bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoplasmic genome substitution in wheat affects the nuclear-cytoplasmic cross-talk leading to transcript and metabolite alterations
Authors: Crosatti Cristina , Quansah Lydia , Maré Caterina , Giusti Lorenzo , Roncaglia Enrica , Atienza Sergio G , Cattivelli Luigi , Fait Aaron 
Published: December 2013

Abstract

Background
Alloplasmic lines provide a unique tool to study nuclear-cytoplasmic interactions. Three alloplasmic lines, with nuclear genomes from Triticum aestivum and harboring cytoplasm from Aegilops uniaristata, Aegilops tauschii and Hordeum chilense, were investigated by transcript and metabolite profiling to identify the effects of cytoplasmic substitution on nuclear-cytoplasmic signaling mechanisms.

Results
In combining the wheat nuclear genome with a cytoplasm of H. chilense, 540 genes were significantly altered, whereas 11 and 28 genes were significantly changed in the alloplasmic lines carrying the cytoplasm of Ae. uniaristata or Ae. tauschii, respectively. We identified the RNA maturation-related process as one of the most sensitive to a perturbation of the nuclear-cytoplasmic interaction. Several key components of the ROS chloroplast retrograde signaling, together with the up-regulation of the ROS scavenging system, showed that changes in the chloroplast genome have a direct impact on nuclear-cytoplasmic cross-talk. Remarkably, the H. chilense alloplasmic line down-regulated some genes involved in the determination of cytoplasmic male sterility without expressing the male sterility phenotype. Metabolic profiling showed a comparable response of the central metabolism of the alloplasmic and euplasmic lines to light, while exposing larger metabolite alterations in the H. chilense alloplasmic line as compared with the Aegilops lines, in agreement with the transcriptomic data. Several stress-related metabolites, remarkably raffinose, were altered in content in the H. chilense alloplasmic line when exposed to high light, while amino acids, as well as organic acids were significantly decreased. Alterations in the levels of transcript, related to raffinose, and the photorespiration-related metabolisms were associated with changes in the level of related metabolites.

Conclusion
The replacement of a wheat cytoplasm with the cytoplasm of a related species affects the nuclear-cytoplasmic cross-talk leading to transcript and metabolite alterations. The extent of these modifications was limited in the alloplasmic lines with Aegilops cytoplasm, and more evident in the alloplasmic line with H. chilense cytoplasm. We consider that, this finding might be linked to the phylogenetic distance of the genomes.
Community awareness about risk factors, presentation and prevention and obstetric fistula in Nabitovu village, Iganga district, Uganda
Authors: Kasamba Nassar , Kaye Dan K , Mbalinda Scovia N 
Published: December 2013

Abstract

Background
Obstetric fistula is a worldwide problem that is devastating for women in developing countries. The cardinal cause of obstetric fistula is prolonged obstructed labour and delay in seeking emergency obstetric care. Awareness about obstetric fistula is still low in developing countries. The objective was to assess the awareness about risk factors of obstetric fistulae in rural communities of Nabitovu village, Iganga district, Eastern Uganda.

Methods
A qualitative study using focus group discussion for males and females aged 18-49 years, to explore and gain deeper understanding of their awareness of existence, causes, clinical presentation and preventive measures for obstetric fistula. Data was analyzed by thematic analysis.

Results
The majority of the women and a few men were aware about obstetric fistula, though many had misconceptions regarding its causes, clinical presentation and prevention. Some wrongly attributed fistula to misuse of family planning, having sex during the menstruation period, curses by relatives, sexually transmitted infections, rape and gender-based violence. However, others attributed the fistula to delays to access medical care, induced abortions, conception at an early age, utilization of traditional birth attendants at delivery, and some complications that could occur during surgical operations for difficult deliveries.

Conclusion
Most of the community members interviewed were aware of the risk factors of obstetric fistula. Some respondents, predominantly men, had misconceptions/myths about risk factors of obstetric fistula as being caused by having sex during menstrual periods, poor usage of family planning, being a curse.
Race by Sex Differences in Depression Symptoms and Psychosocial Service Use Among Non-Hispanic Black and White Patients With Lung Cancer
Authors: Traeger Lara , Cannon Sheila , Keating Nancy L. , Pirl William F. , Lathan Christopher , Martin Michelle Y. , He Yulei , Park Elyse R. 
Published: December 2013

Purpose This study examined race by sex differences in depression symptoms and psychosocial service use (pastors, social workers, mental health workers, support groups) among patients with lung cancer. Patients and Methods The multiregional Cancer Care Outcomes Research and Surveillance study surveyed black and white adults with stages I to III lung cancer (n = 1,043) about depression symptoms, interest in help for mood, and psychosocial service use. Multivariable logistic regression was used to evaluate race/sex differences in depression symptoms (modified Center for Epidemiologic Studies Depression Scale ≥ 6) and psychosocial service use, independent of demographic, clinical, psychosocial, and behavioral covariates. Results A total of 18.2% screened positive for depression symptoms. This proportion was highest among black men (24.7%), followed by white women (20.6%), black women (15.8%), and white men (15.0%). In adjusted analyses, white women showed greater risk for depression symptoms relative to black women (P = .01) and white men (P = .002), with no other differences among groups. Black patients were less likely than white patients to receive desired help for mood from their doctors (P = .02), regardless of sex. Among all patients, black women were most likely to have contact with pastoral care and social work. Conclusion Race and sex interacted to predict risk of depression symptoms. Covariates accounted for elevated risk among black men. White women showed greater risk than black women and white men, independent of covariates. Black patients may experience greater barriers to receiving help for mood from their doctors. Race by sex differences in contact with psychosocial services highlight potential differences in the extent to which services are available, acceptable, and/or sought by patients.
Aprepitant Versus Dexamethasone for Preventing Chemotherapy-Induced Delayed Emesis in Patients With Breast Cancer: A Randomized Double-Blind Study
Authors: Roila Fausto , Ruggeri Benedetta , Ballatori Enzo , Del Favero Albano , Tonato Maurizio 
Published: December 2013

Purpose A combination of aprepitant, a 5-HT3 receptor antagonist, and dexamethasone is recommended for the prophylaxis of acute or delayed emesis induced by chemotherapy containing anthracyclines plus cyclophosphamide in patients with breast cancer. The aim of this study was to verify whether dexamethasone is superior to aprepitant in preventing delayed emesis in patients receiving the same prophylaxis for acute emesis. Patients and Methods A randomized double-blind study comparing aprepitant versus dexamethasone was completed in chemotherapy-naive patients with breast cancer treated with anthracyclines plus cyclophosphamide. Before chemotherapy, all patients were treated with intravenous palonosetron 0.25 mg, dexamethasone 8 mg, and oral aprepitant 125 mg. On days 2 and 3, patients randomly received oral dexamethasone 4 mg twice per day or aprepitant 80 mg once per day. Primary end point was rate of complete response (ie, no vomiting or rescue treatment) from days 2 to 5 after chemotherapy. Results Of 580 enrolled patients, 551 were evaluable: 273 received dexamethasone, and 278 received aprepitant. Day 1 complete response rates were similar: 87.6% for dexamethasone and 84.9% for aprepitant (P < .39). From days 2 to 5, complete response rates were the same with both antiemetic prophylaxes (79.5%; P < 1.00), as were results of secondary end points (ie, complete protection, total control, no vomiting, no nausea, score of Functional Living Index–Emesis; P < .24). Incidences of insomnia (2.9% v 0.4%; P < .02) and heartburn (8.1% v 3.6%; P < .03) were significantly greater with dexamethasone on days 2 to 5. Conclusion In patients with breast cancer treated with anthracycline plus cyclophosphamide chemotherapy and receiving the same antiemetic prophylaxis for acute emesis, dexamethasone was not superior to aprepitant but instead had similar efficacy and toxicity in preventing delayed emesis.
Adverse Event Reporting in Cancer Clinical Trial Publications
Authors: Sivendran Shanthi , Latif Asma , McBride Russell B. , Stensland Kristian D. , Wisnivesky Juan , Haines Lindsay , Oh William K. , Galsky Matthew D. 
Published: December 2013

Purpose Reporting adverse events is a critical element of a clinical trial publication. In 2003, the Consolidated Standards of Reporting Trials (CONSORT) group generated recommendations regarding the appropriate reporting of adverse events. The degree to which these recommendations are followed in oncology publications has not been comprehensively evaluated. Methods A review of citations from PubMed, Medline, and Embase published between Jan 1, 2009 and December 31, 2011, identified eligible randomized, controlled phase III trials in metastatic solid malignancies. Publications were assessed for 14 adverse event–reporting elements derived from the CONSORT harms extension statement; a completeness score (range, 0 to 14) was calculated by adding the number of elements reported. Linear regression analysis identified which publication characteristics associated with reporting completeness. Results A total of 175 publications, with data for 96,125 patients, were included in the analysis. The median completeness score was eight (range, three to 12). Most publications (96%) reported only adverse events occurring above a threshold rate or severity, 37% did not specify the criteria used to select which adverse events were reported, and 88% grouped together adverse events of varying severity. Regression analysis revealed that trials without a stated funding source and with an earlier year of publication had significantly lower completeness scores. Conclusion Reporting of adverse events in oncology publications of randomized trials is suboptimal and characterized by substantial selectivity and heterogeneity. The development of oncology-specific standards for adverse event reporting should be established to ensure consistency and provide critical information required for medical decision-making.
A characterisation of almost simple groups with socle 2E6(2) or M(22)
Authors: Parker Chris , Salarian M. Reza , Stroth Gernot 
Published: December 2013

Abstract
We show that the sporadic simple group M(22), the exceptional group of Lie type
2E6(2)
and their automorphism groups are uniquely determined by the approximate structure of the centralizer of an element of order 3 together with some
information about the fusion of this element in the group.
Dynamic structured copula models
Authors: Härdle Wolfgang Karl , Okhrin Ostap , Okhrin Yarema 
Published: December 2013

Abstract
There is an increasing demand for models of multivariate time-series with time-varying and non-Gaussian dependencies. The available models suffer from the curse of dimensionality or from restrictive assumptions on the parameters and distributions.
A promising class of models is that of hierarchical Archimedean copulae (HAC), which allows for non-exchangeable and non-Gaussian dependency structures with a small number of parameters. In this paper we develop a novel adaptive estimation technique of the parameters and of the structure of HAC for time-series. The approach relies on a local change-point detection procedure and a locally constant HAC approximation.
Typical applications are in the financial area but also recently in the spatial analysis of weather parameters.
We analyse the time varying dependency structure of stock indices and exchange rates. Both examples reveal periods with constant and turmoil dependencies. The economic significance of the suggested modelling is evaluated using the Value-at-Risk of a portfolio.
Inducible Defenses Stay Up Late: Temporal Patterns of Immune Gene Expression inTenebrio molitor
Authors: Johnston Paul R , Makarova Olga , Rolff Jens 
Published: December 2013

AbstractThe course of microbial infection in insects is shaped by a two-stage process of immune defense. Constitutive defenses, such as engulfment and melanization, act immediately and are followed by inducible defenses, archetypically the production of antimicrobial peptides, which eliminate or suppress the remaining microbes. By applying RNAseq across a 7-day time course, we sought to characterize the long-lasting immune response to bacterial challenge in the mealworm beetle Tenebrio molitor, a model for the biochemistry of insect immunity and persistent bacterial infection. By annotating a hybrid de novo assembly of RNAseq data, we were able to identify putative orthologs for the majority of components of the conserved insect immune system. Compared with Tribolium castaneum, the most closely related species with a reference genome sequence and a manually curated immune system annotation, the T. molitor immune gene count was lower, with lineage-specific expansions of genes encoding serine proteases and their countervailing inhibitors accounting for the majority of the deficit. Quantitative mapping of RNAseq reads to the reference assembly showed that expression of genes with predicted functions in cellular immunity, wound healing, melanization, and the production of reactive oxygen species was transiently induced immediately after immune challenge. In contrast, expression of genes encoding antimicrobial peptides or components of the Toll signaling pathway and iron sequestration response remained elevated for at least 7 days. Numerous genes involved in metabolism and nutrient storage were repressed, indicating a possible cost of immune induction. Strikingly, the expression of almost all antibacterial peptides followed the same pattern of long-lasting induction, regardless of their spectra of activity, signaling possible interactive roles in vivo.
Early Puberty, Negative Peer Influence, and Problem Behaviors in Adolescent Girls
Authors: Mrug Sylvie , Elliott Marc N. , Davies Susan , Tortolero Susan R. , Cuccaro Paula , Schuster Mark A. 
Published: December 2013

OBJECTIVE:
To determine how early puberty and peer deviance relate to trajectories of aggressive and delinquent behavior in early adolescence and whether these relationships differ by race/ethnicity.

METHODS:
In this longitudinal study, 2607 girls from 3 metropolitan areas and their parents were interviewed at ages 11, 13, and 16 years. Girls reported on their age of onset of menarche, best friend’s deviant behavior, delinquency, and physical, relational, and nonphysical aggression. Parents provided information on family sociodemographic characteristics and girls’ race/ethnicity.

RESULTS:
Sixteen percent of girls were classified as early maturers (defined by onset of menarche before age 11 years). Overall, relational and nonphysical aggression increased from age 11 to age 16, whereas delinquency and physical aggression remained stable. Early puberty was associated with elevated delinquency and physical aggression at age 11. The relationship with early puberty diminished over time for physical aggression but not for delinquency. Best friend’s deviant behavior was linked with higher levels of all problem behaviors, but the effect lessened over time for most outcomes. Early puberty was associated with a stronger link between best friend’s deviance and delinquency, suggesting increased vulnerability to negative peer influences among early-maturing girls. A similar vulnerability was observed for relational and nonphysical aggression among girls in the “other” racial/ethnic minority group only.

CONCLUSIONS:
Early puberty and friends’ deviance may increase the risk of problem behavior in young adolescent girls. Although many of these associations dissipate over time, early-maturing girls are at risk of persistently higher delinquency and stronger negative peer influences.
Comorbidity Clusters in Autism Spectrum Disorders: An Electronic Health Record Time-Series Analysis
Authors: Doshi-Velez Finale , Ge Yaorong , Kohane Isaac 
Published: December 2013

OBJECTIVE:The distinct trajectories of patients with autism spectrum disorders (ASDs) have not been extensively studied, particularly regarding clinical manifestations beyond the neurobehavioral criteria from the Diagnostic and Statistical Manual of Mental Disorders. The objective of this study was to investigate the patterns of co-occurrence of medical comorbidities in ASDs.METHODS:International Classification of Diseases, Ninth Revision codes from patients aged at least 15 years and a diagnosis of ASD were obtained from electronic medical records. These codes were aggregated by using phenotype-wide association studies categories and processed into 1350-dimensional vectors describing the counts of the most common categories in 6-month blocks between the ages of 0 to 15. Hierarchical clustering was used to identify subgroups with distinct courses.RESULTS:Four subgroups were identified. The first was characterized by seizures (n = 120, subgroup prevalence 77.5%). The second (n = 197) was characterized by multisystem disorders including gastrointestinal disorders (prevalence 24.3%) and auditory disorders and infections (prevalence 87.8%), and the third was characterized by psychiatric disorders (n = 212, prevalence 33.0%). The last group (n = 4316) could not be further resolved. The prevalence of psychiatric disorders was uncorrelated with seizure activity (P = .17), but a significant correlation existed between gastrointestinal disorders and seizures (P &lt; .001). The correlation results were replicated by using a second sample of 496 individuals from a different geographic region.CONCLUSIONS:Three distinct patterns of medical trajectories were identified by unsupervised clustering of electronic health record diagnoses. These may point to distinct etiologies with different genetic and environmental contributions. Additional clinical and molecular characterizations will be required to further delineate these subgroups.
Comparative Effectiveness of Empiric Antibiotics for Community-Acquired Pneumonia
Authors: Queen Mary Ann , Myers Angela L. , Hall Matthew , Shah Samir S. , Williams Derek J. , Auger Katherine A. , Jerardi Karen E. , Statile Angela M. , Tieder Joel S. 
Published: December 2013

BACKGROUND AND OBJECTIVE:Narrow-spectrum antibiotics are recommended as the first-line agent for children hospitalized with community-acquired pneumonia (CAP). There is little scientific evidence to support that this consensus-based recommendation is as effective as the more commonly used broad-spectrum antibiotics. The objective was to compare the effectiveness of empiric treatment with narrow-spectrum therapy versus broad-spectrum therapy for children hospitalized with uncomplicated CAP.METHODS:This multicenter retrospective cohort study using medical records included children aged 2 months to 18 years at 4 children's hospitals in 2010 with a discharge diagnosis of CAP. Patients receiving either narrow-spectrum or broad-spectrum therapy in the first 2 days of hospitalization were eligible. Patients were matched by using propensity scores that determined each patient’s likelihood of receiving empiric narrow or broad coverage. A multivariate logistic regression analysis evaluated the relationship between antibiotic and hospital length of stay (LOS), 7-day readmission, standardized daily costs, duration of fever, and duration of supplemental oxygen.RESULTS:Among 492 patients, 52% were empirically treated with a narrow-spectrum agent and 48% with a broad-spectrum agent. In the adjusted analysis, the narrow-spectrum group had a 10-hour shorter LOS (P = .04). There was no significant difference in duration of oxygen, duration of fever, or readmission. When modeled for LOS, there was no difference in average daily standardized cost (P = .62) or average daily standardized pharmacy cost (P = .26).CONCLUSIONS:Compared with broad-spectrum agents, narrow-spectrum antibiotic coverage is associated with similar outcomes. Our findings support national consensus recommendations for the use of narrow-spectrum antibiotics in children hospitalized with CAP.
Barriers and Challenges to Global Clinical Cancer Research
Authors: Seruga Bostjan , Sadikov Aleksander , Cazap Eduardo L. , Delgado Lucia Beatriz , Digumarti Raghunadharao , Leighl Natasha B. , Meshref Mohamed M. , Minami Hironobu , Robinson Eliezer , Yamaguchi Nise Hitomi , Pyle Doug , Cufer Tanja 
Published: December 2013

Abstract

Background.
There are concerns about growing barriers to cancer research. We explored the characteristics of and barriers to global clinical cancer research.

Methods.
The American Society of Clinical Oncology International Affairs Committee invited 300 selected oncologists with research experience from 25 countries to complete a Web-based survey. Fisher's exact test was used to compare answers between participants from high-income countries (HICs) and low- and middle-income countries (LMICs). Barriers to clinical cancer research were ranked from 1 (most important) to 8 (least important). Mann-Whitney's nonparametric test was used to compare the ranks describing the importance of investigated obstacles.

Results.
Eighty oncologists responded, 41 from HICs and 39 from LMICs. Most responders were medical oncologists (62%) at academic hospitals (90%). Researchers from HICs were more involved with academic and industry-driven research than were researchers from LMICs. Significantly higher proportions of those who considered their ability to conduct academic research and industry-driven research over the past 5 years more difficult were from HICs (73% vs. 27% and 70% vs. 30%, respectively). Concerning academic clinical cancer research, a lack of funding was ranked the most important (score: 3.16) barrier, without significant differences observed between HICs and LMICs. Lack of time or competing priorities and procedures from competent authorities were the second most important barriers to conducting academic clinical research in HICs and LMICs, respectively.

Conclusion.
Lack of funding, lack of time and competing priorities, and procedures from competent authorities might be the main global barriers to academic clinical cancer research.