bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism
Authors: Guo Xiaoli , Hou Xiaomei , Fang Jun , Wei Piwei , Xu Bo , Chen Mingluan , Feng Yuqi , Chu Chengcai 
Published: April 2013

SummaryIt has been shown that seed development is regulated by a network of transcription factors in Arabidopsis including LEC1 (LEAFY COTYLEDON1), L1L (LEC1‐like) and the B3 domain factors LEC2, FUS3 (FUSCA3) and ABI3 (ABA‐INSENSITIVE3); however, molecular and genetic regulation of seed development in cereals is poorly understood. To understand seed development and seed germination in cereals, a large‐scale screen was performed using our T–DNA mutant population, and a mutant germination‐defective1 (gd1) was identified. In addition to the severe germination defect, the gd1 mutant also shows a dwarf phenotype and abnormal flower development. Molecular and biochemical analyses revealed that GD1 encodes a B3 domain‐containing transcription factor with repression activity. Consistent with the dwarf phenotype of gd1, expression of the gibberelic acid (GA) inactivation gene OsGA2ox3 is increased dramatically, accompanied by reduced expression of GA biosynthetic genes including OsGA20ox1, OsGA20ox2 and OsGA3ox2 in gd1, resulting in a decreased endogenous GA4 level. Exogenous application of GA not only induced GD1 expression, but also partially rescued the dwarf phenotype of gd1. Furthermore, GD1 binds to the promoter of OsLFL1, a LEC2/FUS3‐like gene of rice, via an RY element, leading to significant up‐regulation of OsLFL1 and a large subset of seed maturation genes in the gd1 mutant. Plants over‐expressing OsLFL1 partly mimic the gd1 mutant. In addition, expression of GD1 was induced under sugar treatment, and the contents of starch and soluble sugar are altered in the gd1 mutant. These data indicate that GD1 participates directly or indirectly in regulating GA and carbohydrate homeostasis, and further regulates rice seed germination and seedling development.
The impact of donor cytomegalovirus DNA on transfusion strategies for at‐risk patients
Authors: Ziemann Malte , Juhl David , Görg Siegfried , Hennig Holger 
Published: April 2013

BackgroundCytomegalovirus (CMV) DNA is frequently detected in plasma of newly seropositive donors. Selection of leukoreduced blood products from donors with remote CMV infection could avoid transfusion‐transmitted CMV infections (TT‐CMV) due to primarily infected donors. However, there are no data about the prevalence of reactivations in long‐term seropositive donors compared to the incidence of window period donations in seronegative donors. Therefore, the optimal transfusion strategy for at‐risk patients is unclear.Study Design and MethodsWhole blood samples from 22,904 donations were tested for CMV DNA, and CMV DNA–positive donations were categorized as donations from 1) seronegative donors, 2) newly seropositive donors, and 3) long‐term seropositive donors.ResultsTwenty‐one donors were reproducibly CMV DNA–positive (0.09%). Frequency of detection and concentration of CMV DNA in whole blood were comparable for seronegative and long‐term seropositive donors. Nonreproducibly positive results for CMV DNA in whole blood were more frequent in long‐term seropositive donors (0.16% vs. 0.01%, p < 0.01). Only low concentrations of CMV DNA in plasma were detectable in two seronegative donors and one long‐term seropositive donor. Highest concentrations of CMV DNA in both whole blood and plasma, however, were found in newly seropositive donors.ConclusionPrevalences of window period donations among seronegative donors and reactivations among long‐term seropositive donors, as well as the CMV DNA concentration in whole blood and plasma samples from these donors, are comparable. Therefore, blood products from both groups could be used for patients at risk for TT‐CMV, while those of newly seropositive donors seem to bear an increased risk.
Production of cloned NIBS (Nippon Institute for Biological Science) and α‐1, 3‐galactosyltransferase knockout MGH miniature pigs by somatic cell nuclear transfer using the NIBS breed as surrogates
Authors: Shimatsu Yoshiki , Yamada Kazuhiko , Horii Wataru , Hirakata Atsushi , Sakamoto Yuji , Waki Shiori , Sano Junichi , Saitoh Toshiki , Sahara Hisashi , Shimizu Akira , Yazawa Hajime , Sachs David H. , Nunoya Tetsuo 
Published: April 2013

AbstractBackgroundNuclear transfer (NT) technologies offer a means for producing the genetically modified pigs necessary to develop swine models for mechanistic studies of disease processes as well as to serve as organ donors for xenotransplantation. Most previous studies have used commercial pigs as surrogates.Method and ResultsIn this study, we established a cloning technique for miniature pigs by somatic cell nuclear transfer (SCNT) using Nippon Institute for Biological Science (NIBS) miniature pigs as surrogates. Moreover, utilizing this technique, we have successfully produced an α‐1, 3‐galactosyltransferase knockout (GalT‐KO) miniature swine. Fibroblasts procured from a NIBS miniature pig fetus were injected into 1312 enucleated oocytes. The cloned embryos were transferred to 11 surrogates of which five successfully delivered 13 cloned offspring; the production efficiency was 1.0% (13/1312). In a second experiment, lung fibroblasts obtained from neonatal GalT‐KO MGH miniature swine were used as donor cells and 1953 cloned embryos were transferred to 12 surrogates. Six cloned offspring were born from five surrogates, a production efficiency of 0.3% (6/1953).ConclusionsThese results demonstrate successful establishment of a miniature pig cloning technique by SCNT using NIBS miniature pigs as surrogates. To our knowledge, this is the first demonstration of successful production of GalT‐KO miniature swine using miniature swine surrogates. This technique could help to ensure a stable supply of the cloned pigs through the use of miniature pig surrogates and could expand production in countries with limited space or in facilities with special regulations such as specific pathogen‐free or good laboratory practice.
A Large-Eddy Simulation Study of Bottom-Heating Effects on Scalar Dispersion in and above a Cubical Building Array
Authors: Park Seung-Bu , Baik Jong-Jin , Ryu Young-Hee 
Published: April 2013

AbstractThermal effects on scalar dispersion in and above a cubical building array are numerically investigated using the parallelized large-eddy simulation model (PALM). Two cases (no heating and bottom heating) are simulated, and scalar dispersion patterns in the two cases are compared. In the no-heating case, scalar ejections in the low-speed flow structures play an important role in transporting scalar upward above the building array. In the bottom-heating case, streamwise elongated and isolated scalar ejections appear below upper low-speed and upper high-speed regions above the building array. In both cases, bottom-emitted scalar flux is balanced by streamwise scalar advection and vertical turbulent scalar flux at the rooftop height. The vertical turbulent scalar flux at the rooftop height is mainly composed of scalar ejections and scalar sweeps that are related to low- and high-speed flow structures, respectively. Furthermore, the low- and high-speed flow structures at the rooftop height induce spanwise converging and spanwise diverging flow in the building array in both the no-heating and bottom-heating cases. Thus, the mean scalar concentration in the building array is high below the low-speed flow structures (above the building array) in both cases. Dominant scalar dispersion patterns in the building array are found to be spanwise scalar transport events that are composed of negative scalar concentration perturbation and spanwise flow therein. In the bottom-heating case, a large-scale secondary circular flow develops, causing stronger spanwise scalar dispersion patterns in the building array.
Large-Scale Distinctions between MJO and Non-MJO Convective Initiation over the Tropical Indian Ocean
Authors: Ling Jian , Zhang Chidong , Bechtold Peter 
Published: April 2013

AbstractIn this study, the authors seek large-scale signals that may distinguish MJO from non-MJO convective events before they start over the Indian Ocean. Three such signals were found. Low-level easterly anomalies extend from the surface to the midtroposphere and move from the western to eastern Indian Ocean. Surface pressure anomalies exhibit a zonal structure of wavenumber 1 with an equatorial low-pressure surge penetrating eastward from Africa through the Indian Ocean and reaching the Maritime Continent. Negative temperature anomalies in the middle to upper troposphere start over the Indian Ocean and move eastward. All of them emerge 20 days before convective initiation of the MJO and move eastward at speeds close to that of the MJO without any direct connection to MJO convection. They are not obviously related to the extratropics in any discernible way or any preceding MJO events. They are absent in non-MJO convective events. These signals provide useful information for forecasting MJO initiation over the Indian Ocean. They can be signatures of a dry dynamics mode of the MJO, if it exists.
Near–Sea Surface Temperature Stratification from SVP Drifters
Authors: Reverdin G. , Morisset S. , Bellenger H. , Boutin J. , Martin N. , Blouch P. , Rolland J. , Gaillard F. , Bouruet-Aubertot P. , Ward B. 
Published: April 2013

Abstract
This study describes how the hull temperature (Ttop) measurements from multisensor surface velocity program (SVP) drifters can be combined with other measurements to provide quantitative information on near-surface vertical temperature stratification during large daily cycles. First, Ttop is compared to the temperature measured at 17 -cm depth from a float tethered to the SVP drifter. These 2007–12 SVP drifters present a larger daily cycle by 1%–3% for 1°–2°C daily cycle amplitudes, with a maximum difference close to the local noon. The difference could result from flow around the SVP drifter in the presence of temperature stratification in the top 20 cm of the water column but also from a small influence of internal drifter temperature on Ttop. The largest differences were found for small drifters (Technocean) for very large daily cycles, as expected from their shallower measurements. The vertical stratification is estimated by comparing these hull data with the deeper T or conductivity C measurements from Sea-Bird sensors 25 (Pacific Gyre) to 45 cm (MetOcean) below the top temperature sensor. The largest stratification is usually found near local noon and early afternoon. For a daily cycle amplitude of 1°C, these differences with the upper level are in the range of 3%–5% of the daily cycle for the Pacific Gyre drifters and 6%–10% for MetOcean drifters with the largest values occurring when the midday sun elevation is lowest. The relative differences increase for larger daily cycles, and the vertical profiles become less linear. These estimated stratifications are well above the uncertainty on Ttop.
The role of axon guidance factor semaphorin 6B in the invasion and metastasis of gastric cancer
Authors: Ge Changqing , Li Quanfu , Wang Lipu , Xu Xu 
Published: April 2013

Objective To investigate the role of semaphorin 6B in gastric cancer invasion and metastasis. Methods Immunohistochemistry for semaphorin 6B was performed on gastric cancer tumour tissue samples in this retrospective study. Levels of semaphorin 6B protein and mRNA were determined in gastric cancer cell lines by Western blotting and quantitative reverse transcription–polymerase chain reaction, respectively. The human gastric cancer cell line SGC-7901 was transfected with small interfering RNA targeting semaphorin 6B; effects on cell adhesion, migration and invasion were determined by cell adhesion assay, transwell chamber migration assay and wound healing assay, respectively. Results Tumour tissue samples from 220 patients were analysed. In vivo, semaphorin 6B immunopositivity correlated with tumour differentiation, lymph node metastasis and distant metastasis but not patient age, sex or tumour stage. Semaphorin 6B gene silencing significantly suppressed adhesion, migration and invasion of gastric cancer cells in vitro. Conclusions Semaphorin 6B is related to tumour differentiation and metastasis in vivo, and tumour cell migration, adhesion and invasion in vitro. Semaphorin 6B may represent a reliable biomarker for diagnosis, evaluation and gene-targeted therapy of gastric cancer.
Clinicopathological significance of S100A4 expression in human hepatocellular carcinoma
Authors: Liu Zimin , Liu Huamin , Pan Huazheng , Du Qihang , Liang Jun 
Published: April 2013

Objective Prognostic markers for hepatocellular carcinoma (HCC) could help in the clinical management and understanding of its poor prognosis. S100 calcium binding protein A4 (S100A4) is directly involved in tumour metastasis. This study evaluated S100A4 gene expression in human HCC, to identify its role in tumour progression. Methods In this retrospective study, S100A4 protein levels in HCC samples from Chinese patients were evaluated using immunohistochemistry and compared with paired normal tumour-adjacent tissue samples (controls). All patients were evaluated for HCC recurrence. Results S100A4 levels were significantly increased in HCC samples compared with controls ( n = 72, each sample type). Moderately or poorly differentiated tumours had significantly higher levels of S100A4 protein than well-differentiated tumours, and those with tumour vascular invasion showed significantly higher S100A4 levels than those without invasion. Risk of recurrence increased in patients positive for S100A4, and S100A4 positivity correlated with a shorter overall survival time. Conclusion This pilot study suggests S100A4 as a likely tumour marker for HCC that correlates with tumour differentiation, invasion, recurrence and overall survival. S100A4 could be a useful marker of tumour aggressiveness and prognosis.
Rapid plasmid replicon typing by real time PCR melting curve analysis
Authors: Boot Maikel , Raadsen Susanne , Savelkoul Paul HM , Vandenbroucke-Grauls Christina 
Published: April 2013

Abstract

Background
Genes encoding Extended Spectrum Beta Lactamases are usually located on transferable plasmids. Each plasmid contains its own replication mechanism. Carattoli et al. developed an extended PCR-based replicon typing method to characterize and identify the replicons of the major plasmid incompatibility groups in Enterobacteriaceae. Based on this method, we designed a rapid approach with amplicon detection by real-time melting curve analysis. This method appeared to be fast, sensitive, less laborious, less prone to contamination and applicable in a routine laboratory environment.

Results
We successfully integrated the post-PCR analysis of the replicon typing into a closed system, which leads to a 10-fold increase in sensitivity compared to agarose gel visualization. Moreover, the use of crude lysates and SYBR-green saves a considerable amount of hands-on time without decreasing the sensitivity or specificity.

Conclusions
This real-time melting curve replicon typing method appears to be fast, sensitive, less laborious, less prone to contamination and applicable in a routine laboratory environment.
Retinal upregulation of inflammatory and proangiogenic markers in a model of neonatal diabetic rats fed on a high-fat-diet
Authors: Mancini Jorge E , Ortiz Gustavo , Croxatto Juan Oscar , Gallo Juan E 
Published: April 2013

Abstract

Background
The contemporary peak of diabetes seems to be related to obesity, sedentary lifestyle and diet. Diabetic retinopathy is the most leading cause of blindness in adulthood in industrialized countries. Our purpose was to evaluate the effect of a high-fat-diet (HFD) on the retina of diabetic rats.

Methods
Two groups of Wistar rats were injected with streptozotocin (STZ) two days after birth using 45 and 90 mg/kg, respectively. At 8 weeks the group on lower doses started to be fed on a HFD. Animals were sacrificed at 37 weeks of diabetes. A control group was made up of non-diabetic rats. Retinal flat mounts were examined using the trypsin digestion technique. Pericytes counts were compared between diabetic and control rats. Cross retinal sections were analyzed by histological techniques and immunohistochemistry and immunofluorescent technique. Primary antibodies against inflammatory and proangiogenic mediators such as RAGE, GFAP, 5-LO, VEGF and TNF-α were used for immunohistochemistry and Western Blot (WB) analyses.

Results
In the two diabetic groups we observed GFAP-positive cells with a morphology and spatial organization similar to those seen in Müller cells. Both diabetic groups had a significantly lower number of pericytes than non-diabetic animals.Increased retinal immunoreactivity of GFAP, RAGE, TNF-α, VEGF and 5-LO was seen in diabetic animals fed on HFD compared to the other groups of animals. WB analysis revealed a higher expression of 5-LO, VEGF, TNF-α and RAGE in the retina of diabetic rats on HFD than in controls and diabetics fed on a normal diet. The percentage of RAGE-stained ganglion cells and ganglion cells was found to be significantly lower in animals on a HFD than in the other animals.

Conclusions
Diabetic animals fed on a HFD showed an increased upregulation of inflammatory and proangiogenic markers. This animal model may be useful to study mechanisms of diabetic retinopathy and therapeutic targets.
Modular glycosphere assays for high-throughput functional characterization of influenza viruses
Authors: Hobbie Sven N , Viswanathan Karthik , Bachelet Ido , Aich Udayanath , Shriver Zachary , Subramanian Vidya , Raman Rahul , Sasisekharan Ram 
Published: April 2013

Abstract

Background
The ongoing global efforts to control influenza epidemics and pandemics require high-throughput technologies to detect, quantify, and functionally characterize viral isolates. The 2009 influenza pandemic as well as the recent in-vitro selection of highly transmissible H5N1 variants have only increased existing concerns about emerging influenza strains with significantly enhanced human-to-human transmissibility. High-affinity binding of the virus hemagglutinin to human receptor glycans is a highly sensitive and stringent indicator of host adaptation and virus transmissibility. The surveillance of receptor-binding characteristics can therefore provide a strong additional indicator for the relative hazard imposed by circulating and newly emerging influenza strains.

Results
Streptavidin-coated microspheres were coated with selected biotinylated glycans to mimic either human or avian influenza host-cell receptors. Such glycospheres were used to selectively capture influenza virus of diverse subtypes from a variety of samples. Bound virus was then detected by fluorescently labelled antibodies and analyzed by quantitative flow cytometry. Recombinant hemagglutinin, inactivated virus, and influenza virions were captured and analyzed with regards to receptor specificity over a wide range of analyte concentration. High-throughput analyses of influenza virus produced dose–response curves that allow for functional assessment of relative receptor affinity and thus transmissibility.

Conclusions
Modular glycosphere assays for high-throughput functional characterization of influenza viruses introduce an important tool to augment the surveillance of clinical and veterinarian influenza isolates with regards to receptor specificity, host adaptation, and virus transmissibility.
Development and validation of an algorithm to recalibrate mental models and reduce diagnostic errors associated with catheter-associated bacteriuria
Authors: Trautner Barbara W , Bhimani Rupal D , Amspoker Amber B , Hysong Sylvia J , Garza Armandina , Kelly P Adam , Payne Velma L , Naik Aanand D 
Published: April 2013

Abstract

Background
Overtreatment of catheter-associated bacteriuria is a quality and safety problem, despite the availability of evidence-based guidelines. Little is known about how guidelines-based knowledge is integrated into clinicians’ mental models for diagnosing catheter-associated urinary tract infection (CA-UTI). The objectives of this research were to better understand clinicians’ mental models for CA-UTI, and to develop and validate an algorithm to improve diagnostic accuracy for CA-UTI.

Methods
We conducted two phases of this research project. In phase one, 10 clinicians assessed and diagnosed four patient cases of catheter associated bacteriuria (n= 40 total cases). We assessed the clinical cues used when diagnosing these cases to determine if the mental models were IDSA guideline compliant. In phase two, we developed a diagnostic algorithm derived from the IDSA guidelines. IDSA guideline authors and non-expert clinicians evaluated the algorithm for content and face validity. In order to determine if diagnostic accuracy improved using the algorithm, we had experts and non-experts diagnose 71 cases of bacteriuria.

Results
Only 21 (53%) diagnoses made by clinicians without the algorithm were guidelines-concordant with fair inter-rater reliability between clinicians (Fleiss’ kappa = 0.35, 95% Confidence Intervals (CIs) = 0.21 and 0.50). Evidence suggests that clinicians’ mental models are inappropriately constructed in that clinicians endorsed guidelines-discordant cues as influential in their decision-making: pyuria, systemic leukocytosis, organism type and number, weakness, and elderly or frail patient. Using the algorithm, inter-rater reliability between the expert and each non-expert was substantial (Cohen’s kappa = 0.72, 95% CIs = 0.52 and 0.93 between the expert and non-expert #1 and 0.80, 95% CIs = 0.61 and 0.99 between the expert and non-expert #2).

Conclusions
Diagnostic errors occur when clinicians’ mental models for catheter-associated bacteriuria include cues that are guidelines-discordant for CA-UTI. The understanding we gained of clinicians’ mental models, especially diagnostic errors, and the algorithm developed to address these errors will inform interventions to improve the accuracy and reliability of CA-UTI diagnoses.