populations. Today there are 146,000 fewer Californians in prison, jail, parole, or probation. Initially driven largely by a period of lengthy litigation, a rare federal court order to depopulate, several other reforms, reflecting a sticks and carrots approach, were introduced beginning in 2007 to lower imprisonment rates. Among them was “Realignment,” which relocated approximately 27,000 state prisoners to the counties. However, it required another stick in the form of a ballot initiative (Proposition 47) to further reduce the prison population and meet compliance with the federal court order. In the end, it was the externally imposed dual “sticks” of litigation and a ballot initiative that proved to be the driving forces in reducing California’s use of mass incarceration.
Who Are the People in Your Neighborhood? Neighborhood Age Composition and Age Discrimination
Authors: Stokes Jeffrey E. , Moorman Sara M.
Published: February 2016

Age discrimination is pervasive in the United States, yet little is known about the social contexts in which it occurs. Older persons spend much of their time in their neighborhoods, where a density of other older persons may protect against age discrimination. Extending group density theory to age, we analyze data from 1,561 older adults from the second wave of the National Survey of Midlife Development in the United States, using neighborhood-level data from the 2010 U.S. census. We examine (1) whether the concentration of older neighborhood residents influences perceived age discrimination and (2) whether that influence varies by age. Results indicate that the density of older residents protects against age discrimination for individuals entering old age but it is decreasingly influential as individuals approach oldest-old age and report less age discrimination regardless of neighborhood age composition. We discuss the implications of these findings for theory on age discrimination.
The Age-Graded Nature of Advice
Authors: Schafer Markus H. , Upenieks Laura
Published: February 2016

Drawing from life course, social networks, and developmental social psychology scholarship, this article considers how advice transmission varies across age groups and examines the age-contingent associations between advice-giving and life meaning. Binomial and ordered logistic regression using the 2006 Portraits of American Life Study ( n = 2,583) reveal that adults in their twenties are most likely to report offering advice to multiple social targets. Notably, however, the connection between advice-giving and life meaning is most pronounced for late-middle age adults—even as changes during this part of the life course reduce the odds of advice exchange. Consistent with developmental theory and the mattering perspective, we argue that advice is a mechanism for contributing to others’ welfare and for cultivating life meaning. Yet opportunity structures for advice transmission also shift over life course, leaving adults in late-middle age and beyond with fewer opportunities to engage in such generative practices.
Reverse Integration in Wheelchair Basketball
Authors: Hutzler Yeshayahu , Barda Rachel , Mintz Ahuva , Hayosh Tali
Published: February 2016

Wheelchair basketball is one of the most popular sport activities among persons with disabilities. The current study focuses on “reverse integration” (RI) groups of athletes with and without disabilities playing wheelchair basketball in Israel. A qualitative analysis approach was chosen to examine whether the able-bodied participants in RI wheelchair basketball training and competition identify their participation as a “serious leisure” (SL) activity, and to determine which additional insights could be gained about this activity from participants’ perspectives. Eight male able-bodied participants, who have taken part in three Israeli wheelchair basketball leagues (divisions), were interviewed. All eight participants in this study played longer than a year. The findings revealed support for the SL premise within all six SL criteria. Participation of our informants was categorized within the establishment and maintenance phases. All participants reported sustained perseverance in spite of having to deal with significant challenges, including the physical strain and mental difficulties associated with the game, coping with dual roles of participation as player and coach, and finally, having to face the same economical and social barriers typically reported by athletes with disability.
African attitudes toward foreign countries: A hierarchical approach
Authors: Inman Kris L.
Published: February 2016

This study uses a hierarchical statistical model to explore what drives African attitudes toward foreign countries, an understudied and underappreciated topic in the fields of African studies, political psychology and international relations. Enabled by increasing access to information, technology and resources, African peoples across the continent are directing their national stages like never before. Yet when it comes to international engagements on the continent, there is little scholarly focus on African sentiment toward foreign countries. The present study finds that the drivers of attitudes toward foreign countries vary, depending on which foreign country is under consideration by the respondent. For China, positive sentiment is associated with individuals who report having assets, belong to the president’s party, view domestic governance positively, are more politically interested, are more trusting, are educated and are more frequent news consumers. While political interest, trust, education, news consumption and positive evaluation of domestic governance also correspond to positive attitudes toward the USA, so does being employed and perceiving the domestic government as corrupt. When it comes to attitudes toward former colonies, trust, education, news consumption, positive evaluations of domestic governance, perceiving the domestic government as corrupt, employment, identification with the president’s party and support for democracy are associated with positive sentiment. For China, the USA and former colonies, negative sentiment is associated with individuals who identify as Muslim.
Admission to the Intensive Care Unit is Associated With Changes in the Oral Mycobiome
Authors: Watkins Richard R. , Mukherjee Pranab K. , Chandra Jyotsna , Retuerto Mauricio A. , Guidry Chrissy , Haller Nairmeen , Paranjape Charudutt , Ghannoum Mahmoud A.
Published: February 2016

A prospective exploratory study was conducted to characterize the oral mycobiome at baseline and determine whether changes occur after admission to the intensive care unit (ICU). We found that ICU admission is associated with alterations in the oral mycobiome, including an overall increase in Candida albicans.
A solution to transient failures of HVI track circuits caused by inrush interference based on wavelet analysis
Authors: Huang Zanwu , Roberts Clive , Chen Lei , Li Shaobin , Wang Hongguang
Published: February 2016

A track circuit never reporting block failure means a track section is reported as vacant to a railway control system, even if it is occupied by a train. This is a wrong side failure which may cause an accident. A high-voltage impulse (HVI) track circuit based on the fast Fourier transform is currently in use in China to solve this problem, but it has been observed that when used in electric railway systems large inrush currents can lead to another track circuit failure mode, which is referred to as a transient reporting block (TRB) in this paper. The root causes and impact of TRB track circuit failures are analyzed and a solution to the TRB failure mode based on wavelet analysis is proposed. Computer simulations and onsite experiments are carried out and the results show that the proposed approach can accurately extract the feature frequency and then effectively avoid the TRB failure, even if the HVI track signal is disturbed by a significant inrush of traction-return current.
Disability and HIV in Africa: Breaking the barriers to sexual health care
Authors: Rohleder Poul
Published: February 2016

Three decades into the HIV pandemic, the issues affecting people with disabilities remain less known. Increasing attention has been given to this overlooked population when it comes to HIV prevention, treatment and care. This is related to the significant unmet sexual and reproductive healthcare needs facing people with disabilities worldwide. This article discusses the barriers to sexual health for people with disabilities in Africa and presents an argument about how mainstream HIV prevention work and research do not adequately attend to the sorts of systemic barriers that exclude people with disabilities, which a more targeted and critical approach could.
Gaze direction when driving after dark on main and residential roads: Where is the dominant location?
Authors: Winter J , Fotios S , Völker S
Published: February 2016

CIE Joint Technical Committee JTC-1 has requested data regarding the size and shape of the distribution of drivers’ eye movement in order to characterize visual adaptation. This paper reports the eye movement of drivers along two routes in Berlin after dark, a main road and a residential street, captured using eye tracking. It was found that viewing behaviour differed between the two types of road. On the main road eye movement was clustered within a circle of approximately 10° diameter, centred at the horizon of the lane. On the residential street eye movement is clustered slightly (3.8°) towards the near side, eye movements were best captured with either an ellipse of approximate axes 10° vertical and 20° horizontal, centred on the lane ahead, or a 10° circle centred 3.8° towards the near side. These distributions reflect a driver’s tendency to look towards locations of anticipated hazards.
An overall ablation model of ethylene-propylene-diene monomer based on porous characteristics in char layer
Authors: Liu Yang , Yang Sa , He Guoqiang , Li Jiang
Published: February 2016

A numerical methodology has been developed to simulate the overall ablation process of the insulator material named ethylene-propylene-diene monomer. Special attention is focused on the char layers of ethylene-propylene-diene monomer formed in different ablation environments by analyzing the characters of the char layers, which was defined as an uneven porous medium. An overall ablation model has been developed to describe the simultaneous thermo-chemical ablation and particle erosion of ethylene-propylene-diene monomer using porous medium equation methodology. A total of six calculations of one kind of ethylene-propylene-diene monomer material have been performed to obtain the theory erosion properties in two lab-scale solid rocket motors, and all the submodels of overall ablation model have been validated.
The Dan Rather Maxim: Collective identity and news coverage of human rights and international law
Authors: Major Mark
Published: February 2016

This article examines the influence of national identity on coverage of human rights and international law. Based on a content analysis of New York Times, Washington Post, and USA Today’s coverage of torture at Abu Ghraib and the Obama administration’s expansion of drone warfare, it is argued that the news media largely protects the American identity by ignoring or marginalizing considerations of human rights and international law, despite these issues being central to the events. This research posits that the news media adheres to the Dan Rather Maxim named after long-time CBS news anchor, Dan Rather, who noted that in times of conflict the press tends to ‘follow the flag’. In other words, national identity informs and ultimately skews coverage of conflicts. This article adds to the existing scholarship on social and national identity biases in the news by giving primacy to international law and human rights frames during controversial periods. The content analysis finds that the actions of US political actors and institutions do not receive ample treatment when viewed through the lens of human rights and international humanitarian law.
Inhaled nitric oxide decreases pulmonary endothelial nitric oxide synthase expression and activity in normal newborn rat lungs
Authors: Hua-Huy Thông , Duong-Quy Sy , Pham Hoa , Pansiot Julien , Mercier Jean-Christophe , Baud Olivier , Dinh-Xuan Anh Tuan
Published: February 2016

Inhaled nitric oxide (iNO) is commonly used in the treatment of very ill pre-term newborns. Previous studies showed that exogenous NO could affect endothelial NO synthase (eNOS) activity and expression in vascular endothelial cell cultures or adult rat models, but this has never been fully described in newborn rat lungs. We therefore aimed to assess the effects of iNO on eNOS expression and activity in newborn rats.

Rat pups, post-natal day (P) 0 to P7, and their dams were placed in a chamber containing NO at 5 ppm (iNO-5 ppm group) or 20 ppm (iNO-20 ppm group), or in room air (control group). Rat pups were sacrificed at P7 and P14 for evaluation of lung eNOS expression and activity.

At P7, eNOS protein expression in total lung lysates, in bronchial and arterial sections, was significantly decreased in the iNO-20 ppmversuscontrol group. At P14, eNOS expression was comparable among all three groups. The amounts of eNOS mRNA significantly differed at P7 between the iNO-20 ppm and control groups. NOS activity decreased in the iNO-20 ppm group at P7 and returned to normal levels at P14. There was an imbalance between superoxide dismutase and NOS activities in the iNO-20 ppm group at P7.

Inhalation of NO at 20 ppm early after birth decreases eNOS gene transcription, protein expression and enzyme activity. This decrease might account for the rebound phenomenon observed in patients treated with iNO.
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
Authors: Kim Minji , Zhang Xiejia , Ligo Jonathan G. , Farnoud Farzad , Veeravalli Venugopal V. , Milenkovic Olgica
Published: February 2016

Background

Metagenomics is a genomics research discipline devoted to the study of microbial communities in environmental samples and human and animal organs and tissues. Sequenced metagenomic samples usually comprise reads from a large number of different bacterial communities and hence tend to result in large file sizes, typically ranging between 1–10 GB. This leads to challenges in analyzing, transferring and storing metagenomic data. In order to overcome these data processing issues, we introduce MetaCRAM, the first de novo, parallelized software suite specialized for FASTA and FASTQ format metagenomic read processing and lossless compression.

Results

MetaCRAM integrates algorithms for taxonomy identification and assembly, and introduces parallel execution methods; furthermore, it enables genome reference selection and CRAM based compression. MetaCRAM also uses novel reference-based compression methods designed through extensive studies of integer compression techniques and through fitting of empirical distributions of metagenomic read-reference positions. MetaCRAM is a lossless method compatible with standard CRAM formats, and it allows for fast selection of relevant files in the compressed domain via maintenance of taxonomy information. The performance of MetaCRAM as a stand-alone compression platform was evaluated on various metagenomic samples from the NCBI Sequence Read Archive, suggesting 2- to 4-fold compression ratio improvements compared to gzip. On average, the compressed file sizes were 2-13 percent of the original raw metagenomic file sizes.

Conclusions

We described the first architecture for reference-based, lossless compression of metagenomic data. The compression scheme proposed offers significantly improved compression ratios as compared to off-the-shelf methods such as zip programs. Furthermore, it enables running different components in parallel and it provides the user with taxonomic and assembly information generated during execution of the compression pipeline.

Availability

The MetaCRAM software is freely available at http://web.engr.illinois.edu/~mkim158/metacram.html. The website also contains a README file and other relevant instructions for running the code. Note that to run the code one needs a minimum of 16 GB of RAM. In addition, virtual box is set up on a 4GB RAM machine for users to run a simple demonstration.
Treatment of periodontal intrabony defects using autologous periodontal ligament stem cells: a randomized clinical trial
Authors: Chen Fa-Ming , Gao Li-Na , Tian Bei-Min , Zhang Xi-Yu , Zhang Yong-Jie , Dong Guang-Ying , Lu Hong , Chu Qing , Xu Jie , Yu Yang , Wu Rui-Xin , Yin Yuan , Shi Songtao , Jin Yan
Published: February 2016

Background

Periodontitis, which progressively destroys tooth-supporting structures, is one of the most widespread infectious diseases and the leading cause of tooth loss in adults. Evidence from preclinical trials and small-scale pilot clinical studies indicates that stem cells derived from periodontal ligament tissues are a promising therapy for the regeneration of lost/damaged periodontal tissue. This study assessed the safety and feasibility of using autologous periodontal ligament stem cells (PDLSCs) as an adjuvant to grafting materials in guided tissue regeneration (GTR) to treat periodontal intrabony defects. Our data provide primary clinical evidence for the efficacy of cell transplantation in regenerative dentistry.

Methods

We conducted a single-center, randomized trial that used autologous PDLSCs in combination with bovine-derived bone mineral materials to treat periodontal intrabony defects. Enrolled patients were randomly assigned to either the Cell group (treatment with GTR and PDLSC sheets in combination with Bio-oss®) or the Control group (treatment with GTR and Bio-oss® without stem cells). During a 12-month follow-up study, we evaluated the frequency and extent of adverse events. For the assessment of treatment efficacy, the primary outcome was based on the magnitude of alveolar bone regeneration following the surgical procedure.

Results

A total of 30 periodontitis patients aged 18 to 65 years (48 testing teeth with periodontal intrabony defects) who satisfied our inclusion and exclusion criteria were enrolled in the study and randomly assigned to the Cell group or the Control group. A total of 21 teeth were treated in the Control group and 20 teeth were treated in the Cell group. All patients received surgery and a clinical evaluation. No clinical safety problems that could be attributed to the investigational PDLSCs were identified. Each group showed a significant increase in the alveolar bone height (decrease in the bone-defect depth) over time (p < 0.001). However, no statistically significant differences were detected between the Cell group and the Control group (p > 0.05).

Conclusions

This study demonstrates that using autologous PDLSCs to treat periodontal intrabony defects is safe and does not produce significant adverse effects. The efficacy of cell-based periodontal therapy requires further validation by multicenter, randomized controlled studies with an increased sample size.

Trial Registration

NCT01357785 Date registered: 18 May 2011.
Functioning of drug-metabolizing microsomal cytochrome P450s: In silico probing of proteins suggests that the distal heme ‘active site’ pocket plays a relatively ‘passive role’ in some enzyme-substrate interactions
Authors: Venkatachalam Avanthika , Parashar Abhinav , Manoj Kelath Murali
Published: February 2016

Purpose

The currently held mechanistic understanding of microsomal cytochrome P450s (CYPs) seeks that diverse drug molecules bind within the deep-seated distal heme pocket and subsequently react at the heme centre. To explain a bevy of experimental observations and meta-analyses, we indulge a hypothesis that involves a “diffusible radical mediated” mechanism. This new hypothesis posits that many substrates could also bind at alternate loci on/within the enzyme and be reacted without the pertinent moiety accessing a bonding proximity to the purported catalytic Fe-O enzyme intermediate.

Methods

Through blind and heme-distal pocket centered dockings of various substrates and non-substrates (drug molecules of diverse sizes, classes, topographies etc.) of microsomal CYPs, we explored the possibility of access of substrates via the distal channels, its binding energies, docking orientations, distance of reactive moieties (or molecule per se) to/from the heme centre, etc. We investigated specific cases like- (a) large drug molecules as substrates, (b) classical marker drug substrates, (c) class of drugs as substrates (Sartans, Statins etc.), (d) substrate preferences between related and unrelated CYPs, (e) man-made site-directed mutants’ and naturally occurring mutants’ reactivity and metabolic disposition, (f) drug-drug interactions, (g) overall affinities of drug substrate versus oxidized product, (h) meta-analysis ofin silicoversus experimental binding constants and reaction/residence times etc.

Results

It was found that heme-centered dockings of the substrate/modulator drug molecules with the available CYP crystal structures gave poor docking geometries and distances from Fe-heme centre. In conjunction with several other arguments, the findings discount the relevance of erstwhile hypothesis in many CYP systems. Consequently, the newly proposed hypothesis is deemed a viable alternate, as it satisfies Occam’s razor.

Conclusions

The new proposal affords expanded scope for explaining the mechanism, kinetics and overall phenomenology of CYP mediated drug metabolism. It is now understood that the heme-iron and the hydrophobic distal pocket of CYPs serve primarily to stabilize the reactive intermediate (diffusible radical) and the surface or crypts of the apoprotein bind to the xenobiotic substrate (and in some cases, the heme distal pocket could also serve the latter function). Thus, CYPs enhance reaction rates and selectivity/specificity via a hitherto unrecognized modality.
Joint stochastic constraint of a large data set from a salt dome
Authors: Roberts Alan W. , Hobbs Richard W. , Goldstein Michael , Moorkamp Max , Jegen Marion , Heincke Bjørn
Published: February 2016

Understanding the uncertainty associated with large joint geophysical surveys, such as 3D seismic, gravity, and magnetotelluric (MT) studies, is a challenge, conceptually and practically. By demonstrating the use of emulators, we have adopted a Monte Carlo forward screening scheme to globally test a prior model space for plausibility. This methodology means that the incorporation of all types of uncertainty is made conceptually straightforward, by designing an appropriate prior model space, upon which the results are dependent, from which to draw candidate models. We have tested the approach on a salt dome target, over which three data sets had been obtained; wide-angle seismic refraction, MT and gravity data. We have considered the data sets together using an empirically measured uncertain physical relationship connecting the three different model parameters: seismic velocity, density, and resistivity, and we have indicated the value of a joint approach, rather than considering individual parameter models. The results were probability density functions over the model parameters, together with a halite probability map. The emulators give a considerable speed advantage over running the full simulator codes, and we consider their use to have great potential in the development of geophysical statistical constraint methods.