bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of Brain ATP-Binding Cassette Transporter A-1 Exacerbates Blood–Brain Barrier and White Matter Damage After Stroke
Authors: Cui Xu , Chopp Michael , Zacharek Alex , Karasinska Joanna M. , Cui Yisheng , Ning Ruizhuo , Zhang Yi , Wang Yun , Chen Jieli 
Published: January 2015

Background and Purpose—
The ATP-binding cassette transporter A-1 (ABCA1) gene is a key target of the transcription factors liver X receptors. Liver X receptor activation has anti-inflammatory and neuroprotective effects in animal ischemic stroke models. Here, we tested the hypothesis that brain ABCA1 reduces blood–brain barrier (BBB) and white matter (WM) impairment in the ischemic brain after stroke.

Methods—

Adult brain-specific ABCA1–deficient (ABCA1
−B/−B
) and floxed-control (ABCA1
fl/fl
) mice were subjected to permanent distal middle cerebral artery occlusion and were euthanized 7 days after distal middle cerebral artery occlusion. Functional outcome, infarct volume, BBB leakage, and WM damage were analyzed.

Results—

Compared with ABCA1
fl/fl
mice, ABCA1
−B/−B
mice showed marginally (
P
=0.052) increased lesion volume but significantly increased BBB leakage and WM damage in the ischemic brain and more severe neurological deficits. Brain ABCA1–deficient mice exhibited increased the level of matrix metalloproteinase-9 and reduced the level of insulin-like growth factor 1 in the ischemic brain. BBB leakage was inversely correlated (
r
=−0.073;
P
<0.05) with aquaporin-4 expression. Reduction of insulin-like growth factor 1 and aquaporin-4, but upregulation of matrix metalloproteinase-9 expression were also found in the primary astrocyte cultures derived from ABCA1
−B/−B
mice. Cultured primary cortical neurons derived from C57BL/6 wild-type mice with ABCA1
−B/−B
astrocyte–conditioned medium exhibited decreased neurite outgrowth compared with culture with ABCA1
fl/fl
astrocyte–conditioned medium. ABCA1
−B/−B
primary cortical neurons show significantly decreased neurite outgrowth, which was attenuated by insulin-like growth factor 1 treatment.

Conclusions—
We demonstrate that brain ABCA1 deficiency increases BBB leakage, WM/axonal damage, and functional deficits after stroke. Concomitant reduction of insulin-like growth factor 1 and upregulation of matrix metalloproteinase-9 may contribute to brain ABCA1 deficiency–induced BBB and WM/axonal damage in the ischemic brain.
Outcome in Patients Previously on Antithrombotic Therapy in the SAMMPRIS Trial
Authors: Lutsep Helmi L. , Barnwell Stanley L. , Larsen Darren T. , Lynn Michael J. , Hong Mindy , Turan Tanya N. , Derdeyn Colin P. , Fiorella David , Janis L. Scott , Chimowitz Marc I. 
Published: January 2015

Background and Purpose—
Stenting has been used as a rescue therapy in patients with intracranial arterial stenosis and a transient ischemic attack or stroke when on antithrombotic therapy (AT). We determined whether the stenting versus aggressive medical therapy for intracranial arterial stenosis (SAMMPRIS) trial supported this approach by comparing the treatments within subgroups of patients whose qualifying event (QE) occurred on versus off of AT.

Methods—
The primary outcome, 30-day stroke and death and later strokes in the territory of the qualifying artery, was compared between (1) percutaneous transluminal angioplasty and stenting plus aggressive medical therapy (PTAS) versus aggressive medical management therapy alone (AMM) for patients whose QE occurred on versus off AT and between (2) patients whose QE occurred on versus off AT separately for the treatment groups.

Results—

Among the 284/451 (63%) patients who had their QE on AT, the 2-year primary end point rates were 15.6% for those randomized to AMM (n=140) and 21.6% for PTAS (n=144;
P
=0.043, log-rank test). In the 167 patients not on AT, the 2-year primary end point rates were 11.6% for AMM (n=87) and 18.8% for PTAS (n=80;
P
=0.31, log-rank test). Within both treatment groups, there was no difference in the time to the primary end point between patients who were on or off AT (AMM,
P
=0.96; PTAS,
P
=0.52; log-rank test).

Conclusions—
SAMMPRIS results indicate that the benefit of AMM over PTAS is similar in patients on versus off AT at the QE and that failure of AT is not a predictor of increased risk of a primary end point.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00576693.
Daily Precipitation Extreme Events in the Iberian Peninsula and Its Association with Atmospheric Rivers*
Authors: Ramos Alexandre M. , Trigo Ricardo M. , Liberato Margarida L. R. , Tomé Ricardo 
Published: January 2015

Abstract
An automated atmospheric rivers (ARs) detection algorithm is used for the North Atlantic Ocean basin that allows the identification and a comprehensive characterization of the major AR events that affected the Iberian Peninsula over the 1948–2012 period. The extreme precipitation days in the Iberian Peninsula and their association (or not) with the occurrence of ARs is analyzed in detail. The extreme precipitation days are ranked by their magnitude and are obtained after considering 1) the area affected and 2) the precipitation intensity. Different rankings are presented for the entire Iberian Peninsula, for Portugal, and for the six largest Iberian river basins (Minho, Duero, Tagus, Guadiana, Guadalquivir, and Ebro) covering the 1950–2008 period. Results show that the association between ARs and extreme precipitation days in the western domains (Portugal, Minho, Tagus, and Duero) is noteworthy, while for the eastern and southern basins (Ebro, Guadiana, and Guadalquivir) the impact of ARs is reduced. In addition, the contribution from ARs toward the extreme precipitation ranking list is not homogenous, playing an overwhelming role for the most extreme precipitation days but decreasing significantly with the less extreme precipitation days. Moreover, and given the narrow nature of the ARs, the location of the ARs over each subdomain is closely related to the occurrence (or not) of extreme precipitation days.
Modelling the Impact of Squall on Wind Waves with the Generalized Kinetic Equation
Authors: Annenkov Sergei , Shrira Victor 
Published: January 2015

AbstractThis is a first study of short-lived transient sea states, arising from fast variations of wind fields. This study considers the response of a wind-wave field to a sharp increase of wind over a short time interval (a squall). Conventional wind-wave models based on the Hasselmann equation assume quasi stationarity of a random wave field and are a priori inapplicable for such transient states. To describe fast spectral changes, the authors use the generalized kinetic equation (GKE) derived without the quasi-stationarity assumption. A novel efficient highly parallelized algorithm for the numerical simulation of the GKE is presented. Simulations with the GKE and the Hasselmann equation are examined and compared. While under steady wind, the spectral evolution in both cases is shown to be practically identical, but after the squall the qualitative difference emerges: the GKE predicts formation of a transient sea state with a considerably narrower peak.
A 35-GHz Polarimetric Doppler Radar for Long-Term Observations of Cloud Parameters—Description of System and Data Processing
Authors: Görsdorf Ulrich , Lehmann Volker , Bauer-Pfundstein Matthias , Peters Gerhard , Vavriv Dmytro , Vinogradov Vladimir , Volkov Vadim 
Published: January 2015

AbstractA 35-GHz radar has been operating at the Meteorological Observatory Lindenberg (Germany) since 2004, measuring cloud parameters continuously. The radar is equipped with a powerful magnetron transmitter and a high-gain antenna resulting in a high sensitivity of −55 dBZ at 5-km height for a 10-s averaging time. The main purpose of the radar is to provide long-term datasets of cloud parameters for model evaluation, satellite validation, and climatological studies. Therefore, the system operates with largely unchanged parameter settings and a vertically pointing antenna. The accuracy of the internal calibration (budget calibration) has been appraised to be 1.3 dB. Cloud parameters are derived by two different approaches: macrophysical parameters have been deduced for the complete period of operation through combination with ceilometer measurements; a more enhanced target classification and the calculation of liquid and ice water contents are realized by algorithms developed in the framework of the European CloudNet project.
Morphological Pattern Classification System for Plantar Thermography of Patients with Diabetes
Authors: Mori Taketoshi , Nagase Takashi , Takehara Kimie , Oe Makoto , Ohashi Yumiko , Amemiya Ayumi , Noguchi Hiroshi , Ueki Kohjiro , Kadowaki Takashi , Sanada Hiromi 
Published: January 2015

Background: A plantar temperature distribution can be obtained by thermography; however, the advantage has not been effectively utilized in the past. We previously proposed a classification method based on the angiosome concept, but the method was insufficient because it was too subjective and complicated for clinicians. In this study, we propose a new classification system of plantar forepart thermographic patterns using an image segmentation technique. Methods: A cross-sectional observational study was conducted including 32 healthy volunteers and 129 patients with diabetes mellitus (DM). Individual thermographic variations and trends were evaluated. A comparison was conducted between the patterns obtained by our previous angiosome-based research and the patterns found by the new classification system. Results: The system objectively found wider variations of the plantar forepart thermographic patterns in the patients with DM compared with those in the control subjects. In patients with DM, the system showed that the whole-high pattern was most frequent (46%), followed by the butterfly pattern (12%). In the control group, the butterfly pattern was most frequent (44%), followed by the whole-high pattern (19%). Both ankle and toe brachial indices were higher in feet with high temperature area in the inner side of the plantar. Conclusions: Thermographic patterns found by the new computer-based system were similar to those obtained in our previous subjective work. The classification system found forefoot-low pattern and tiptoe-low pattern objectively. The system based on infrared thermography will be a screening tool to assess circulatory status in daily foot care of patients with DM.
Plantar Pressure Distribution Patterns of Individuals with Prediabetes in Comparison with Healthy Individuals and Individuals with Diabetes
Authors: Robinson Caroline Cabral , Balbinot Luciane Fachin , Silva Marcelo Faria , Achaval Matilde , Zaro Milton Antônio 
Published: January 2015

Background: Since elevated mechanical stress along with loss of plantar protective sensation are considered relevant factors in skin breakdown resulting in diabetic foot ulcerations, the assessment of plantar pressure is important for the prevention of diabetic foot complications. Prediabetes subjects are at risk of chronic hyperglycemia complications, among them neuropathy, but information about plantar loading in this population is not available. We aimed to compare baropodometric parameters of individuals with prediabetes versus healthy persons and persons with diabetes mellitus (DM). Methods: Baropodometric data from 73 subjects (15 with prediabetes (pre-DM), 28 with type 2 DM, 30 healthy) aged between 29 and 69 years of both genders were registered through a pressure platform with self-selected gait speed and first-step protocol. Peak plantar pressure, stance time, percentage of contact time, percentage of contact area and pressure-time integral were assessed in five plantar foot regions: Heel, midfoot, metatarsals, hallux, and toes 2 to 5. Groups were compared by one-way analysis of variance with Scheffé post hoc (α = 0.05). Results: Age, body mass index, gender, and arch height index did not differ between groups. Pre-DM and DM subjects presented increased peak pressure and pressure-time integral in metatarsals ( p = .010; p > .001), as well as increased percentage of contact time in midfoot ( p = .006) and metatarsals ( p = .004) regions when compared with healthy subjects. Stance time was significantly higher ( p = .017) in DM subjects. Conclusions: Pre-DM subjects seem to exhibit an altered plantar pressure distribution pattern similar to that often found in DM subjects.
Novel Wearable Technology for Assessing Spontaneous Daily Physical Activity and Risk of Falling in Older Adults with Diabetes
Authors: Najafi Bijan , Armstrong David G. , Mohler Jane 
Published: January 2015

Background: As baby boomers age and their expected life span increases, there is an unprecedented need to better manage the health care of elders with diabetes who are at increased risk of falling due to diabetes complications, frailty, or other conditions. New clinical and research tools are needed to measure functioning accurately and to identify early indicators of risk of falling, thus translating into more effective and earlier intervention. Methods: The objective of this pilot study was to validate a significant change in hardware and algorithm to track activity patterns using a single triaxial accelerometer through validation of timed up and go and standard measures of balance and gait. We recruited a convenience sample of eight older adults with diabetes and peripheral neuropathy (age, 77 ±7 years old) who were asked to wear the sensor for imposed daytime activity performed in our gait laboratory. Subjects were stratified into risk of falling categories based on Tinetti scores. We examined the accuracy of the suggested technology for discrimination of high- versus low-risk groups. Results: The system was accurate in identifying the number of steps taken and walking duration (random error <5%). The proposed algorithm allowed accurate identification and stratification of those at highest risk of falling, suggesting that subjects with high risk of falling required a substantially longer duration for rising from a chair when compared with those with low risk of falling ( p < .05). Conclusions: Our new single triaxial accelerometer algorithm successfully tracked postural transition, allowing accurate identification of those at high risk of falling, and could be useful for intermittent or even continuous monitoring of older adults with diabetes. Other potential applications could include activity monitoring of the diabetes population with lower extremity disease and of patients undergoing surgical procedures or as an objective measure during rehabilitation.
Electrical Stimulation as an Adjunctive Treatment of Painful and Sensory Diabetic Neuropathy
Authors: Thakral Gaurav , Kim Paul J. , LaFontaine Javier , Menzies Robert , Najafi Bijan , Lavery Lawrence A. 
Published: January 2015

Background: The objective of this review is to evaluate the use of electrical stimulation to treat diabetic neuropathy. Application of electrical stimulation may provide a novel treatment option for large and small fiber neuropathy in persons with diabetes. Large and small nerve neuropathy alters pain, proprioception, touch perception, and motor function, which cause burning foot pain and serve as protective mechanisms from ulcerations. Methods: A content search for clinical trials involving electrical stimulation, neuropathy, and diabetes was conducted through PubMed. Randomized clinical trials and prospective studies with outcome measures affecting the lower extremity function were selected for review. Results: We identified eight studies in which electrical stimulation was used to treat diabetic neuropathy. Six studies evaluated small fiber neuropathy. Two studies evaluated patients with both small and large fiber neuropathy and reported significant improvement in vibration and monofilament testing and reduction in symptoms in the electrical stimulation treatment group. Six of the eight painful neuropathy studies identified significant improvement in symptoms. There were no studies that evaluated electrical stimulation to treated diabetic motor neuropathy, fall prevention or postural instability. Conclusions: Electrical stimulation may be an effective alternative and adjunctive therapy to current interventions for diabetic peripheral neuropathy.
Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice
Authors: Zhang Bin , Ye Weijun , Ren Deyong , Tian Peng , Peng Youlin , Gao Yang , Ruan Banpu , Wang Li , Zhang Guangheng , Guo Longbiao , Qian Qian , Gao Zhenyu 
Published: January 2015

Abstract

Background
Flag leaf is the most essential organ for photosynthesis in rice and its size plays an important role in rice breeding for ideal plant-type. Flag leaf size affect photosynthesis to a certain extent, thereby influencing rice production. Several genes controlling leaf size and shape have been identified with mutants. Although a number of quantitative trait loci (QTLs) for leaf size and shape have been detected on 12 chromosomes with different populations of rice, few of them were cloned.

Results
The pair-wise correlation analysis was conducted on length, width and length-width ratio of the flag leaf, and yield per plant in the core recombinant inbred lines of Liang-You-Pei-Jiu (LYP9) developed in Hainan and Hangzhou. There were significant correlations among the three flag leaf size and shape traits. Interestingly, a positive correlation was found between flag leaf width and yield per plant. Based on the high-resolution linkage map we constructed before, 43 QTLs were detected for three flag leaf size and shape traits and yield per plant, among which 31 QTLs were unreported so far. Seven QTLs were identified common in two environments. And qFLW7.2, a new major QTL for flag leaf width, was fine mapped within 27.1 kb region on chromosome 7. Both qFLW7.2 and qPY7 were located in the interval of 45.30 ~ 53.34 cM on chromosome 7, which coincided with the relationship between yield per plant (PY) and flag leaf width (FLW).

Conclusion

qFLW7.2, which explained 14% of the phenotypic variation, increased flag leaf width with 93–11 allele. Two candidate genes were selected based on sequence variation and expression difference between two parents, which facilitated further QTL cloning and molecular breeding in super rice.
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Authors: Kelly Benjamin J , Fitch James R , Hu Yangqiu , Corsmeier Donald J , Zhong Huachun , Wetzel Amy N , Nordquist Russell D , Newsom David L , White Peter 
Published: January 2015

AbstractWhile advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.
VERSE: a novel approach to detect virus integration in host genomes through reference genome customization
Authors: Wang Qingguo , Jia Peilin , Zhao Zhongming 
Published: January 2015

AbstractFueled by widespread applications of high-throughput next generation sequencing (NGS) technologies and urgent need to counter threats of pathogenic viruses, large-scale studies were conducted recently to investigate virus integration in host genomes (for example, human tumor genomes) that may cause carcinogenesis or other diseases. A limiting factor in these studies, however, is rapid virus evolution and resulting polymorphisms, which prevent reads from aligning readily to commonly used virus reference genomes, and, accordingly, make virus integration sites difficult to detect. Another confounding factor is host genomic instability as a result of virus insertions. To tackle these challenges and improve our capability to identify cryptic virus-host fusions, we present a new approach that detects Virus intEgration sites through iterative Reference SEquence customization (VERSE). To the best of our knowledge, VERSE is the first approach to improve detection through customizing reference genomes. Using 19 human tumors and cancer cell lines as test data, we demonstrated that VERSE substantially enhanced the sensitivity of virus integration site detection. VERSE is implemented in the open source package VirusFinder 2 that is available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
Expression of citrulline and homocitrulline residues in the lungs of non-smokers and smokers: implications for autoimmunity in rheumatoid arthritis
Authors: Lugli Elena B , Correia Raquel ESM , Fischer Roman , Lundberg Karin , Bracke Ken R , Montgomery Anna B , Kessler Benedikt M , Brusselle Guy G , Venables Patrick J 
Published: January 2015

Abstract
Introduction
Smoking is a well-established risk factor for rheumatoid arthritis (RA), and it has been proposed that smoking-induced citrullination renders autoantigens immunogenic. To investigate this mechanism, we examined human lung tissue from 40 subjects with defined smoking status, with or without chronic obstructive pulmonary disease (COPD), and control tissues from other organs for citrullinated proteins and the deiminating enzymes peptidylarginine deiminase type-2 (PAD2) and -4 (PAD4).

Methods
Lung tissue samples, dissected from lobectomy specimens from 10 never smokers, 10 smokers without airflow limitation, 13 COPD smokers and eight COPD ex-smokers, and control tissue samples (spleen, skeletal muscle, liver, ovary, lymph node, kidney and heart), were analysed for citrullinated proteins, PAD2 and PAD4 by immunoblotting. Citrulline and homocitrulline residues in enolase and vimentin were analysed by partial purification by gel electrophoresis followed by mass spectrometry in 12 of the lung samples and one from each control tissues. Band intensities were scored semi-quantitatively and analysed by two-tailed Mann-Whitney T-test.

Results
Within the lung tissue samples, citrullinated proteins, PAD2 and PAD4 were found in all samples, with an increase in citrullination in COPD (P = 0.039), but minimal difference between smokers and non-smokers (P = 0.77). Citrullination was also detected at lower levels in the tissues from other organs, principally in lymph node, kidney and skeletal muscle. Mass spectrometry of the lung samples showed that vimentin was citrullinated at positions 71, 304, 346, 410 and 450 in non-smokers and smokers both with and without COPD. A homocitrulline at position 104 was found in four out of six COPD samples and one out of six non-COPD. Citrulline-450 was also found in three of the control tissues. There were no citrulline or homocitrulline residues demonstrated in α-enolase.

Conclusions
We have shown evidence of citrullination of vimentin, a major autoantigen in RA, in both non-smokers and smokers. The increase in citrullinated proteins in COPD suggests that citrullination in the lungs of smokers is mainly due to inflammation. The ubiquity of citrullination of vimentin in the lungs and other tissues suggests that the relationship between smoking and autoimmunity in RA may be more complex than previously thought.