bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses
Authors: Briddon Rob W , Patil Basavaprabhu L , Bagewadi Basavaraj , Nawaz-ul-Rehman Muhammad Shah , Fauquet Claude M 
Published: April 2010

Abstract

Background
Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a view to unraveling their evolutionary histories and providing information on the possible origin of the DNA-B component.

Results
Comparative phylogenetic and exhaustive pairwise sequence comparison of all DNA-A and DNA-B components of begomoviruses demonstrates that the two molecules have very distinct molecular evolutionary histories and likely are under very different evolutionary pressures. The analysis highlights that component exchange has played a far greater role in diversification of begomoviruses than previously suspected, although there are distinct differences in the apparent ability of different groups of viruses to utilize this "sexual" mechanism of genetic exchange. Additionally we explore the hypothesis that DNA-B originated as a satellite that was captured by the monopartite progenitor of all extant bipartite begomoviruses and subsequently evolved to become the integral (essential) genome component that we recognize today. The situation with present-day satellites associated with begomoviruses provides some clues to the processes and selection pressures that may have led to the "domestication" of a wild progenitor of the DNA-B component.

Conclusions
The analysis has highlighted the greater genetic variation of DNA-B components, in comparison to the DNA-A components, and that component exchange is more widespread than previously demonstrated and confined to viruses from the Old World. Although the vast majority of New World and some Old World begomoviruses show near perfect co-evolution of the DNA-A and DNA-B components, this is not the case for the majority of Old World viruses. Genetic differences between Old and New World begomoviruses and the cultivation of exotic crops in the Old World are likely factors that have led to this dichotomy.
α-Synuclein overexpression increases dopamine toxicity in BE(2)-M17 cells
Authors: Bisaglia Marco , Greggio Elisa , Maric Dragan , Miller David W , Cookson Mark R , Bubacco Luigi 
Published: April 2010

AbstractBackgroundOxidative stress has been proposed to be involved in the pathogenesis of Parkinson's disease (PD). A plausible source of oxidative stress in nigral dopaminergic neurons is the redox reactions that specifically involve dopamine and produce various toxic molecules, i.e., free radicals and quinone species. α-Synuclein, a protein found in Lewy bodies characteristic of PD, is also thought to be involved in the pathogenesis of PD and point mutations and multiplications in the gene coding for α-synuclein have been found in familial forms of PD.ResultsWe used dopaminergic human neuroblastoma BE(2)-M17 cell lines stably transfected with WT or A30P mutant α-synuclein to characterize the effect of α-synuclein on dopamine toxicity. Cellular toxicity was analyzed by lactate dehydrogenase assay and by fluorescence-activated cell sorter analysis. Increased expression of either wild-type or mutant α-synuclein enhances the cellular toxicity induced by the accumulation of intracellular dopamine or DOPA.ConclusionsOur results suggest that an interplay between dopamine and α-synuclein can cause cell death in a neuron-like background. The data presented here are compatible with several models of cytotoxicity, including the formation of α-synuclein oligomers and impairment of the lysosomal degradation.
Quality of cause-of-death reporting using ICD-10 drowning codes: a descriptive study of 69 countries
Authors: Lu Tsung-Hsueh , Lunetta Philippe , Walker Sue 
Published: April 2010

Abstract

Background
The systematic collection of high-quality mortality data is a prerequisite in designing relevant drowning prevention programmes. This descriptive study aimed to assess the quality (i.e., level of specificity) of cause-of-death reporting using ICD-10 drowning codes across 69 countries.

Methods
World Health Organization (WHO) mortality data were extracted for analysis. The proportion of unintentional drowning deaths coded as unspecified at the 3-character level (ICD-10 code W74) and for which the place of occurrence was unspecified at the 4th character (.9) were calculated for each country as indicators of the quality of cause-of-death reporting.

Results
In 32 of the 69 countries studied, the percentage of cases of unintentional drowning coded as unspecified at the 3-character level exceeded 50%, and in 19 countries, this percentage exceeded 80%; in contrast, the percentage was lower than 10% in only 10 countries. In 21 of the 56 countries that report 4-character codes, the percentage of unintentional drowning deaths for which the place of occurrence was unspecified at the 4th character exceeded 50%, and in 15 countries, exceeded 90%; in only 14 countries was this percentage lower than 10%.

Conclusion
Despite the introduction of more specific subcategories for drowning in the ICD-10, many countries were found to be failing to report sufficiently specific codes in drowning mortality data submitted to the WHO.
CD133 expression in chemo-resistant Ewing sarcoma cells
Authors: Jiang Xiaohua , Gwye Ynnez , Russell Darren , Cao Christine , Douglas Dorothea , Hung Long , Kovar Heinrich , Triche Timothy J , Lawlor Elizabeth R 
Published: April 2010

Abstract

Background
Some human cancers demonstrate cellular hierarchies in which tumor-initiating cancer stem cells generate progeny cells with reduced tumorigenic potential. This cancer stem cell population is proposed to be a source of therapy-resistant and recurrent disease. Ewing sarcoma family tumors (ESFT) are highly aggressive cancers in which drug-resistant, relapsed disease remains a significant clinical problem. Recently, the cell surface protein CD133 was identified as a putative marker of tumor-initiating cells in ESFT. We evaluated ESFT tumors and cell lines to determine if high levels of CD133 are associated with drug resistance.

Methods
Expression of the CD133-encoding PROM1 gene was determined by RT-PCR in ESFT tumors and cell lines. CD133 protein expression was assessed by western blot, FACS and/or immunostaining. Cell lines were FACS-sorted into CD133+ and CD133- fractions and proliferation, colony formation in soft agar, and in vivo tumorigenicity compared. Chemosensitivity was measured using MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxy-methoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assays.

Results

PROM1 expression was either absent or extremely low in most tumors. However, PROM1 was highly over-expressed in 4 of 48 cases. Two of the 4 patients with PROM1 over-expressing tumors rapidly succumbed to primary drug-resistant disease and two are long-term, event-free survivors. The expression of PROM1 in ESFT cell lines was similarly heterogeneous. The frequency of CD133+ cells ranged from 2-99% and, with one exception, no differences in the chemoresistance or tumorigenicity of CD133+ and CD133- cell fractions were detected. Importantly, however, the STA-ET-8.2 cell line was found to retain a cellular hierarchy in which relatively chemo-resistant, tumorigenic CD133+ cells gave rise to relatively chemo-sensitive, less tumorigenic, CD133- progeny.

Conclusions
Up to 10% of ESFT express high levels of PROM1. In some tumors and cell lines the CD133+ fraction is relatively more drug-resistant, while in others there is no apparent difference between CD133+ and CD133- cells. These studies reveal heterogeneity in PROM1/CD133 expression in ESFT tumors and cell lines and confirm that high levels of PROM1 expression are, in at least some cases, associated with chemo-resistant disease. Further studies are required to elucidate the contribution of PROM1/CD133 expressing cells to therapeutic resistance in a large, prospective cohort of primary ESFT.
Health-related quality of life in overweight and obese youths: Results of a multicenter study
Authors: Wille Nora , Bullinger Monika , Holl Reinhard , Hoffmeister Ulrike , Mann Reinhard , Goldapp Cornelia , Reinehr Thomas , Westenhöfer Joachim , Egmond-Froehlich Andreas , Ravens-Sieberer Ulrike 
Published: April 2010

Abstract

Background
We examined treatment-seeking overweight and obese youths to better understand the gender, age, and treatment modality differences in generic and disease-specific health-related quality of life (HRQOL).

Methods
This multicenter study included 1,916 patients (mean = 12.6 years; 57% females; mean zBMI = 2.4) who started treatment for overweight and obesity in 48 treatment facilities between July 2005 and October 2006. The facilities offered either inpatient treatment or outpatient programs. Prior to treatment, all participants completed the generic KIDSCREEN-27 HRQOL-questionnaire, the self-perception subscale of the generic KIDSCREEN-52 and the disease-specific obesity module of the KINDLR.
The patients' HRQOL was compared to the KIDSCREEN reference sample from the general population by one-way analyses of variance, adjusting for age, gender, and socioeconomic status. Independent t-tests were conducted to compare disease-specific HRQOL scores between patients by gender and age group. Significant mean differences in HRQOL between inpatients and outpatients were explored by one-way analyses of variance, adjusting for age, gender, and zBMI. Effect sizes 'd' were calculated employing the estimated marginal means and the pooled standard deviation (mtreatment - mnorm/SDpooled).

Results
The patients' HRQOL scores were impaired relative to German norms, with effect sizes up to d = 1.12. The pattern of impairment was similar in boys and girls as well as in children and adolescents. In each of the analyses, at least three of six KIDSCREEN subscales were affected. Regardless of gender and age group, the highest impairments were found in self-perception and physical well-being. Because of the strong decrease in HRQOL in the general population during adolescence, compared to age-specific norms, adolescents were less impaired than were children. However, overweight and obese adolescents (especially females) reported the lowest absolute HRQOL scores. HRQOL varied with the intensity of treatment. Inpatients had significantly lower scores than did outpatients, even after adjusting for age, gender and zBMI.

Conclusions
The results suggest the presence of differences in HRQOL with regard to gender, age, and treatment modality in treatment-seeking overweight and obese youths. Research and clinical practice must consider the particular impairments of inpatients as well as the impairments of (especially female) adolescents.
Integrated network analysis of transcriptomic and proteomic data in psoriasis
Authors: Piruzian Eleonora , Bruskin Sergey , Ishkin Alex , Abdeev Rustam , Moshkovskii Sergey , Melnik Stanislav , Nikolsky Yuri , Nikolskaya Tatiana 
Published: April 2010

AbstractBackgroundPsoriasis is complex inflammatory skin pathology of autoimmune origin. Several cell types are perturbed in this pathology, and underlying signaling events are complex and still poorly understood.ResultsIn order to gain insight into molecular machinery underlying the disease, we conducted a comprehensive meta-analysis of proteomics and transcriptomics of psoriatic lesions from independent studies. Network-based analysis revealed similarities in regulation at both proteomics and transcriptomics level. We identified a group of transcription factors responsible for overexpression of psoriasis genes and a number of previously unknown signaling pathways that may play a role in this process. We also evaluated functional synergy between transcriptomics and proteomics results.ConclusionsWe developed network-based methodology for integrative analysis of high throughput data sets of different types. Investigation of proteomics and transcriptomics data sets on psoriasis revealed versatility in regulatory machinery underlying pathology and showed complementarities between two levels of cellular organization.
Environmental risk mapping of canine leishmaniasis in France
Authors: Chamaillé Lise , Tran Annelise , Meunier Anne , Bourdoiseau Gilles , Ready Paul , Dedet Jean-Pierre 
Published: April 2010

AbstractBackgroundCanine leishmaniasis (CanL) is a zoonotic disease caused byLeishmania infantum, a Trypanosomatid protozoan transmitted by phlebotomine sandflies. Leishmaniasis is endemic in southern France, but the influences of environmental and climatic factors on its maintenance and emergence remain poorly understood. From a retrospective database, including all the studies reporting prevalence or incidence of CanL in France between 1965 and 2007, we performed a spatial analysis in order to i) map the reported cases in France, and ii) produce an environment-based map of the areas at risk for CanL. We performed a Principal Component Analysis (PCA) followed by a Hierarchical Ascendant Classification (HAC) to assess if the locations of CanL could be grouped according to environmental variables related to climate, forest cover, and human and dog densities. For each group, the potential distribution of CanL in France was mapped using a species niche modelling approach (Maxent model).ResultsResults revealed the existence of two spatial groups of CanL cases. The first group is located in the Cévennes region (southern Massif Central), at altitudes of 200-1000 m above sea level, characterized by relatively low winter temperatures (1.9°C average), 1042 mm average annual rainfall and much forest cover. The second group is located on the Mediterranean coastal plain, characterized by higher temperatures, lower rainfall and less forest cover. These two groups may correspond to the environments favoured by the two sandfly vectors in France,Phlebotomus ariasiandPhlebotomus perniciosusrespectively. Our niche modelling of these two eco-epidemiological patterns was based on environmental variables and led to the first risk map for CanL in France.ConclusionResults show how an ecological approach can help to improve our understanding of the spatial distribution of CanL in France.
Experimental infection and co-infection of dogs with Anaplasma platys and Ehrlichia canis: hematologic, serologic and molecular findings
Authors: Gaunt SD , Beall MJ , Stillman BA , Lorentzen L , Diniz PPVP , Chandrashekar R , Breitschwerdt EB 
Published: April 2010

AbstractBackgroundRhipicephalus sanguineusis a ubiquitous tick responsible for transmittingEhrlichia canisand most likelyAnaplasma platysto dogs, as either single or co-infections. The objective of this study was to assess the effects of either simultaneous or sequential experimental infections withE. canisandA. platyson hematological and serological parameters, duration of infection, and efficacy of doxycycline therapy in dogs infected with one or both organisms. Six dogs per group were either uninfected,A. platysinfected,E. canisinfected,A. platysandE. canisco-infected,A. platysinfected andE. canischallenged orE. canisinfected andA. platyschallenged at day 112 post-infection (PI). Doxycycline treatment was initiated at 211 days PI, followed by dexamethasone immunosuppression beginning 410 days PI.ResultsInitially, transient decreases in hematocrit occurred in all groups infected withE. canis, but the mean hematocrit was significantly lower in theA. platysandE. canisco-infected group. All dogs except the controls developed marked thrombocytopenia after initial infection followed by gradually increased platelet counts by 112 days PI in groups with the single infections, while platelet counts remained significantly lower in theA. platysandE. canisco-infected group. Both sequential and simultaneous infections ofA. platysandE. canisproduced an enhanced humoral immune response toA. platyswhen compared to infection withA. platysalone. Likewise, co-infection withE. canisandA. platysresulted in a more persistentA. platysinfection compared to dogs infected withA. platysonly, but nearly allA. platysinfected dogs becameA. platys PCR negative prior to doxycycline treatment.E. canisinfected dogs, whether single or co-infected, remained thrombocytopenic andE. canisPCR positive in blood for 420 days. When treated with doxycycline, allE. canisinfected dogs becameE. canisPCR negative and the thrombocytopenia resolved. Despite immunosuppression, neitherA. platysnorE. canisDNA was PCR amplified from doxycycline-treated dogs.ConclusionsThe results of this study demonstrate that simultaneous or sequential infection withA. platysandE. caniscan alter various pathophysiological parameters in experimentally infected dogs, and because natural exposure to multiple tick-borne pathogens occurs frequently in dogs, awareness of co-infection is important in clinical practice.
Pneumococcal and influenza vaccination rates and their determinants in children with chronic medical conditions
Authors: Giannattasio Antonietta , Squeglia Veronica , Lo Vecchio Andrea , Russo Maria Teresa , Barbarino Alessandro , Carlomagno Raffaella , Guarino Alfredo 
Published: April 2010

Abstract

Background
To investigate the rates of pneumococcal and influenza vaccinations and their determinants in children with chronic medical conditions.

Patients and Methods
Children with HIV infection, cystic fibrosis, liver transplantation and diabetes mellitus were enrolled. Physicians of regional Reference Centres for each condition, primary care paediatricians and caregivers of children provided information through specific questionnaires. For diabetes, 3 Reference Centres were included.

Results
Less than 25% of children in each group received pneumococcal vaccination. Vaccination rates against influenza were 73% in patients with HIV-infection, 90% in patients with cystic fibrosis, 76% in patients with liver transplantation, and ranged from 21% to 61% in patients with diabetes mellitus. Reference Centres rather than primary care paediatricians had a major role in promoting vaccinations. Lack of information was the main reason for missing vaccination. Awareness of the severity of pneumococcus infection by key informants of at-risk children was associated with higher vaccination rate.

Conclusions
Vaccination rates in children with chronic conditions were poor for pneumococcus and slightly better for influenza. Barriers to vaccination include lack of awareness, health care and organization problems.
A systematic review of the impact of sedation practice in the ICU on resource use, costs and patient safety
Authors: Jackson Daniel L , Proudfoot Clare W , Cann Kimberley F , Walsh Tim 
Published: April 2010

Abstract
Introduction
Patients in intensive care units (ICUs) often receive sedation for prolonged periods. In order to better understand the impact of sub-optimal sedation practice on outcomes, we performed a systematic review, including observational studies and controlled trials which were conducted in sedated patients in the ICU and which compared the impact of changes in or different protocols for sedation management on economic and patient safety outcomes.

Methods
We searched Medline, Embase and CINAHL online literature databases from 1988 to 15th May 2008 and hand searched conferences. English-language studies set in the ICU, in sedated adult humans on mechanical ventilation, which reported the impact of sedation practice on cost and resource use and patient safety outcomes, were included. All abstracts were reviewed twice by two independent reviewers, with all conflicts resolved by a third reviewer, to check that they met the review inclusion criteria. Full-text papers of all included studies were retrieved and again reviewed twice against inclusion criteria. Data were doubly extracted from studies. Study aims, design, population, and outcomes including duration of mechanical ventilation, length of stay in ICU and hospital, costs and rates of mortality and adverse events were extracted. Due to heterogeneity between study designs and outcomes reported, no quantitative data synthesis such as meta-analysis was possible.

Results
Included studies varied in design, patient population and aim, with the majority being before-after studies. Overall, studies showed that improvements in sedation practice, such as the introduction of guidelines and protocols, or daily interruption of sedation, were associated with improvements in outcomes including ICU and hospital length of stay, duration of mechanical ventilation, and costs. Mortality and the incidence of nosocomial infections were also reduced.

Conclusions
Systematic interventions to improve sedation practice and maintain patients at an optimal sedation level in the ICU may improve patient outcomes and optimize resource usage.
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Authors: Weinberg Zasha , Wang Joy X , Bogue Jarrod , Yang Jingying , Corbino Keith , Moy Ryan H , Breaker Ronald R 
Published: April 2010

AbstractBackgroundStructured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure.ResultsBy applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzymeS-adenosylmethionine. Newly identifiedcis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection byHelicobacter, and many other physiological processes. A candidate riboswitch termedcrcBis represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act intransare also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences.ConclusionsThis work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.