bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans
Authors: Zuluaga Andrea P. , Vega‐Arreguín Julio C. , Fei Zhangjun , Matas Antonio J. , Patev Sean , Fry William E. , Rose Jocelyn K. C. 
Published: March 2015

SummaryThe infection of plants by hemibiotrophic pathogens involves a complex and highly regulated transition from an initial biotrophic, asymptomatic stage to a later necrotrophic state, characterized by cell death. Little is known about how this transition is regulated, and there are conflicting views regarding the significance of the plant hormones jasmonic acid (JA) and salicylic acid (SA) in the different phases of infection. To provide a broad view of the hemibiotrophic infection process from the plant perspective, we surveyed the transcriptome of tomato (Solanum lycopersicum) during a compatible interaction with the hemibiotrophic oomycete Phytophthora infestans during three infection stages: biotrophic, the transition from biotrophy to necrotrophy, and the necrotrophic phase. Nearly 10 000 genes corresponding to proteins in approximately 400 biochemical pathways showed differential transcript abundance during the three infection stages, revealing a major reorganization of plant metabolism, including major changes in source–sink relations, as well as secondary metabolites. In addition, more than 100 putative resistance genes and pattern recognition receptor genes were induced, and both JA and SA levels and associated signalling pathways showed dynamic changes during the infection time course. The biotrophic phase was characterized by the induction of many defence systems, which were either insufficient, evaded or suppressed by the pathogen.
Efficacy of combination therapy with probiotics and mosapride in patients with IBS without diarrhea: a randomized, double‐blind, placebo‐controlled, multicenter, phase II trial
Authors: Choi C. H. , Kwon J. G. , Kim S. K. , Myung S.‐J. , Park K. S. , Sohn C.‐I. , Rhee P.‐L. , Lee K. J. , Lee O. Y. , Jung H.‐K. , Jee S. R. , Jeen Y. T. , Choi M.‐G. , Choi S. C. , Huh K. C. , Park H. 
Published: March 2015

AbstractBackgroundProbiotics can be beneficial in irritable bowel syndrome (IBS). Mosapride citrate, a selective 5‐HT4 receptor agonist, stimulates gastrointestinal motility. We investigated the efficacy of combination therapy with probiotics and mosapride for non‐diarrheal‐type IBS.MethodsTwo hundred and eighty‐five IBS patients were randomly assigned to either a combination of probiotics (Bacillus subtilis and Streptococcus faecium) and mosapride at one of four different doses or a placebo for 4 weeks. The primary outcome was the proportion of patients experiencing adequate relief (AR) of global IBS symptoms at week 4. The secondary outcomes included subject's global assessment (SGA) of IBS symptom relief, individual symptoms, stool parameters, and IBS‐quality of life.Key ResultsThe proportion of AR at week 4 was significantly higher in all treatment groups compared to the placebo group (53.7% in group 1, 55.0% in group 2, 55.2% in group 3, 53.6% in group 4 [the highest dose], and 35.1% in placebo group, respectively, p < 0.05). The proportion of patients reporting ‘completely or considerably relieved’ in the SGA was higher in the treatment groups than in the placebo group. The abdominal pain/discomfort score in the treatment group 4 was more prominently improved compared with that of the placebo group. In patients with constipation‐predominant IBS, the improvements in stool frequency and consistency were significantly higher in the treatment groups 4 and 1, respectively, than those in the placebo group.Conclusions & InferencesCombination therapy with probiotics and mosapride is effective for relief of symptoms in patients with non‐diarrheal‐type IBS. The study has been registered in the US National Library of Medicine (http://www.clinicaltrials.gov, NCT01505777).
Population genetics of freeze tolerance among natural populations of Populus balsamifera across the growing season
Authors: Menon Mitra , Barnes William J. , Olson Matthew S. 
Published: March 2015

Summary

Protection against freeze damage during the growing season influences the northern range limits of plants. Freeze tolerance and freeze avoidance are the two major freeze resistance strategies. Winter survival strategies have been extensively studied in perennials, but few have addressed them and their genetic basis during the growing season.

We examined intraspecific phenotypic variation in freeze resistance of Populus balsamifera across latitude and the growing season. To investigate the molecular basis of this variation, we surveyed nucleotide diversity and examined patterns of gene expression in the poplar C‐repeat binding factor (CBF) gene family.

Foliar freeze tolerance exhibited latitudinal and seasonal variation indicative of natural genotypic variation. CBF6 showed signatures of recent selective sweep. Of the 46 SNPs surveyed across the six CBF homologs, only CBF2_619 exhibited latitudinal differences consistent with increased freeze tolerance in the north. All six CBF genes were cold inducible, but showed varying patterns of expression across the growing season.

Some Poplar CBF homologs exhibited patterns consistent with historical selection and clinal variation in freeze tolerance documented here. However, the CBF genes accounted for only a small amount of the variation, indicating that other genes in this and other molecular pathways likely play significant roles in nature.
Screening for secondhand smoke in schoolchildren in Japan
Authors: Ino Toshihiro , Kurosawa Kazuo 
Published: March 2015

AbstractBackgroundThere is no systematic screening for secondhand smoke exposure in children.MethodsIn 2002, we began a secondhand smoke screening (SSS) program for grade 4 elementary schoolchildren with the cooperation of public administration. The SSS program consisted of urinary cotinine measurement in children and a questionnaire survey of their parents.ResultsMore than 1200 schoolchildren were enrolled in this program annually. The level of urinary cotinine in 30% of the children was >5 ng/mL, whereas in half of them it was undetectable. The major risk factor affecting cotinine level was mother's smoking. Average cotinine was significantly high in children who had a history of “short stature”, “decayed tooth and/or periodontal disease,” and “frequent stridor”. In addition, the highest level of cotinine was detected in children whose father and/or mother smoked in the living room and the lowest level of cotinine was detected in children whose father and/or mother smoked on the veranda or outside the door. These levels, however, were two–fivefold higher than in children whose parents did not smoke. On follow‐up questionnaire survey 4 years after initial SSS, significant elevated motivation for smoking cessation was noted.ConclusionsThe SSS program is a very simple mass screen that can be done using only a urine test and is very effective for motivating parents to stop smoking with regard to cost benefit.
Differences Between High‐ and Low‐Motility Buffalo Sperm Identified by Comparative Proteomics
Authors: Huang Y‐L , Fu Q , Yang L , Guan J‐L , Pan H , Chen F‐M , Lu K‐L , Zhang M 
Published: March 2015

ContentsThis study was undertaken to investigate differences in protein expression between high‐ and low‐motility sperm of swamp buffalo. The research used two‐dimensional gel electrophoresis (2DE) coupled to matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (MALDI‐TOF/TOF‐MS) to analyse the different proteins. The results showed 18 different expression protein spots between high‐ and low‐motility buffalo sperm; eight of these proteins were up‐regulated in low‐motility sperm, five were down‐regulated, one deleted and four proteins specifically expressed. Finally, four proteins were successfully identified by MS as belonging to three unique proteins; they are outer dense fibre of sperm tails protein 2 (ODF2), ATP synthase subunit alpha (ATP5A1) and succinyl‐CoA synthetase subunit beta (SUCLG2). In summary, these results help to develop an understanding of the molecular mechanisms associated with low‐motility sperm and provide clues for finding molecular markers associated with sperm motility.
Identification of a Taraxacum brevicorniculatum rubber elongation factor protein that is localized on rubber particles and promotes rubber biosynthesis
Authors: Laibach Natalie , Hillebrand Andrea , Twyman Richard M. , Prüfer Dirk , Schulze Gronover Christian 
Published: March 2015

SummaryTwo protein families required for rubber biosynthesis in Taraxacum brevicorniculatum have recently been characterized, namely the cis‐prenyltransferases (TbCPTs) and the small rubber particle proteins (TbSRPPs). The latter were shown to be the most abundant proteins on rubber particles, where rubber biosynthesis takes place. Here we identified a protein designated T. brevicorniculatum rubber elongation factor (TbREF) by using mass spectrometry to analyze rubber particle proteins. TbREF is homologous to the TbSRPPs but has a molecular mass that is atypical for the family. The promoter was shown to be active in laticifers, and the protein itself was localized on the rubber particle surface. In TbREF‐silenced plants generated by RNA interference, the rubber content was significantly reduced, correlating with lower TbCPT protein levels and less TbCPT activity in the latex. However, the molecular mass of the rubber was not affected by TbREF silencing. The colloidal stability of rubber particles isolated from TbREF‐silenced plants was also unchanged. This was not surprising because TbREF depletion did not affect the abundance of TbSRPPs, which are required for rubber particle stability. Our findings suggest that TbREF is an important component of the rubber biosynthesis machinery in T. brevicorniculatum, and may play a role in rubber particle biogenesis and influence rubber production.
Transforming growth factor‐β released by apoptotic white blood cells during red blood cell storage promotes transfusion‐induced alloimmunomodulation
Authors: Vallion Romain , Bonnefoy Francis , Daoui Anna , Vieille Loredane , Tiberghien Pierre , Saas Philippe , Perruche Sylvain 
Published: March 2015

BACKGROUNDRed blood cell (RBC) alloimmunization is a major immunologic risk of transfusion. However, RBC storage facilitates white blood cell (WBC) apoptosis and apoptotic cells have immunomodulatory properties. We investigated the behavior of WBCs, and apoptosis in particular, in RBC units during storage and then studied the impact of WBC apoptosis on the modulation of posttransfusion alloimmunization in RBC products stored short term.STUDY DESIGN AND METHODSWe used a mouse model of alloimmunization to transfused HEL‐ovalbumin‐Duffy (HOD) surface antigen expressed specifically on RBCs. The presence of circulating anti‐HOD immunoglobulin G detected by flow cytometry confirmed immunization to HOD+ RBCs. WBC apoptosis and factors released by apoptotic WBCs during storage were determined and in particular the role of transforming growth factor (TGF)‐β was assessed on RBC alloimmunization.RESULTSIn blood stored 72 hours, 30% of WBCs were apoptotic, and transfusion of short‐term‐stored blood resulted in lesser immunization than did fresh blood or stored leukoreduced (LR) RBCs. WBCs undergoing apoptosis released during short‐term storage factors modulating RBC alloimmunization. Indeed apoptotic cell–released factors modulate alloimmunization whereas exogenous apoptotic cells directly transfused with LR RBCs did not. While microparticles released during RBC storage had no immunomodulatory role, TGF‐β found in the supernatant of stored blood demonstrated the capacity to favor Treg polarization of naïve CD4+CD25– T cells in vitro and limited RBC alloimmunization in vivo. Indeed, addition of recombinant TGF‐β to stored LR RBC transfusion strongly limited posttransfusion RBC alloimmunization.CONCLUSIONOur findings show that short‐term storage of non‐LR blood facilitates WBC apoptosis therefore releasing TGF‐β that modulates posttransfusion RBC alloimmunization.
Molecular signalling pathways in canine gliomas
Authors: Boudreau C. E. , York D. , Higgins R. J. , LeCouteur R. A. , Dickinson P. J. 
Published: March 2015

AbstractIn this study, we determined the expression of key signalling pathway proteins TP53, MDM2, P21, AKT, PTEN, RB1, P16, MTOR and MAPK in canine gliomas using western blotting. Protein expression was defined in three canine astrocytic glioma cell lines treated with CCNU, temozolamide or CPT‐11 and was further evaluated in 22 spontaneous gliomas including high and low grade astrocytomas, high grade oligodendrogliomas and mixed oligoastrocytomas. Response to chemotherapeutic agents and cell survival were similar to that reported in human glioma cell lines. Alterations in expression of key human gliomagenesis pathway proteins were common in canine glioma tumour samples and segregated between oligodendroglial and astrocytic tumour types for some pathways. Both similarities and differences in protein expression were defined for canine gliomas compared to those reported in human tumour counterparts. The findings may inform more defined assessment of specific signalling pathways for targeted therapy of canine gliomas.
Vaginal Microbiota of Adolescent Girls Prior to the Onset of Menarche Resemble Those of Reproductive-Age Women
Authors: Hickey Roxana J. , Zhou Xia , Settles Matthew L. , Erb Julie , Malone Kristin , Hansmann Melanie A. , Shew Marcia L. , Van Der Pol Barbara , Fortenberry J. Dennis , Forney Larry J. 
Published: March 2015

ABSTRACT

Puberty is an important developmental stage wherein hormonal shifts mediate the physical and physiological changes that lead to menarche, but until now, the bacterial composition of vaginal microbiota during this period has been poorly characterized. We performed a prospective longitudinal study of perimenarcheal girls to gain insight into the timing and sequence of changes that occur in the vaginal and vulvar microbiota during puberty. The study enrolled 31 healthy, premenarcheal girls between the ages of 10 and 12 years and collected vaginal and vulvar swabs quarterly for up to 3 years. Bacterial composition was characterized by Roche 454 pyrosequencing and classification of regions V1 to V3 of 16S rRNA genes. Contrary to expectations, lactic acid bacteria, primarily Lactobacillus spp., were dominant in the microbiota of most girls well before the onset of menarche in the early to middle stages of puberty.
Gardnerella vaginalis
was detected at appreciable levels in approximately one-third of subjects, a notable finding considering that this organism is commonly associated with bacterial vaginosis in adults. Vulvar microbiota closely resembled vaginal microbiota but often exhibited additional taxa typically associated with skin microbiota. Our findings suggest that the vaginal microbiota of girls begin to resemble those of adults well before the onset of menarche.

IMPORTANCE
This study addresses longitudinal changes in vaginal and vulvar microbial communities prior to and immediately following menarche. The research is significant because microbial ecology of the vagina is an integral aspect of health, including resistance to infections. The physiologic changes of puberty and initiation of cyclic menstruation are likely to have profound effects on vaginal microbiota, but almost nothing is known about changes that normally occur during this time. Our understanding has been especially hampered by the lack of thorough characterization of microbial communities using techniques that do not rely on the cultivation of fastidious bacteria, as well as a dearth of studies on girls in the early to middle stages of puberty. This study improves our understanding of the normal development of vaginal microbiota during puberty and onset of menarche and may better inform clinical approaches to vulvovaginal care of adolescent girls.
Laparoscopic assistance for primary transanal pull-through in Hirschsprung's disease: a systematic review and meta-analysis
Authors: Thomson David , Allin Benjamin , Long Anna-May , Bradnock Tim , Walker Gregor , Knight Marian 
Published: March 2015

ObjectiveTo compare outcomes following totally transanal endorectal pull-through (TTERPT) versus pull-through with any form of laparoscopic assistance (LAPT) for infants with uncomplicated Hirschsprung's disease.DesignSystematic review and meta-analysis.SettingFive hospitals with a paediatric surgical service.Participants405 infants with uncomplicated Hirschsprung's disease.InterventionsTTERPT versus LAPT.Primary and secondary outcome measuresPrimary outcomes: mortality, postoperative enterocolitis, faecal incontinence, constipation, unplanned laparotomy or stoma formation, and injury to abdominal viscera.Secondary outcomesHaemorrhage requiring transfusion of blood products, abscess formation, intestinal obstruction, intestinal ischaemia, enteric fistula formation, urinary incontinence or retention, impotency and duration of procedure.ResultsFive eligible studies comprising 405 patients were identified from 2107 studies. All studies were retrospective case series, with variability in outcome assessment quality and length of follow-up. Operative duration was 50.29 min shorter with TTERPT (95% CI 39.83 to 60.74, p<0.00001). There were no significant differences identified between TTERPT and LAPT for incidence of postoperative enterocolitis (OR=0.78, 95% CI 0.44 to 1.38, p=0.39), faecal incontinence (OR=0.44, 95% CI 0.09 to 2.20, p=0.32) or constipation (OR=0.84, 95% CI 0.32 to 2.17, p=0.71).ConclusionsThis meta-analysis did not find any evidence to suggest a higher rate of enterocolitis, incontinence or constipation following TTERPT compared with LAPT. Further long-term comparative studies and multicentre data pooling are needed to determine whether a purely transanal approach offers any advantages over a laparoscopically assisted approach to rectosigmoid Hirschsprung's disease.Trial registration numberPROSPERO registry- CRD42013005698.
Clinical, ultrasonographic and postmortem findings in a goat with abscessation of the mesenteric lymph nodes
Authors: Braun Ueli , Hilbe Monika , Nuss Karl , Tschoner Theresa 
Published: March 2015

This case report describes the clinical, ultrasonographic and pathological findings in a 4.5‐year‐old Grisons striped goat with abscessation of the mesenteric lymph nodes. The goat had a poor appetite, tense abdomen and reduced ruminal motility. There was neutrophilic leukocytosis, and a serological test forCorynebacterium pseudotuberculosiswas positive. Abdominal ultrasonography in the right flank revealed multifocal, circular to oval masses with a diameter of 4–7 cm, heterogeneous content and irregular cavitation. Diagnostic laparotomy revealed multiple mesenteric abscesses. The goat was euthanised, and a diagnosis of severe, multifocal, purulent lymphadenitis involving the mesenteric lymph nodes was made. The onion‐ring appearance of the abscesses and the creamy white to green pus suggested caseous lymphadenitis.
Autonomous Soft-Error Tolerance of FPGA Configuration Bits
Authors: Das Anup , Venkataraman Shyamsundar , Kumar Akash 
Published: March 2015

Field-programmable gate arrays (FPGAs) are increasingly susceptible to radiation-induced single event upsets (SEUs). These upsets are predominant in a space environment; however, with increasing use of static RAM (SRAM) in modern FPGAs, these SEUs are gaining prominence even in a terrestrial environment. SEUs can flip SRAM bits of FPGA, potentially altering the functionality of the implemented design. This has motivated FPGA designers to investigate techniques to protect the FPGA configuration bits against such inadvertent bit flips (soft error). Traditionally, triple modular redundancy (TMR) is used to protect the FPGA bit flips. Increasing design complexity and limited battery life motivate for alternative approaches for soft-error tolerance. In this article, we propose a technique to improve autonomous fault-masking capabilities of a design by maximizing the number of zeros or ones in lookup tables (LUTs). The technique analyzes critical configuration bits and utilizes spare resources (XOR gates and carry chains) of FPGAs to selectively manipulate the logic implemented in LUTs using two operations: LUT restructuring and LUT decomposition. We implemented the proposed approach for Xilinx Virtex-6 FPGAs and validated the same with a wide set of designs from the MCNC, IWLS 2005, and ITC99 benchmark suites. Results demonstrate that the proposed logic restructuring maximizes logic 0 (or 1) of LUTs by an average of 20%, achieving 80% fault masking with no area overhead. The fault rate of the entire design is reduced by 60% on average as compared to the existing techniques. Furthermore, the logic decomposition algorithm provides incremental fault-tolerance capabilities and achieves an additional 5% fault masking with an average 7% increase in slice usage.
The complete methodology is implemented into a tool for Xilinx FPGA and is made available online for the benefit of the research community. The algorithms are lightweight, and the whole design flow (including Xilinx Place and Route) was completed in 75 minutes for the largest benchmark in the set.
A Hash Table for Line-Rate Data Processing
Authors: István Zsolt , Alonso Gustavo , Blott Michaela , Vissers Kees 
Published: March 2015

FPGA-based data processing is becoming increasingly relevant in data centers, as the transformation of existing applications into dataflow architectures can bring significant throughput and power benefits. Furthermore, a tighter integration of computing and network is appealing, as it overcomes traditional bottlenecks between CPUs and network interfaces, and dramatically reduces latency.
In this article, we present the design of a novel hash table, a fundamental building block used in many applications, to enable data processing on FPGAs close to the network. We present a fully pipelined design capable of sustaining consistent 10Gbps line-rate processing by deploying a concurrent mechanism to handle hash collisions. We address additional design challenges such as support for a broad range of key sizes without stalling the pipeline through careful matching of lookup time with packet reception time. Finally, the design is based on a scalable architecture that can be easily parameterized to work with different memory types operating at different access speeds and latencies.
We have tested the proposed hash table in an FPGA-based memcached appliance implementing a main-memory key-value store in hardware. The hash table is used to index 2 million entries in 24GB of external DDR3 DRAM while sustaining 13 million requests per second, the maximum packet rate that can be achieved with UDP packets on a 10Gbps link for this application.