bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic evaluation of oxalate‐degrading transgenic soybean in response to Sclerotinia sclerotiorum infection
Authors: Calla Bernarda , Blahut‐Beatty Laureen , Koziol Lisa , Zhang Yunfang , Neece David J. , Carbajulca Doris , Garcia Alexandre , Simmonds Daina H. , Clough Steven J. 
Published: January 2014

SummaryOxalate oxidases (OxO) catalyse the degradation of oxalic acid (OA). Highly resistant transgenic soybean carrying an OxO gene and its susceptible parent soybean line, AC Colibri, were tested for genome‐wide gene expression in response to the necrotrophic, OA‐producing pathogen Sclerotinia sclerotiorum using soybean cDNA microarrays. The genes with changed expression at statistically significant levels (overall F‐test P‐value cut‐off of 0.0001) were classified into functional categories and pathways, and were analysed to evaluate the differences in transcriptome profiles. Although many genes and pathways were found to be similarly activated or repressed in both genotypes after inoculation with S. sclerotiorum, the OxO genotype displayed a measurably faster induction of basal defence responses, as observed by the differential changes in defence‐related and secondary metabolite genes compared with its susceptible parent AC Colibri. In addition, the experiment presented provides data on several other transcripts that support the hypothesis that S. sclerotiorum at least partially elicits the hypersensitive response, induces lignin synthesis (cinnamoyl CoA reductase) and elicits as yet unstudied signalling pathways (G‐protein‐coupled receptor and related). Of the nine genes showing the most extreme opposite directions of expression between genotypes, eight were related to photosynthesis and/or oxidation, highlighting the importance of redox in the control of this pathogen.
Optimization of virus‐induced gene silencing in Catharanthus roseus
Authors: Sung Y.‐C. , Lin C.‐P. , Chen J.‐C. 
Published: January 2014

Catharanthus roseus (periwinkle) contains abundant alkaloids and is the only commercial source of two cancer drugs, vinblastine and vincristine. The plant is also used as an experimental host for phytoplasmas because it can be infected by most phytoplasmas and shows distinctive symptoms. Abundant gene sequences for periwinkle have become available through high‐throughput transcriptome sequencing, so periwinkle has become an ideal model for studies of alkaloid metabolism and plant–phytoplasma interactions. Tobacco rattle virus (TRV)‐based virus‐induced gene silencing (VIGS) for functional genomics studies has been established, but the duration of the system was too short for plant–phytoplasma interaction studies. To improve the system, several factors were analysed, including culture temperature, plant age, leaf age, organ preferences and virus distribution, for their effects on VIGS efficacy. A new agroinfiltration method was also used for inoculating entire seedlings. High temperature (30°C) strongly inhibited VIGS, but low temperature (16°C) inhibited plant growth. VIGS efficacy was reduced in old leaves but was not affected by plant age. VIGS occurred in all examined organs, including roots, stems, leaves and flowers, but was most effective in leaves and flowers. The TRV‐based system required the existence of TRV2 to maintain gene silencing, so TRV2 concentration may be used as an indicator of successful gene silencing. The optimized VIGS system was useful for studies of plant–phytoplasma interactions and conferred gene silencing for more than 6 months.
The Lymphoid Chemokine CCL21 Enhances the Cytotoxic T Lymphocyte‐Inducing Functions of Dendritic Cells
Authors: Hong C. Y. , Lee H.‐J. , Kim H.‐J. , Lee J.‐J 
Published: January 2014

AbstractThe potential use of lymphoid chemokines to generate a dendritic cell (DC) cancer vaccine is not yet clear. We investigated the effect of lymphoid chemokines on DC function and on the production of effective cytotoxic T lymphocytes (CTLs) for application of cancer vaccine using monocyte‐derived mature DCs (mDCs) prestimulated with lymphoid chemokines. mDCs exposed to a secondary lymphoid organ chemokine (SLC/CCL21) dramatically induced CTL response by increasing cytolytic activity without any significant alterations on expression of cell surface markers (e.g. CD80, CD83, CD86 and CCR7) or on the production of cytokines (e.g. IL‐12p70, IL‐10 and IL‐23). Interestingly, mDCs prestimulated with CCL21 showed higher levels of CXCL10 (IP‐10) production, but not the production of CCL22, compared with untreated mDCs. IP‐10 treatment during CTL generation with DCs dramatically enhanced tumour‐specific CTL response compared with untreated CTLs, and these enhanced CTL‐inducing functions of CCL21‐treated DCs were inhibited by anti‐IP‐10 treatment. Taken together, our data suggested an important role of the lymphoid‐endothelium‐associated chemokine, CCL21, on DCs in the induction of CTL responses.
IL‐17 and Glutamate Excitotoxicity in the Pathogenesis of Multiple Sclerosis
Authors: Kostic M. , Dzopalic T. , Zivanovic S. , Zivkovic N. , Cvetanovic A. , Stojanovic I. , Vojinovic S. , Marjanovic G. , Savic V. , Colic M. 
Published: January 2014

AbstractImmunoinflammatory‐mediated demyelination, the main pathological feature of multiple sclerosis (MS), is regularly accompanied by neurodegenerative processes, mostly in the form of axonal degeneration, which could be initiated by glutamate excitotoxicity. In the current study, the relationship between Th17‐mediated inflammatory and excitotoxic events was investigated during an active phase of MS. Cerebrospinal fluid (CSF) of patients with MS and control subjects was collected, and IL‐17A and glutamate levels were determined. IL‐17A level was significantly higher in patients with MS; whereas no statistically significant changes in glutamate concentrations were found. There was a direct correlation between IL‐17A and glutamate levels; IL‐17A levels were also associated with the neutrophil expansion in CSF and blood–brain barrier disruption. However, IL‐17A level and the number of neutrophils tended to fall with disease duration. The results suggest that Th17 cells might enhance and use glutamate excitotoxicity as an effector mechanism in the MS pathogenesis. Furthermore, Th17 immune response, as well as neutrophils, could be more important for MS onset rather than further disease development and progression, what could explain why some MS clinical trials, targeting Th17 cells in the later stage of the disease, failed to provide any clinical benefit.
Quinoline‐3‐Carboxamides Modulate Primary T Cell‐Dependent B Cell Responses but do not Inhibit Functional Immunity
Authors: Källberg E. , Ivars F. , Leanderson T. 
Published: January 2014

AbstractThe effect of a quinoline‐3‐carboxamide on the T cell‐dependent B cell response was investigated in C57BL/6 mice after NP‐CGG immunization. The primary serum response to the hapten was slightly inhibited by treatment with a quinoline‐3‐carboxamide. This inhibition was paralleled by reduced numbers of germinal centre (GC) B cells and follicular T cells in the spleen up to 21 days after immunization. Also, both the number of GCs formed and their size were reduced by quinoline‐3‐carboxamide treatment. In contrast to the observation in the primary immune response, there was no inhibitory effect on the secondary immune response. These data could help to explain how quinoline‐3‐carboxamides can modulate immune function in autoimmune diseases without being immunosuppressive.
The Role of T cell Immunoglobulin and Mucin Domain‐3 in Immune Thrombocytopenia
Authors: Zhang X.‐M. , Shan N.‐N. 
Published: January 2014

AbstractT cell immunoglobulin and mucin domain‐3 (TIM‐3), originally identified as a T helper (Th) 1‐specific type I membrane protein, plays a vital role in Th1 immunity and tolerance induction through interaction with its ligand, galectin‐9. The binding of TIM‐3 by galectin‐9 serves to downregulate Th1 responses. Moreover, the regulatory function of TIM‐3 has been extended to other cells, such as Th17 cells, CD4+CD25+ regulatory T cells (Tregs), CD8+ T cells and certain innate immune cells. Previous studies have acknowledged that the TIM‐3 pathway is involved in the pathogenesis of several human autoimmune diseases, such as systemic lupus erythematous, rheumatoid arthritis and aplastic anaemia. Moreover, genetic data suggest a role for TIM‐3 in human autoimmune diseases. However, in immune thrombocytopenia (ITP), a common Th1‐ and possibly Th17‐biased autoimmune disorder, the role of TIM‐3 has not been explored. Recently, our data have demonstrated that TIM‐3 expression is reduced in ITP patients, and we have found a potential link between ITP and the TIM‐3 pathway. In this article, we discuss and speculate on the role of the TIM‐3 pathway in ITP.
Fates of Setaria faberi and Abutilon theophrasti seeds in three crop rotation systems
Authors: Liebman M , Miller Z J , Williams C L , Westerman P R , Dixon P M , Heggenstaller A , Davis A S , Menalled F D , Sundberg D N 
Published: January 2014

SummaryWeed seeds in and on the soil are the primary cause of weed infestations in arable fields. Previous studies have documented reductions in weed seedbanks due to cropping system diversification through extended rotation sequences, but the impacts of different rotation systems on additions to and losses from weed seedbanks remain poorly understood. We conducted an experiment in Iowa, USA, to determine the fates of Setaria faberi and Abutilon theophrasti seeds in 2‐, 3‐ and 4‐year crop rotation systems when seed additions to the soil seedbank were restricted to a single pulse at the initiation of the study. Over the course of the experiment, seedlings were removed as they emerged and prevented from producing new seeds. After 41 months, seed population densities dropped >85% for S. faberi and >65% for A. theophrasti, but differences between rotation systems in the magnitude of seedbank reductions were not detected. Most of the reductions in seedbank densities took place from autumn through early spring in the first 5 months following seed deposition, before seedling emergence occurred, suggesting that seed predation and/or seed decay was important. For S. faberi, total cumulative seedling emergence and total seed mortality did not differ between rotation systems. In contrast, for A. theophrasti, seedling emergence was 71% lower and seed mortality was 83% greater in the 3‐ and 4‐year rotation systems than in the 2‐year system. Results of this study indicate that for certain weed species, such as A. theophrasti, crop rotation systems can strongly affect life‐history processes associated with soil seedbanks.
Draft Genome Sequence of the Alga-Aggregating Bacterium
Bacillus
sp. Strain RP1137
Authors: Powell Ryan J. , Bachvaroff Tsvetan R. , Hill Russell T. 
Published: January 2014

ABSTRACT

Bacillus
sp. strain RP1137 is a bacterium that is able to rapidly and efficiently aggregate biofuel-producing microalgae. By 16S rRNA gene sequencing, it was found to be related to the industrially important
Bacillus megaterium
. Here, we report the draft genome sequence of
Bacillus
sp. strain RP1137.
Association of early adult modifiable cardiovascular risk factors with left atrial size over a 20-year follow-up period: the CARDIA study
Authors: Armstrong Anderson C , Gidding Samuel S , Colangelo Laura A , Kishi Satoru , Liu Kiang , Sidney Stephen , Konety Suma , Lewis Cora E , Correia Luís C L , Lima Joao A C 
Published: January 2014

ObjectivesWe investigate how early adult and 20-year changes in modifiable cardiovascular risk factors (MRF) predict left atrial dimension (LAD) at age 43–55 years.MethodsThe Coronary Artery Risk Development in Young Adults (CARDIA) study enrolled black and white adults (1985–1986). We included 2903 participants with echocardiography and MRF assessment in follow-up years 5 and 25. At years 5 and 25, LAD was assessed by M-mode echocardiography, then indexed to body surface area (BSA) or height. Blood pressure (BP), body mass index (BMI), heart rate (HR), smoking, alcohol use, diabetes and physical activity were defined as MRF. Associations of MRF with LAD were assessed using multivariable regression adjusted for age, ethnicity, gender and year-5 left atrial (LA) size.ResultsThe participants were 30±4 years; 55% white; 44% men. LAD and LAD/height were modest but significantly higher over the follow-up period, but LAD/BSA decreased slightly. Increased baseline and 20-year changes in BP were related to enlargement of LAD and indices. Higher baseline and changes in BMI were also related to higher LAD and LAD/height, but the opposite direction was found for LAD/BSA. Increase in baseline HR was related to lower LAD but not LAD indices, when only baseline covariates were included in the model. However, baseline and 20-year changes in HR were significantly associated to LA size.ConclusionsIn a biracial cohort of young adults, the most robust predictors for LA enlargement over a 20-year follow-up period were higher BP and BMI. However, an inverse direction was found for the relationship between BMI and LAD/BSA. HR showed an inverse relation to LA size.
Safety and availability of clofazimine in the treatment of multidrug and extensively drug-resistant tuberculosis: analysis of published guidance and meta-analysis of cohort studies
Authors: Hwang Thomas J , Dotsenko Svetlana , Jafarov Azizkhon , Weyer Karin , Falzon Dennis , Lunte Kaspars , Nunn Paul , Jaramillo Ernesto , Keshavjee Salmaan , Wares Douglas F 
Published: January 2014

ObjectivesGiven the spread of multidrug-resistant tuberculosis (MDR-TB), new therapies are urgently needed, including the repurposing of existing drugs. We aimed to assess key considerations for the clinical and programmatic use of clofazimine (Cfz), a riminophenazine with antimycobacterial activity currently used to treat leprosy.DesignFixed and random effects meta-analysis of cohort studies and systematic review.SettingElectronic and manual searches were combined.Inclusion criteriaObservational studies on treatment of multidrug-resistant and extremely drug-resistant tuberculosis with Cfz or a Cfz-containing regimen, and published guidance and documents relating to cost and availability were eligible.Results5 observational studies enrolled 861 patients, of which 602 received Cfz. The pooled proportion of adverse drug reactions requiring discontinuation of Cfz treatment was 0.1% (95% CI (0.0 to 0.6%)), and the median frequency of all adverse events was 5.1%. Cfz showed in vitro efficacy againstMycobacterium tuberculosis, and Cfz-containing regimens may have had a useful role in the treatment of patients with drug-resistant strains and who had limited alternative treatment options. However, Cfz uptake remains insufficient to meet global needs; there is only one internationally quality-assured manufacturer, which produces a limited quantity of the drug prioritised for treatment of leprosy, the only indication for which the drug is registered.ConclusionsWhile the data were limited, Cfz was associated with a risk for adverse drug reactions comparable to that of first-line TB treatment, which could be reasonably managed under programmatic conditions. However, low market availability and high cost are important barriers to access to Cfz for patients with MDR-TB.
RECENT RESULTS ON HIGH-ENERGY SPIN PHENOMENA OF GLUONS AND SEA-QUARKS IN POLARIZED PROTON-PROTON COLLISIONS AT RHIC AT BNL
Authors: SURROW BERND 
Published: January 2014

The STAR experiment at the Relativistic Heavy-Ion Collider at Brookhaven National Laboratory is carrying out a spin physics program in high-energy polarized proton collisions at [Formula: see text] GeV and [Formula: see text] GeV to gain a deeper insight into the spin structure and dynamics of the proton. One of the main objectives of the spin physics program at RHIC is the precise determination of the polarized gluon distribution function. The STAR detector is well suited for the reconstruction of various final states involving jets, π0, π±, e± and γ, which allows to measure several different processes. Recent results suggest a gluon spin contribution to the proton spin at the same level as the quark spin contribution itself. The production of W bosons in polarized p+p collisions at [Formula: see text] GeV opens a new era in the study of the spin-flavor structure of the proton. W-(+) bosons are produced in [Formula: see text] collisions and can be detected through their leptonic decays, [Formula: see text], where only the respective charged lepton is measured. Results of W-(+) production suggest a large asymmetry between the polarization of anti-u and anti-d quarks.
Making Consensus Tractable
Authors: Mossel Elchanan , Tamuz Omer 
Published: January 2014

We study a model of consensus decision making in which a finite group of Bayesian agents has to choose between one of two courses of action. Each member of the group has a private and independent signal at his or her disposal, giving some indication as to which action is optimal. To come to a common decision, the participants perform repeated rounds of voting. In each round, each agent casts a vote in favor of one of the two courses of action, reflecting his or her current belief, and observes the votes of the rest.
We provide an efficient algorithm for the calculation the agents have to perform and show that consensus is always reached and that the probability of reaching a wrong decision decays exponentially with the number of agents.
Personalized tag recommendation based on generalized rules
Authors: Cagliero Luca , Fiori Alessandro , Grimaudo Luigi 
Published: January 2014

Tag recommendation is focused on recommending useful tags to a user who is annotating a Web resource. A relevant research issue is the recommendation of additional tags to partially annotated resources, which may be based on either personalized or collective knowledge. However, since the annotation process is usually not driven by any controlled vocabulary, the collections of user-specific and collective annotations are often very sparse. Indeed, the discovery of the most significant associations among tags becomes a challenging task.
This article presents a novel personalized tag recommendation system that discovers and exploits generalized association rules, that is, tag correlations holding at different abstraction levels, to identify additional pertinent tags to suggest. The use of generalized rules relevantly improves the effectiveness of traditional rule-based systems in coping with sparse tag collections, because: (i) correlations hidden at the level of individual tags may be anyhow figured out at higher abstraction levels and (ii) low-level tag associations discovered from collective data may be exploited to specialize high-level associations discovered in the user-specific context.
The effectiveness of the proposed system has been validated against other personalized approaches on real-life and benchmark collections retrieved from the popular photo-sharing system Flickr.
Active learning strategies for rating elicitation in collaborative filtering
Authors: Elahi Mehdi , Ricci Francesco , Rubens Neil 
Published: January 2014

The accuracy of collaborative-filtering recommender systems largely depends on three factors: the quality of the rating prediction algorithm, and the quantity and quality of available ratings. While research in the field of recommender systems often concentrates on improving prediction algorithms, even the best algorithms will fail if they are fed poor-quality data during training, that is, garbage in, garbage out. Active learning aims to remedy this problem by focusing on obtaining better-quality data that more aptly reflects a user's preferences. However, traditional evaluation of active learning strategies has two major flaws, which have significant negative ramifications on accurately evaluating the system's performance (prediction error, precision, and quantity of elicited ratings). (1) Performance has been evaluated for each user independently (ignoring system-wide improvements). (2) Active learning strategies have been evaluated in isolation from unsolicited user ratings (natural acquisition).
In this article we show that an elicited rating has effects across the system, so a typical user-centric evaluation which ignores any changes of rating prediction of other users also ignores these cumulative effects, which may be more influential on the performance of the system as a whole (system centric). We propose a new evaluation methodology and use it to evaluate some novel and state-of-the-art rating elicitation strategies. We found that the system-wide effectiveness of a rating elicitation strategy depends on the stage of the rating elicitation process, and on the evaluation measures (MAE, NDCG, and Precision). In particular, we show that using some common user-centric strategies may actually degrade the overall performance of a system. Finally, we show that the performance of many common active learning strategies changes significantly when evaluated concurrently with the natural acquisition of ratings in recommender systems.
The Association between Hearing Loss and Social Isolation in Older Adults
Authors: Mick Paul , Kawachi Ichiro , Lin Frank R. 
Published: January 2014

ObjectiveTo determine if age‐related hearing loss is associated with social isolation and whether factors such as age, gender, income, race, or hearing aid use moderated the association.Study DesignCross‐sectional.SettingRandomly sampled United States communities.Subjects and MethodsCross‐sectional data on adults 60 to 84 years old from the 1999 to 2006 cycles of the National Health and Nutrition Examination Survey were analyzed. The dependent variable was social isolation, which was defined using the social isolation score (SIS), a 4‐point composite index consisting of items pertaining to strength of social network and support. SIS scores ≥2 were considered indicative of social isolation. The independent (predictor) variable was the pure tone average of speech frequency (0.5‐4 kHz) hearing thresholds in the better‐hearing ear. Covariates included potential medical, demographic, and otologic confounders. We used multivariate logistic regression to evaluate the association between hearing loss and the odds of having social isolation. An exploratory analysis was performed to assess the strength of associations between hearing loss and individual items of the SIS scale.ResultsGreater hearing loss was associated with increased odds of social isolation in women aged 60 to 69 years (odds ratio [OR], 3.49 per 25‐dB of hearing loss; 95% confidence interval, 1.91, 6.39;P<. 001). Effect modification by gender was significant in this age group (P=. 003). Hearing loss was not significantly associated with social isolation in other age and gender groups.ConclusionsGreater hearing loss is associated with increased odds of being social isolated in a nationally representative sample of women aged 60 to 69 years.