bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Land Model Calibration on Coupled Land–Atmosphere Prediction
Authors: Santanello Joseph A. , Kumar Sujay V. , Peters-Lidard Christa D. , Harrison Ken , Zhou Shujia 
Published: July 2013

Abstract
Land–atmosphere (LA) interactions play a critical role in determining the diurnal evolution of both planetary boundary layer (PBL) and land surface heat and moisture budgets, as well as controlling feedbacks with clouds and precipitation that lead to the persistence of dry and wet regimes. In this study, the authors examine the impact of improved specification of land surface states, anomalies, and fluxes on coupled Weather Research and Forecasting Model (WRF) forecasts during the summers of extreme dry (2006) and wet (2007) land surface conditions in the U.S. southern Great Plains. The improved land initialization and surface flux parameterizations are obtained through calibration of the Noah land surface model using the new optimization and uncertainty estimation subsystems in NASA's Land Information System (LIS-OPT/LIS-UE). The impact of the calibration on the 1) spinup of the land surface used as initial conditions and 2) the simulated heat and moisture states and fluxes of the coupled WRF simulations is then assessed. In addition, the sensitivity of this approach to the period of calibration (dry, wet, or average) is investigated. Results show that the offline calibration is successful in providing improved initial conditions and land surface physics for the coupled simulations and in turn leads to systematic improvements in land–PBL fluxes and near-surface temperature and humidity forecasts. Impacts are larger during dry regimes, but calibration during either primarily wet or dry periods leads to improvements in coupled simulations due to the reduction in land surface model bias. Overall, these results provide guidance on the questions of what, how, and when to calibrate land surface models for coupled model prediction.
Assessment of Spatial Rainfall Variability over the Lower Mississippi River Alluvial Valley
Authors: Dyer Jamie , Mercer Andrew 
Published: July 2013

Abstract
A large portion of the lower Mississippi River alluvial valley (LMRAV) relies on irrigation from the regional alluvial aquifer for crop sustainability, which is expensive both in terms of water resources and farmer expenditures because of the large volume of water necessary to maintain crop production. As a result, knowledge of the seasonal frequency and distribution of precipitation over the LMRAV is critical for water resources management, the development of irrigation strategies, and economic planning. This project addresses the need for a detailed assessment of regional precipitation patterns through the use of rotated principal component analysis (RPCA) of high-resolution gridded radar-derived rainfall data, which provides quantification of the spatial and temporal characteristics of rainfall over the LMRAV from 1996 to 2011. Results of the project show that precipitation depths over the LMRAV are generally lower and more variable than adjacent eastern areas throughout the year, although there is substantial variability between seasons. This pattern seems to be influenced more by variations during the cool season (January–March), which has a higher overall precipitation depth and lower spatial variability than the warm season (July–September). Results further indicate that warm season rainfall is generally lower and less predictable over the LMRAV as compared to the cool season, which may be detrimental to regional water resources since irrigation planning and permitting is heavily based on seasonal rainfall predictions.
Assessment of Model Error in Limited-Area Simulations of Shallow Water Test Cases on the C-Grid Plane and Sphere
Authors: Jeffery Christopher A. 
Published: July 2013

AbstractA suite of limited-area test cases for the solution of the shallow water (SW) equations on the plane and sphere is collected and evaluated using the Model for Prediction Across Scales (MPAS) modeling system. Included are regional simulations of standard test cases, as well as new viscous and linearized test cases with exact analytic solutions. Four different aspects of model error are isolated and thereby assessed: 1) error generated by grid nonuniformity on the plane and sphere, 2) time-independent (balanced) error and time-dependent (propagating wave) error, 3) lateral boundary implementation error, and 4) error reduction due to a viscous equation set or an absorbing sponge layer. Results show that the nature of model error for these test cases is specific to the geophysical regime: SW flows on a rotating sphere with Froude numbers of O(0.1) and Rossby numbers also of O(0.1). For SW simulations in this context, inward reflection of gravity waves at the domain boundary does not appear to be a driver of instability or a determining factor in solution accuracy. This conclusion has important implications for idealized studies that exclude this geophysical regime, in particular one-dimensional studies of lateral boundary conditions for limited-area models and studies of the absorption of linearized gravity waves at domain boundaries using dynamical relaxation. An old debate over the efficacy of dynamical relaxation for a viscous equation set is addressed; MPAS simulations of an SW test case with and without dynamical relaxation support claims that eddy viscosity does not notably improve solution accuracy or stability.
Treatment of acquired von Willebrand syndrome in childhood
Authors: Callaghan Michael U. , Wong Trisha E. , Federici Augusto B. 
Published: July 2013

Abstract
A 3-1/2-year-old male with no personal or family history of bleeding disorders presented with abdominal distension, epistaxis, and anemia (hemoglobin 8.2 g/dL). A magnetic resonance imaging scan of the abdomen demonstrated a mass arising from the left kidney. Preoperative laboratory studies revealed a prolonged activated partial thromboplastin time of 49.2 seconds, a normal prothrombin time of 12.4 seconds, and a platelet count of 230 000/μL. Further testing revealed factor VIII (FVIII) activity of 16%, factor IX (FIX) activity of 74%, von Willebrand factor (VWF) activity of 12%, VWF antigen activity of 31%, and decreased high-molecular-weight VWF multimers consistent with acquired von Willebrand syndrome (AVWS). What is the best treatment for this child?
On some inequalities for s-convex functions and applications
Authors: Özdemir Muhamet Emin , Yıldız Çetin , Akdemir Ahmet Ocak , Set Erhan 
Published: July 2013

Abstract
Some new results related to the left-hand side of the Hermite-Hadamard type inequalities for the class of functions whose second derivatives at certain powers are s-convex functions in the second sense are obtained. Also, some applications to special means of real numbers are provided.

MSC:26A51, 26D15.
Strong convergence for solving a general system of variational inequalities and fixed point problems in Banach spaces
Authors: Ceng Lu-Chuan , Hussain Nawab , Latif Abdul , Yao Jen-Chih 
Published: July 2013

Abstract
In this paper, we propose and analyze some iterative algorithms by hybrid viscosity approximation methods for solving a general system of variational inequalities and a common fixed point problem of an infinite family of nonexpansive mappings in a uniformly convex Banach space which has a uniformly Gâteaux differentiable norm, and we prove some strong convergence theorems under appropriate conditions. The results presented in this paper improve, extend, supplement and develop the corresponding results recently obtained in the literature.

MSC:49J30, 47H09, 47J20.
Blockade of bovine PD-1 increases T cell function and inhibits bovine leukemia virus expression in B cells in vitro
Authors: Ikebuchi Ryoyo , Konnai Satoru , Okagawa Tomohiro , Yokoyama Kazumasa , Nakajima Chie , Suzuki Yasuhiko , Murata Shiro , Ohashi Kazuhiko 
Published: July 2013

AbstractProgrammed death-1 (PD-1) is a known immunoinhibitory receptor that contributes to immune evasion of various tumor cells and pathogens causing chronic infection, such as bovine leukemia virus (BLV) infection. First, in this study, to establish a method for the expression and functional analysis of bovine PD-1, hybridomas producing monoclonal antibodies (mAb) specific for bovine PD-1 were established. Treatment with these anti-PD-1 mAb enhanced interferon-gamma (IFN-γ) production of bovine peripheral blood mononuclear cells (PBMC). Next, to examine whether PD-1 blockade by anti-PD-1 mAb could upregulate the immune reaction during chronic infection, the expression and functional analysis of PD-1 in PBMC isolated from BLV-infected cattle with or without lymphoma were performed using anti-PD-1 mAb. The frequencies of both PD-1+CD4+T cells in blood and lymph node and PD-1+CD8+T cells in lymph node were higher in BLV-infected cattle with lymphoma than those without lymphoma or control uninfected cattle. PD-1 blockade enhanced IFN-γ production and proliferation and reduced BLV-gp51 expression and B-cell activation in PBMC from BLV-infected cattle in response to BLV-gp51 peptide mixture. These data show that anti-bovine PD-1 mAb could provide a new therapy to control BLV infection via upregulation of immune response.
Phenotypic characterisation of the cellular immune infiltrate in placentas of cattle following experimental inoculation with Neospora caninum in late gestation
Authors: Cantón Germán J , Katzer Frank , Benavides-Silván Julio , Maley Stephen W , Palarea-Albaladejo Javier , Pang Yvonne , Smith Sionagh , Bartley Paul M , Rocchi Mara , Innes Elisabeth A , Chianini Francesca 
Published: July 2013

AbstractDespiteNeospora caninumbeing a major cause of bovine abortion worldwide, its pathogenesis is not completely understood.Neosporainfection stimulates host cell-mediated immune responses, which may be responsible for the placental damage leading to abortion. The aim of the current study was to characterize the placental immune response following an experimental inoculation of pregnant cattle withN. caninumtachyzoites at day 210 of gestation. Cows were culled at 14, 28, 42 and 56 days post inoculation (dpi). Placentomes were examined by immunohistochemistry using antibodies against macrophages, T-cell subsets (CD4, CD8 and γδ), NK cells and B cells. Macrophages were detected mainly at 14 days post inoculation. Inflammation was generally mild and mainly characterized by CD3+, CD4+and γδ T-cells; whereas CD8+and NK cells were less numerous. The immune cell repertoire observed in this study was similar to those seen in pregnant cattle challenged withN. caninumat early gestation. However, cellular infiltrates were less severe than those seen during first trimesterNeosporainfections. This may explain the milder clinical outcome observed when animals are infected late in gestation.
Suppression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic Spo11 allele
Authors: Smagulova Fatima , Brick Kevin , Pu Yongmei , Sengupta Uttara , Camerini-Otero R Daniel , Petukhova Galina V 
Published: July 2013

Abstract

Background
Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome called recombination hotspots. The hotspot locations are largely determined by the DNA binding specificity of the PRDM9 protein in human, mice and most other mammals. In budding yeast Saccharomyces cerevisae, which lacks a Prdm9 gene, meiotic breaks are formed opportunistically in the regions of accessible chromatin, primarily at gene promoters. The genome-wide distribution of hotspots in this organism can be altered by tethering Spo11 protein to Gal4 recognition sequences in the strain expressing Spo11 attached to the DNA binding domain of the Gal4 transcription factor. To establish whether similar re-targeting of meiotic breaks can be achieved in PRDM9-containing organisms we have generated a Gal4BD-Spo11 mouse that expresses SPO11 protein joined to the DNA binding domain of yeast Gal4.

Results
We have mapped the genome-wide distribution of the recombination initiation sites in the Gal4BD-Spo11 mice. More than two hundred of the hotspots in these mice were novel and were likely defined by Gal4BD, as the Gal4 consensus motif was clustered around the centers in these hotspots. Surprisingly, meiotic DNA breaks in the Gal4BD-Spo11 mice were significantly depleted near the ends of chromosomes. The effect is particularly striking at the pseudoautosomal region of the X and Y chromosomes – normally the hottest region in the genome.

Conclusions
Our data suggest that specific, yet-unidentified factors influence the initiation of meiotic recombination at subtelomeric chromosomal regions.
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Authors: Trinh Quang M , Jen Fei-Yang Arthur , Zhou Ziru , Chu Kar Ming , Perry Marc D , Kephart Ellen T , Contrino Sergio , Ruzanov Peter , Stein Lincoln D 
Published: July 2013

Abstract

Background
Funded by the National Institutes of Health (NIH), the aim of the Mod el Organism ENC yclopedia o f D NA E lements (modENCODE) project is to provide the biological research community with a comprehensive encyclopedia of functional genomic elements for both model organisms C. elegans (worm) and D. melanogaster (fly). With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data set. While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using modifications and enhancements of the original protocols, or combine modENCODE data with other data sets. Unfortunately this can be a time consuming and logistically challenging proposition.

Results
In recognition of this challenge, the modENCODE DCC has released uniform computing resources for analyzing modENCODE data on Galaxy (https://github.com/modENCODE-DCC/Galaxy), on the public Amazon Cloud (http://aws.amazon.com), and on the private Bionimbus Cloud for genomic research (http://www.bionimbus.org). In particular, we have released Galaxy workflows for interpreting ChIP-seq data which use the same quality control (QC) and peak calling standards adopted by the modENCODE and ENCODE communities. For convenience of use, we have created Amazon and Bionimbus Cloud machine images containing Galaxy along with all the modENCODE data, software and other dependencies.

Conclusions
Using these resources provides a framework for running consistent and reproducible analyses on modENCODE data, ultimately allowing researchers to use more of their time using modENCODE data, and less time moving it around.
Predictors of treatment failure and time to detection and switching in HIV-infected Ethiopian children receiving first line anti-retroviral therapy
Authors: Bacha Tigist , Tilahun Birkneh , Worku Alemayehu 
Published: July 2013

Abstract

Background
The emergence of resistance to first line antiretroviral therapy (ART) regimen leads to the need for more expensive and less tolerable second line drugs. Hence, it is essential to identify and address factors associated with an increased probability of first line ART regimen failure. The objective of this article is to report on the predictors of first line ART regimen failure, the detection rate of ART regime failure, and the delay in switching to second line ART drugs.

Methods
A retrospective cohort study was conducted from 2005 to 2011. All HIV infected children under the age of 15 who took first line ART for at least six months at the four major hospitals of Addis Ababa, Ethiopia were included. Data were collected, entered and analyzed using Epi info/ENA version 3.5.1 and SPSS version 16. The Cox proportional-hazard model was used to assess the predictors of first line ART failure.

Results
Data of 1186 children were analyzed. Five hundred seventy seven (48.8%) were males with a mean age of 6.22 (SD = 3.10) years. Of the 167(14.1%) children who had treatment failure, 70 (5.9%) had only clinical failure, 79 (6.7%) had only immunologic failure, and 18 (1.5%) had both clinical and immunologic failure. Patients who had height for age in the third percentile or less at initiation of ART were found to have higher probability of ART treatment failure [Adjusted Hazard Ratio (AHR), 3.25 95% CI, 1.00-10.58]. Patients who were less than three years old [AHR, 1.85 95% CI, 1.24-2.76], chronic diarrhea after initiation of antiretroviral treatment [AHR, 3.44 95% CI, 1.37-8.62], ART drug substitution [AHR, 1.70 95% CI, 1.05-2.73] and base line CD4 count below 50 cells/mm3 [AHR, 2.30 95% CI, 1.28-4.14] were also found to be at higher risk of treatment failure. Of all the 167 first line ART failure cases, only 24 (14.4%) were switched to second line ART with a mean delay of 24 (SD = 11.67) months. The remaining 143 (85.6%) cases were diagnosed to have treatment failure retrospectively by the authors based on their records. Hence, they were not detected and these patients were not offered second line ARTs.

Conclusions
Having chronic malnutrition, low CD4 at base line, chronic diarrhea after initiation of first line ART, substitution of ART drugs and age less than 3 years old were found to be independent predictors of first line ART failure in children. Most of the first line ART failure cases were not detected early and those that were detected were not switched to second line drugs in a timely fashion. Children with the above risk factors should be closely monitored for a timely switch to second line highly active anti-retroviral therapy.
Characterisation and analysis of thioredoxin peroxidase as a potential antigen for the serodiagnosis of sarcoptic mange in rabbits by dot-ELISA
Authors: Zhang Runhui , Zheng Wanpeng , Wu Xuhang , Jise Quwu , Ren Yongjun , Nong Xiang , Gu Xiaobin , Wang Shuxian , Peng Xuerong , Lai Songjia , Yang Guangyou 
Published: July 2013

Abstract

Background
Scabies caused by Sarcoptes scabiei is a widespread but a neglected tropical zoonosis. In this study, we characterised a S. scabiei thioredoxin peroxidase (SsTPx) and evaluated a recombinant SsTPx as a diagnostic antigen in rabbits.

Methods
The open reading frame of the gene encoding SsTPx-2 was amplified and the recombinant protein was expressed in Escherichia coli cells and purified. SsTPx was localized in mite tissue by immunolocalisation using the purified recombinant protein. Serodiagnosis assays were carried out in 203 New Zealand White rabbit serum samples by dot-ELISA.

Result
The open reading frame (489 bp) of the gene encodes an 18.11 kDa protein, which showed highly homology to that of Psoroptes cuniculi (98.77% identity) and belongs to the 2-Cys family of peroxiredoxins. SsTPx was mainly distributed in muscle tissues of mites, integument of the epidermis and the anterior end of S. scabiei. Although SsTPx cross-reactivity with psoroptic mites was observed, the SsTPx dot-ELISA showed excellent diagnostic ability, with 95.3% sensitivity and 93.8% specificity in mange-infected and uninfected groups.

Conclusions
This study showed that the purified SsTPx is a highly sensitive antigen for the diagnosis of mange infection by dot-ELISA. This technique is a rapid and convenient method that can be used worldwide for the clinical diagnosis of sarcoptic mange in rabbits, and is especially useful in developing regions.
Surveillance study of species distribution, antifungal susceptibility and mortality of nosocomial candidemia in a tertiary care hospital in China
Authors: Ma Chun-fang , Li Fang-qiu , Shi Li-ning , Hu Yu-an , Wang Ying , Huang Mei , Kong Qian-qian 
Published: July 2013

Abstract

Background
Bloodstream infections due to Candida species cause significant morbidity and mortality, and the epidemiology of Candida infection is changing. Surveillance for candidemia is necessary to detect trends in species distribution and antifungal resistance.

Methods
The medical and electronic records of all patients who had candidemia at the authors’ hospital from 2009 to 2011 were reviewed for demographic data and clinical information, including the infecting Candida species, resistance to antifungals and survival, and the presence of risk factors associated with candidemia.

Results
A total of 133 distinct episodes of candidemia were identified over the study period. The annual incidence of candidemia ranged between 0.71 and 0.85 cases/1000 hospital discharges. The most frequent Candida species were C. tropicalis (28.6%), followed by C. albicans (23.3%) and C. parapsilosis (19.5%). The rates of susceptibility to antifungal agents were as followed: voriconazole (97.8%), itraconazole (69.5%), fluconazole (46.1%), ketoconazole (38.9%). Out of 131 evaluable patients, 34 (26.0%) died within 30 days from the onset of candidemia. C. tropicalis candidemia was associated with the highest mortality rate (44.7%). Regarding the crude mortality in the different units, patients in Hemato-Oncology ward had the highest mortality rate (66.7%), followed by patients in cardiovascular wards and ICU (57.1% and 25.6%, respectively). Predictors of 30-day mortality were identified by uni- and multivariate analyses. Complicated abdominal surgery, presence of central venous catheter (CVC), neutropenia, candidemia due to C. tropicalis and poor treatment with fluconazole were significantly associated with the 30-day mortality. Presence of CVC (odds ratio[OR] = 4.177; 95% confidence interval [CI] = 1.698 to 10.278; P = 0.002) was the only independent predictor for mortality in the multivariate analysis.

Conclusion
This report provides baseline data for future epidemiological and susceptibility studies and for the mortality rates associated with candidemia in our hospital. The knowledge of the local epidemiological trends in Candida species isolated in blood cultures is important to guide therapeutic choices.
Internal jugular venous abnormalities in transient monocular blindness
Authors: Cheng Chun-Yu , Chang Feng-Chi , Chao A-Ching , Chung Chih-Ping , Hu Han-Hwa 
Published: July 2013

Abstract

Background
The etiology of transient monocular blindness (TMB) in patients without carotid stenosis has been linked to ocular venous hypertension, for their increased retrobulbar vascular resistance, sustained retinal venule dilatation and higher frequency of jugular venous reflux (JVR). This study aimed to elucidate whether there are anatomical abnormalities at internal jugular vein (IJV) in TMB patients that would contribute to impaired cerebral venous drainage and consequent ocular venous hypertension.

Methods
Contrast-enhanced axial T1-weighted magnetic resonance imaging (MRI) was performed in 23 TMB patients who had no carotid stenosis and 23 age- and sex-matched controls. The veins were assessed at the upper IJV (at C1–3 level) and the middle IJV (at C3–5 level). Grading of IJV compression/stenosis was determined bilaterally as follows: 0 = normal round or ovoid appearance; 1 = mild flattening; 2 = moderate flattening; and 3 = severe flattening or not visualized.

Results
There was significantly more moderate or severe IJV compression/stenosis in the TMB patients at the left upper IJV level and the bilateral middle IJV level. Defining venous compression/stenosis scores ≥ 2 as a significant cerebral venous outflow impairment, TMB patients were found to have higher frequency of significant venous outflow impairment at the upper IJV level (56.5% vs. 8.7%, p = 0.0005) and the middle IJV level (69.6% vs. 21.7%, p=0.0011).

Conclusions
TMB Patients with the absence of carotid stenosis had higher frequency and greater severity of IJV compression/stenosis which could impair cerebral venous outflow. Our results provide evidence supporting that the cerebral venous outflow abnormality is one of the etiologies of TMB.