bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stroke vision, aphasia, neglect (VAN) assessment—a novel emergent large vessel occlusion screening tool: pilot study and comparison with current clinical severity indices
Authors: Teleb Mohamed S , Ver Hage Anna , Carter Jaqueline , Jayaraman Mahesh V , McTaggart Ryan A 
Published: February 2016

BackgroundIdentification of emergent large vessel occlusion (ELVO) stroke has become increasingly important with the recent publications of favorable acute stroke thrombectomy trials. Multiple screening tools exist but the length of the examination and the false positive rate range from good to adequate. A screening tool was designed and tested in the emergency department using nurse responders without a scoring system.MethodsThe vision, aphasia, and neglect (VAN) screening tool was designed to quickly assess functional neurovascular anatomy. While objective, there is no need to calculate or score with VAN. After training participating nurses to use it, VAN was used as an ELVO screen for all stroke patients on arrival to our emergency room before physician evaluation and CT scan.ResultsThere were 62 consecutive code stroke activations during the pilot study. 19 (31%) of the patients were VAN positive and 24 (39%) had a National Institutes of Health Stroke Scale (NIHSS) score of ≥6. All 14 patients with ELVO were either VAN positive or assigned a NIHSS score ≥6. While both clinical severity thresholds had 100% sensitivity, VAN was more specific (90% vs 74% for NIHSS ≥6). Similarly, while VAN and NIHSS ≥6 had 100% negative predictive value, VAN had a 74% positive predictive value while NIHSS ≥6 had only a 58% positive predictive value.ConclusionsThe VAN screening tool accurately identified ELVO patients and outperformed a NIHSS ≥6 severity threshold and may best allow clinical teams to expedite care and mobilize resources for ELVO patients. A larger study to both validate this screening tool and compare with others is warranted.
Ascending Aortic Aneurysm in Angiotensin II–Infused Mice
Authors: Trachet Bram , Piersigilli Alessandra , Fraga-Silva Rodrigo A. , Aslanidou Lydia , Sordet-Dessimoz Jessica , Astolfo Alberto , Stampanoni Marco F.M. , Segers Patrick , Stergiopulos Nikolaos 
Published: February 2016

Objective—

To understand the anatomy and physiology of ascending aortic aneurysms in angiotensin II–infused ApoE
−/−
mice.

Approach and Results—

We combined an extensive in vivo imaging protocol (high-frequency ultrasound and contrast-enhanced microcomputed tomography at baseline and after 3, 10, 18, and 28 days of angiotensin II infusion) with synchrotron-based ultrahigh resolution ex vivo imaging (phase contrast X-ray tomographic microscopy) in n=47 angiotensin II–infused mice and 6 controls. Aortic regurgitation increased significantly over time, as did the luminal volume of the ascending aorta. In the samples that were scanned ex vivo, we observed one or several focal dissections, with the largest located in the outer convex aspect of the ascending aorta. The volume of the dissections moderately correlated to the volume of the aneurysm as measured in vivo (
r
2
=0.46). After 3 days of angiotensin II infusion, we found an interlaminar hematoma in 7/12 animals, which could be linked to an intimal tear. There was also a significant increase in single laminar ruptures, which may have facilitated a progressive enlargement of the focal dissections over time. At later time points, the hematoma was resorbed and the medial and adventitial thickness increased. Fatal transmural dissection occurred in 8/47 mice at an early stage of the disease, before adventita remodeling.

Conclusions—
We visualized and quantified the dissections that lead to ascending aortic aneurysms in angiotensin II–infused mice and provided unique insight into the temporal evolution of these lesions.
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.
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.
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.
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

Abstract
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

Abstract
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

AbstractUnderstanding 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

AbstractHigh 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.
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

Abstract
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.