bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations
Authors: Renoult Julien P , Kjellberg Finn , Grout Cinderella , Santoni Sylvain , Khadari Bouchaïb 
Published: October 2009

Abstract

Background
Hybridization events are relatively common in vascular plants. However, the frequency of these events is unevenly distributed across the plant phylogeny. Plant families in which individual species are pollinated by specific pollinator species are predicted to be less prone to hybridization than other families. However, exceptions may occur within these families, when pollinators shift host-plant species. Indeed, host shifts are expected to increase the rate of hybridization events. Pollinators of Ficus section Galoglychia are suspected to have changed host repeatedly, based on several cases of incongruence between plant phylogeny and taxonomy, and insect phylogeny and taxonomy. We tracked cyto-nuclear discordance across section Galoglychia as evidence for hybridization. To achieve a proper global view, we first clarified the monophyly of section Galoglychia as it had been questioned by recent phylogenetic studies. Moreover, we investigated if fig size could be a factor facilitating host shifts.

Results
Phylogenetic chloroplast and nuclear results demonstrated the monophyly of section Galoglychia. Within section Galoglychia, we detected several cases of statistically significant cyto-nuclear discordance. Discordances concern both terminal nodes of the phylogenetic trees and one deep node defining relationships between subsections. Because nuclear phylogeny is congruent with morphological taxonomy, discordances were caused by the chloroplast phylogeny. Introgressive hybridization was the most likely explanation for these discordances. We also detected that subsections pollinated by several wasp genera had smaller figs and were pollinated by smaller wasps than subsections pollinated by a single wasp genus.

Conclusion
As hypothesized, we discovered evidences of past hybridization in Ficus section Galoglychia. Further, introgression was only detected in subsections presenting incongruence between plant and pollinator phylogenies and taxonomy. This supports the hypothesis that host shift is the cause for plant-pollinator incongruence. Moreover, small fig size could facilitate host shifts. Eventually, this study demonstrates that non-coding chloroplast markers are valuable to resolve deep nodes in Ficus phylogeny.
An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
Authors: Mascarell-Creus Albert , Cañizares Joaquin , Vilarrasa-Blasi Josep , Mora-García Santiago , Blanca José , Gonzalez-Ibeas Daniel , Saladié Montserrat , Roig Cristina , Deleu Wim , Picó-Silvent Belén , López-Bigas Nuria , Aranda Miguel A , Garcia-Mas Jordi , Nuez Fernando , Puigdomènech Pere , Caño-Delgado Ana I 
Published: October 2009

Abstract

Background
Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression.

Results
We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study.

Conclusion
The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia
Authors: Bickhart Derek M , Gogarten Johann P , Lapierre Pascal , Tisa Louis S , Normand Philippe , Benson David R 
Published: October 2009

Abstract

Background
Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families.

Results
Insertion sequences in the Frankia genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder) algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR) events; many of which correlate to transposase clusters.

Conclusion
Analysis of transposase ORFs in Frankia sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this study suggest that IS elements may help drive chromosome differences in different Frankia sp. strains as they have adapted to a variety of hosts and environments.
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades
Authors: Förster Frank , Liang Chunguang , Shkumatov Alexander , Beisser Daniela , Engelmann Julia C , Schnölzer Martina , Frohme Marcus , Müller Tobias , Schill Ralph O , Dandekar Thomas 
Published: October 2009

Abstract

Background
Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.

Results
To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.

Conclusion
Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.
Environmental and intracellular regulation of Francisella tularensis ripA
Authors: Fuller James R , Kijek Todd M , Taft-Benz Sharon , Kawula Thomas H 
Published: October 2009

AbstractBackgroundFrancisella tularensisis a highly virulent, facultative intracellular pathogen and the etiologic agent of the zoonotic disease Tularemia. RipA is a cytoplasmic membrane protein that is conserved amongFrancisellaspecies and is required for intracellular growth.F. tularensis ripAdeletion mutants escape the phagosome of infected cells, but unlike wild type organisms fail to replicate in the host cell cytoplasm.ResultsFurther analysis ofripAwith respect to environmental effects on the growth of mutant strains and expression levels revealed that RipA is required for optimal growth at pH 7.5 but not pH 6.5. Using a combination of RT-PCR,ripA-lacZtranscriptional and translational fusions, and a RipA-tetracysteine tag fusion protein we found that bothripAtranscription and RipA protein levels were elevated in organisms grown at pH 7.5 as compared to organisms grown at pH 5.5. A number of genes, includingiglA, that are required for intracellular growth are regulated by the transcriptional regulators MglA and SspA, and are induced upon infection of host cells. We quantifiedripAandiglAexpression at different stages of intracellular growth and found that the expression of each increased between 1 and 6 hours post infection. Given the similar intracellular expression patterns ofripAandiglAand that MglA and SspA are positive regulators ofiglAwe tested the impact ofmglAandsspAdeletions onripAandiglAexpression. In the deletion mutant strainsiglAexpression was reduced dramatically as expected, howeverripAexpression was increased over 2-fold.ConclusionExpression ofripAis required for growth at neutral pH, is pH sensitive, and is responsive to the intracellular environment. The intracellular expression pattern ofripAcoincided withiglA, which is positively regulated by MglA and SspA. However, in contrast to their positive impact oniglAexpression, MglA and SspA negatively impactedripAexpressionin vitro.
Noninvasive cardiac output and blood pressure monitoring cannot replace an invasive monitoring system in critically ill patients
Authors: Stover John F , Stocker Reto , Lenherr Renato , Neff Thomas A , Cottini Silvia R , Zoller Bernhard , Béchir Markus 
Published: October 2009

Abstract

Background
Monitoring of cardiac output and blood pressure are standard procedures in critical care medicine. Traditionally, invasive techniques like pulmonary artery catheter (PAC) and arterial catheters are widely used. Invasiveness bears many risks of deleterious complications. Therefore, a noninvasive reliable cardiac output (CO) and blood pressure monitoring system could improve the safety of cardiac monitoring. The aim of the present study was to compare a noninvasive versus a standard invasive cardiovascular monitoring system.

Methods
Nexfin HD is a continuous noninvasive blood pressure and cardiac output monitor system and is based on the development of the pulsatile unloading of the finger arterial walls using an inflatable finger cuff. During continuous BP measurement CO is calculated. We included 10 patients with standard invasive cardiac monitoring system (pulmonary artery catheter and arterial catheter) comparing invasively obtained data to the data collected noninvasively using the Nexfin HD.

Results
Correlation between mean arterial pressure measured with the standard arterial monitoring system and the Nexfin HD was r2 = 0.67 with a bias of -2 mmHg and two standard deviations of ± 16 mmHg. Correlation between CO derived from PAC and the Nexfin HD was r2 = 0.83 with a bias of 0.23 l/min and two standard deviations of ± 2.1 l/min; the percentage error was 29%.

Conclusion
Although the noninvasive CO measurement appears promising, the noninvasive blood pressure assessment is clearly less reliable than the invasively measured blood pressure. Therefore, according to the present data application of the Nexfin HD monitoring system in the ICU cannot be recommended generally. Whether such a tool might be reliable in certain critically ill patients remains to be determined.
Genetic factors associated with intestinal metaplasia in a high risk Singapore-Chinese population: a cohort study
Authors: Zhu Feng , Loh Marie , Hill Jeffrey , Lee Sumarlin , Koh King Xin , Lai Kin Wai , Salto-Tellez Manuel , Iacopetta Barry , Yeoh Khay Guan , Soong Richie ,   the Singapore Gastric Cancer Consortium
Published: October 2009

Abstract

Background
Intestinal metaplasia (IM) is an important precursor lesion in the development of gastric cancer (GC). The aim of this study was to investigate genetic factors previously linked to GC risk for their possible association with IM. A total of 18 polymorphisms in 14 candidate genes were evaluated in a Singapore-Chinese population at high risk of developing GC.

Methods
Genotype frequencies were compared between individuals presenting with (n = 128) or without (n = 246) IM by both univariate and multivariate analysis.

Results
Carriers of the NQO1 609 T allele showed an association with IM in individuals who were seropositive for Helicobacter pylori (HP+; OR = 2.61, 95%CI: 1.18-5.80, P = .018). The IL-10 819 C allele was also associated with IM in HP+ individuals (OR = 2.32, 95%CI: 1.21-4.43, P = 0.011), while the PTPN11 A allele was associated with IM in HP- individuals (OR = 2.51, 95%CI: 1.16-5.40, P = 0.019), but showed an inverse association in HP+ subjects (OR = 0.46, 95%CI: 0.21-0.99, P = 0.048).

Conclusion
Polymorphisms in NQO1, IL-10 and PTPN11, in combination with HP status, could be used to identify individuals who are more likely to develop IM and therefore GC.
Adiponectin is associated with cardiovascular disease in male renal transplant recipients: baseline results from the LANDMARK 2 study
Authors: Kaisar Mohd O , Armstrong Kirsty , Hawley Carmel , Campbell Scott , Mudge David , Johnson David W , Prins John B , Isbel Nicole M 
Published: October 2009

Abstract

Background
Adiponectin is a major adipocyte-derived protein with insulin-sensitizing, anti-inflammatory and anti-atherogenic properties. Adiponectin levels correlate inversely with renal function and higher levels are predictive of lower cardiovascular disease (CVD) in patients with normal renal function and chronic kidney disease. No data exists on the association between adiponectin and CVD in renal transplant recipients (RTR).

Methods
Standard biochemistry, clinical data and adiponectin were collected from 137 RTR recruited to the LANDMARK 2 study at baseline. The LANDMARK 2 study is an ongoing randomized controlled study that compares the outcome of aggressive risk factor modification for cardiovascular disease versus standard post-transplant care in renal transplant recipients with impaired glucose tolerance or diabetes mellitus.

Results
Mean patient age was 53.4 ± 12 years and the median post-transplantation period was 5 (0.5-31.9) years. Mean serum adiponectin level was 12.3 ± 7.1 μg/mL. On univariate analysis, adiponectin was positively associated with female gender (P = 0.01) and serum high-density lipoprotein (HDL) concentration (P < 0.001), and inversely with body mass index (P = 0.009), metabolic syndrome (P = 0.047), abnormal glucose tolerance (P = 0.01), C-reactive protein (P = 0.001) and serum triglyceride (P < 0.001). On stepwise multivariate analysis, adiponectin in males was negatively correlated with combined baseline CVD (P = 0.03), waist-hip ratio (P = 0.003) and glomerular filtration rate (P = 0.046), and positively with HDL (P < 0.001). In contrast, in females adiponectin was inversely associated with C-reactive protein (P = 0.001) and serum triglyceride.

Conclusion
In conclusion, adiponectin is positively correlated with inflammation, dyslipidemia and abnormal glucose tolerance in RTR. Furthermore, hypoadiponectinemia correlated with increased baseline CVD in male RTR.
Promoting chlamydia screening with posters and leaflets in general practice - a qualitative study
Authors: Freeman Elaine , Howell-Jones Rebecca , Oliver Isabel , Randall Sarah , Ford-Young William , Beckwith Philippa , McNulty Cliodna 
Published: October 2009

Abstract

Background
General practice staff are reluctant to discuss sexual health opportunistically in all consultations. Health promotion materials may help alleviate this barrier. Chlamydia screening promotion posters and leaflets, produced by the English National Chlamydia Screening Programme (NCSP), have been available to general practices, through local chlamydia screening offices, since its launch. In this study we explored the attitudes of general practice staff to these screening promotional materials, how they used them, and explored other promotional strategies to encourage chlamydia screening.

Methods
Twenty-five general practices with a range of screening rates, were purposively selected from six NCSP areas in England. In focus groups doctors, nurses, administrative staff and receptionists were encouraged to discuss candidly their experiences about their use and opinions of posters, leaflets and advertising to promote chlamydia screening. Researchers observed whether posters and leaflets were on display in reception and/or waiting areas. Data were collected and analysed concurrently using a stepwise framework analytical approach.

Results
Although two-thirds of screening practices reported that they displayed posters and leaflets, they were not prominently displayed in most practices. Only a minority of practices reported actively using screening promotional materials on an ongoing basis. Most staff in all practices were not following up the advertising in posters and leaflets by routinely offering opportunistic screening to their target population. Some staff in many practices thought posters and leaflets would cause offence or embarrassment to their patients. Distribution of chlamydia leaflets by receptionists was thought to be inappropriate by some practices, as they thought patients would be offended when being offered a leaflet in a public area. Practice staff suggested the development of pocket-sized leaflets.

Conclusion
The NCSP should consider developing a range of more discrete but eye catching posters and small leaflets specifically to promote chlamydia screening in different scenarios within general practice; coordinators should audit their use. Practice staff need to discuss, with their screening co-ordinator, how different practice staff can promote chlamydia screening most effectively using the NCSP promotional materials, and change them regularly so that they do not loose their impact. Education to change all practice staff's attitudes towards sexual health is needed to reduce their worries about displaying the chlamydia materials, and how they may follow up the advertising up with a verbal offer of screening opportunistically to 15-24 year olds whenever they visit the practice.
Post partum anxiety and depression in peri-urban communities of Karachi, Pakistan: a quasi-experimental study
Authors: Ali Niloufer S , Ali Badar S , Azam Iqbal S 
Published: October 2009

Abstract

Background
Postpartum anxiety and depression is a major public health concern because of its adverse effects on the cognitive and social development of the infant. Globally postpartum depression has been widely investigated but as anxiety is a more prominent feature of postpartum depression we assessed the prevalence of anxiety and depression and their associated factors in post partum women.

Methods
A quasi-experimental study investigating the impact of postpartum anxiety and depression on child growth and development was conducted in two peri-urban, multiethnic, communities of Karachi, a mega city of Pakistan. A house to house questionnaire based survey was done by trained field workers; 420 consenting pregnant women were identified and data for socio-demographic, home environment and family relationship variables was collected between 36 weeks of pregnancy and within 10 days of childbirth. Mother's levels of anxiety and depression were assessed after one month, two months, six months and twelve months of childbirth; this was two step process: initially an indigenous, validated screening instrument Aga Khan University Anxiety and Depression Scale was used and diagnostic confirmation was done through a psychologist's interview based on DSM IV criteria. Women found to be anxious and depressed at least once out of four assessments were considered for the computation of overall prevalence of postpartum anxiety and depression as well as its risk factors. However, point prevalence's of postpartum anxiety and depression were also reported at each assessment time. Two sixty seven women could be followed for one year. Data was analyzed using SPSS. Chi-square test, simple and multiple logistic regression were used to see the association of different factors.

Results
The overall prevalence of postpartum anxiety and depression was found to be 28.8 percent. Domestic violence, difficulty in breast feeding at birth and unplanned current pregnancy were found to be significantly associated with postpartum anxiety and depression.

Conclusion
Domestic violence and not having the right to plan pregnancy are related to the patriarchal culture and lack of empowerment of women. The association with difficulties in breast feeding needs to be further explored in future studies
Age-related increases in parathyroid hormone may be antecedent to both osteoporosis and dementia
Authors: Braverman Eric R , Chen Thomas JH , Chen Amanda LC , Arcuri Vanessa , Kerner Mallory M , Bajaj Anish , Carbajal Javier , Braverman Dasha , Downs B William , Blum Kenneth 
Published: October 2009

Abstract

Background
Numerous studies have reported that age-induced increased parathyroid hormone plasma levels are associated with cognitive decline and dementia. Little is known about the correlation that may exist between neurological processing speed, cognition and bone density in cases of hyperparathyroidism. Thus, we decided to determine if parathyroid hormone levels correlate to processing speed and/or bone density.

Methods
The recruited subjects that met the inclusion criteria (n = 92, age-matched, age 18-90 years, mean = 58.85, SD = 15.47) were evaluated for plasma parathyroid hormone levels and these levels were statistically correlated with event-related P300 potentials. Groups were compared for age, bone density and P300 latency. One-tailed tests were used to ascertain the statistical significance of the correlations. The study groups were categorized and analyzed for differences of parathyroid hormone levels: parathyroid hormone levels <30 (n = 30, mean = 22.7 ± 5.6 SD) and PTH levels >30 (n = 62, mean = 62.4 ± 28.3 SD, p ≤ 02).

Results
Patients with parathyroid hormone levels <30 showed statistically significantly less P300 latency (P300 = 332.7 ± 4.8 SE) relative to those with parathyroid hormone levels >30, which demonstrated greater P300 latency (P300 = 345.7 ± 3.6 SE, p = .02). Participants with parathyroid hormone values <30 (n = 26) were found to have statistically significantly higher bone density (M = -1.25 ± .31 SE) than those with parathyroid hormone values >30 (n = 48, M = -1.85 ± .19 SE, p = .04).

Conclusion
Our findings of a statistically lower bone density and prolonged P300 in patients with high parathyroid hormone levels may suggest that increased parathyroid hormone levels coupled with prolonged P300 latency may become putative biological markers of both dementia and osteoporosis and warrant intensive investigation.