bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneity and penetration of HIV-1 non-subtype B viruses in an Italian province: public health implications
Authors: TORTI C. , LAPADULA G. , IZZO I. , BRINDICCI G. , LABBATE G. , QUIROS-ROLDAN E. , DIALLO I. , GARGIULO F. , CASTELNUOVO F. , CALABRESI A. , CAROSI G. , MANCA N. , MONNO L. 
Published: January 2010

SUMMARYThis study assessed changes in prevalence and distribution of HIV-1 non-subtype B viruses in Italian and immigrant patients over two decades in a province in Italy. All HIV-positive patients who underwent genotypic resistance testing were selected. Prevalence of non-subtype B viruses in 3-year periods was calculated. All sequences of non-subtype B and those provided by REGA as unassigned were analysed for phylogenetic relationships. In total, 250/1563 (16%) individuals were infected with a non-subtype B virus. Prevalence increased over time, reaching a peak (31·5%) in 2004–2006. In Italian patients, the most frequent subtypes were B (92·5%) and F1 (4%). F1 subtype was also prevalent in patients from South America (13·6%); in patients of African origin, CRF02_AG (54·9%) and G (12·3%) were the most frequent. HIV-1 non-subtype B infections in Italians were mostly found in patients who acquired HIV sexually. A phylogenetic relationship between F subtypes in Italian and representative HIV-1 sequences from Brazil was found. C subtypes in Italians were phylogenetically related to subtypes circulating in Brazil. Inter-subtype recombinants were also found in the latest years. The HIV-1 epidemic in Brescia province evolved to the point where about 1/3 patients recently diagnosed harboured non-B HIV subtypes. The distribution of HIV-1 non-B subtypes in Italian patients resembled that in South American patients and phylogenetic relatedness between some Italian and South American HIV-1 strains was found. The possible epidemiological link between these two populations would have been missed by looking only at risk factors for HIV acquisition declared by patients. The evidence of inter-subtype recombinants points to significant genetic assortment. Overall our results support phylogenetic analysis as a tool for epidemiological investigation in order to guide targeted prevention strategies.
The astrobiological case for our cosmic ancestry
Authors: Wickramasinghe Chandra 
Published: January 2010

AbstractWith steadily mounting evidence that points to a cosmic origin of terrestrial life, a cultural barrier prevails against admitting that such a connection exists. Astronomy continues to reveal the presence of organic molecules and organic dust on a huge cosmic scale, amounting to a third of interstellar carbon tied up in this form. Just as the overwhelming bulk of organics on Earth stored over geological timescales are derived from the degradation of living cells, so it seems likely that interstellar organics in large measure also derive from biology. As we enter a new decade – the year 2010 – a clear pronouncement of our likely alien ancestry and of the existence of extraterrestrial life on a cosmic scale would seem to be overdue.
Assessing genetic diversity in three wildBrachymystax lenokpopulations using AFLP markers
Authors: Di Wang , Shao-Wu Li , Ge-Feng Xu , Yang Liu , Zhen-Bo Mou , Tong-Yan Lu 
Published: January 2010

AbstractThe genetic diversities of 72 individuals from three wild Lenok populations of Mudanjiang River (MD), Yalujiang River (YL) and Wusulijiang River (WSL) in the northeast of China were analysed using amplified fragment length polymorphism (AFLP) markers. The results showed that 541 polymorphic loci out of 559 were amplified by 12 primer pairs and the percentage of polymorphic loci was 96.78%. Shannon indices for the MD, YL and WSL populations were 0.3988±0.2913, 0.3254±0.3037, 0.2125±0.2862, respectively, and Nei's gene diversity indices were 0.2737±0.2062, 0.2229±0.2129, 0.1446±0.1985, respectively. The average total genetic diversity (Ht) was 0.3512±0.0.0208 and the average genetic diversity within populations (Hs) was 0.2137±0.0152. Among the three populations, the average genetic distance (Dst) was 0.1375 and the gene differentiation coefficient (Gst) was 0.3914. The genetic diversity was 60.85% within populations and 39.15% among populations. The gene flow index (Nm) was 0.7776. The analysis of molecular variance (AMOVA) indicated that the average fixation index (Fst) was 0.55336. The variance was 55.16% within populations and 44.84% among populations. The highest polymorphism ratio was in the MD group and the lowest in the WSL group.
Karyotyping ofBrassica oleraceaC genome using Brassica A genomic DNA as blocking agent
Authors: Xiao-Dan Chen , Li-Quan Zhu , Yong Wang , Xiao-Ying Rong , Jun Lu , Xiao-Jia Wang 
Published: January 2010

AbstractIn exploring an effective and reliable karyotyping method in Brassica crop plants,Brassica oleraceawas successfully karyotyped using genomicin situhybridization (GISH).B. oleraceagenomic DNA was labelled as probe using DIG-high prime mix kit, withB. rapagenomic DNA acting as blocking agent. Specific fluorescent signals were detected on each pair of homologous chromosomes, and nine pairs of chromosomes ofB. oleraceawere clearly identified according to the signal characteristics. A practical and accurate method for conducting karyotyping of small chromosomes has been demonstrated.
Collection and preservation of porcine polar bodies
Authors: Gong-Jin Wang , Xiao-Long Zhou , Xiao-Dong Tan , Jian-Ning Yu , Xiao-Bo Xu , Bi-Qin Fan 
Published: January 2010

AbstractMature porcine oocytes containing first polar bodies (Pb I) were obtained byin vitroculture of follicle oocytes from ovaries obtained from a local abattoir, and zygotes with second polar bodies (Pb II) were grown afterin vitrofertilization of the mature oocytes. Extrusion, biological activity and morphology of Pb I and Pb II were statistically analysed. Polar bodies were isolated and collected from oocytes by enzyme digestion or micromanipulation. Their vigour under different preservation conditions was analysed and evaluated using a Trypan blue staining method. The results showed that 66.7% of the oocytes extruded Pb I after 40 h ofin vitromature culture of oocytes, and 49.7% of the zygotes extruded Pb II 20 h afterin vitrofertilization. The efficiency of isolation of Pb II by micromanipulation significantly exceeded that by enzyme digestion, the Pb I and Pb II isolated by micromanipulation presenting with good vigour and normal morphology (95.3% versus 58.9%). The survival rates of Pb I and Pb II were 63.3% and 93.1% for 4 h at 39°C, 85.0% and 72.9% for 40 h at 4°C, and over 95.0% and 84.6% for less than 7 days at −20°C. In comparison with the above preservation conditions for Pb I and Pb II, the results for cryopreservation were best, with rates of survival as high as 89.1% for Pb I and 87.9% for Pb II for preservation periods of over a month, and rates of normal morphology of 97.8% and 95.7%, respectively. The Pb I and Pb II could be isolated and preserved effectively, for use in further research on the recombination of oocytes and zygotes.
PRELIMINARY BASELINE SURVEY OF AVIFAUNAL DIVERSITY IN JIMMA ZONE, SOUTH-WESTERN ETHIOPIA
Authors: Yineger Haile , Hundera Kitessa , Abdu Bruktawit , Beyene Tifases , Ndungu' James Kuria , Sekercioglu Cagan Hakki , Honnay Olivier , Muys Bart , Aerts Raf , Lens Luc 
Published: January 2010

AbstractMultidimensional poverty, which is deeply-rooted within least-developed African countries like Ethiopia, is forcing local people to heavily rely on natural resources for their subsistent livelihoods. As a result, remaining wilderness areas in tropical Africa which support huge but little known biological diversity, are subject to extensive habitat loss, fragmentation and degradation in turn causing loss of plant and animal species and ecosystem services provided by them. Coffee forest fragment within the Jimma Zone of Ethiopia cannot be expected to be an exception to such scenario. Taking this persistent problem into consideration, we carried out a preliminary survey of bird biodiversity in selected areas of Jimma Zone during a short term bird ringing training held from Sept. 30 to Oct. 20, 2008. The main objective of the survey was to identify and document bird species of Jimma Zone, Southwestern Ethiopia, for further in-debth ornithological studies. Survey data were collected through exhaustive observations in and around 10 coffee forest fragments in Garuke, one fragment in Eladale, one urban area site in Jimma town and in scrubland vegetation around Gilgel Ghibe hydropower reservoir, Jimma Zone, Southwestern Ethiopia. In addition, five mist-nets were employed to capture understory forest birds in two purposively selected coffee forest fragments. Mist nets were opened at 5:50 A.M. and checked every 30 minutes until they were closed at 12:00 A.M. Over 196 bird species were identified during this survey and of these, 41 individuals belonging to 20 species were captured in Garuke and 23 individuals of 9 bird species in Eladale. Montane white-eye (Zosterops poliogastrus) followed by Olive sunbird (Nectarinia olivacea), Abyssinian slaty-flycatcher (Melaenornis chocolatinus) and Rupell’s robinchat (Cossypha semirufa) were the most frequently captured bird species. Of the sites surveyed, Gilgel Ghibe hydropower reservoir had strikingly highest bird species diversity. We approached the reservoir almost in a constant site near Bulbul Kebele (the smallest administrative unit in Ethiopia) and recorded over 115 bird species within about 300 meters distance! We learnt that this area was an important and most appropriate site to see a number of migrant and resident species as well as to undertake future bird ringing activities. We believe that the result of this survey will contribute much for the preparation of a comprehensive bird species checklist for Jimma Zone that could serve as important baseline information for more focused future ornithological investigations in the area so as to promote bird conservation through ecotourism activities and improve the livelihood of local people.
BEDTools: a flexible suite of utilities for comparing genomic features
Authors: Quinlan Aaron R. , Hall Ira M. 
Published: January 2010

Abstract
Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner.
Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.
Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools
Contact: aaronquinlan@gmail.com; imh4y@virginia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The two‐component histidine kinase Fhk1 controls stress adaptation and virulence of Fusarium oxysporum
Authors: RISPAIL NICOLAS , DI PIETRO ANTONIO 
Published: January 2010

SUMMARYFungal histidine kinases (HKs) have been implicated in different processes, such as the osmostress response, hyphal development, sensitivity to fungicides and virulence. Members of HK class III are known to signal through the HOG mitogen‐activated protein kinase (MAPK), but possible interactions with other MAPKs have not been explored. In this study, we have characterized fhk1, encoding a putative class III HK from the soil‐borne vascular wilt pathogen Fusarium oxysporum. Inactivation of fhk1 resulted in resistance to phenylpyrrole and dicarboximide fungicides, as well as increased sensitivity to hyperosmotic stress and menadione‐induced oxidative stress. The osmosensitivity of Δfhk1 mutants was associated with a striking and previously unreported change in colony morphology. The Δfhk1 strains showed a significant decrease in virulence on tomato plants. Epistatic analysis between Fhk1 and the Fmk1 MAPK cascade indicated that Fhk1 does not function upstream of Fmk1, but that the two pathways may interact to control the response to menadione‐induced oxidative stress.
Impacts of shellfisheries and nutrient inputs on waterbird communities in the Wash, England
Authors: Atkinson Philip W. , Maclean Ilya M.D. , Clark Nigel A. 
Published: January 2010

Summary 1. Overexploited fisheries threaten many species that depend on the exploited resource. Shorebird populations are in decline globally and here we describe how changing shellfishery management and nutrient inputs have had dramatic influence on waterbird communities on an internationally important wetland. 2. Cockle Cerastoderma edule and mussel Mytilus edulis fisheries conflict with shorebirds by removing prey and increasing mortality amongst non‐target benthic invertebrates. Under intense dredging pressure, evidence suggests that benthic invertebrates such as worms, with rapid growth and short‐generation times, should predominate over species such as bivalves, with slower growth and longer generation times. 3. We investigated the change in the waterbird assemblage in the Wash, eastern England, between 1981–1982 and 2002–2003. This period was characterized by heavy fishing pressure on mussels and cockles, ultimately leading to a crash in the mussel stocks. 4. During the study period, the waterbird assemblage underwent a gradual change from one dominated by those species with a high proportion of bivalves or ‘other’ prey (e.g. crustaceans, fish) in their diet to those with a higher proportion of worms. This gradual change was punctuated by major shifts, corresponding to three winters when oystercatcher Haemotopus ostralegus mortality was 5–13 times normal winter levels. 5. Oystercatcher, knot Calidris canutus and shelduck Tadorna tadorna showed the highest levels of decline. Since the last major oystercatcher mortality event in 1996–1997, the assemblage has not shifted back to that observed prior to the major crash in the mussel stock in 1992. 6. Changes in the waterbird assemblage were significantly related to mussel and cockle stock levels and, to a lesser extent, nutrient levels. Although correlative, evidence from this study indicates that fisheries caused shifts towards a waterbird community dominated by species with a high proportion of worms in their diet. 7.
Synthesis and applications. Mechanical shellfisheries directly conflict with the nature conservation interest of sites holding internationally important waterbird populations. Removal of the mussel beds in the Wash led to major shifts in the waterbird assemblage, with a shift towards worm‐feeders. Setting annual quotas that provide sufficient food for shellfish‐eating birds is essential to maintain the favourable status of this and other internationally important wetlands where shellfish are exploited.
Haemochromatosis genotype and iron overload: association with hypertension and left ventricular hypertrophy
Authors: Ellervik C. , Tybjærg‐Hansen A. , Appleyard M. , Ibsen H. , Nordestgaard B. G. 
Published: January 2010

Abstract.  Ellervik C, Tybjærg‐Hansen A, Appleyard M, Ibsen H, Nordestgaard BG (Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Herlev; Næstved Hospital, University of Copenhagen, Naestved; Copenhagen University Hospital, University of Copenhagen, Copenhagen East; Bispebjerg Hospital, Copenhagen University Hospital, University of Copenhagen, Bispebjerg; and Holbaek Hospital, Holbaek; Denmark). Haemochromatosis genotype and iron overload: association with hypertension and left ventricular hypertrophy. J Intern Med 2010; 268: 252–264.Objective.  We hypothesized that there is an association between haemochromatosis genotype C282Y/C282Y and/or iron overload and risk of hypertension and/or left ventricular hypertrophy (LVH).Methods.  We analysed data from a cross‐sectional study of the general population including 8992 individuals from the Copenhagen City Heart Study (CCHS), a follow‐up study of 36 480 individuals from the Copenhagen General Population Study (CGPS), and a case‐only study of 3815 Scandinavians from the Losartan Intervention For End‐point Reduction in Hypertension Genetic Substudy (LIFEGEN) with LVH and hypertension.Results.  In the CCHS, individuals with C282Y/C282Y versus wild type/wild type had an odds ratio for antihypertensive medication use of 4.8 (1.8–13; P = 0.003). In the CGPS, the corresponding hazard ratio was 1.7 (1.0–2.3; P = 0.003). Also, hazard ratios for antihypertensive medication use in the CGPS were 1.6 (1.0–2.6; P = 0.05) for transferrin saturation ≥80% vs. <50%, and 2.3 (1.3–4.2; P = 0.005) for C282Y/C282Y + transferrin saturation ≥80% vs. wild type/wild type + transferrin saturation <50%. These results were most pronounced in men above 55 years of age. We did not find any association between C282Y/C282Y or iron overload and LVH or hypertension (measured as blood pressure at a single occasion or continuous blood pressure), or LVH with hypertension in the CCHS or with severity of LVH in LIFEGEN.Conclusions.  We found that haemochromatosis genotype C282Y/C282Y and extremely elevated transferrin saturation either separately or combined were associated with increased risk of antihypertensive medication use. Therefore, testing for haemochromatosis genotype C282Y/C282Y and extreme transferrin saturation could be considered in patients with essential hypertension.
Disruption of Nap14, a plastid‐localized non‐intrinsic ABC protein in Arabidopsis thaliana results in the over‐accumulation of transition metals and in aberrant chloroplast structures
Authors: SHIMONI‐SHOR EINAV , HASSIDIM MIRIAM , YUVAL‐NAEH NAOMI , KEREN NIR 
Published: January 2010

ABSTRACTChloroplasts are the major sink for Fe in shoot tissues because of the requirements of the photosynthetic process and to storage in ferritins. Such requirements are common both to plastids and to their evolutionary progenitors, the cyanobacteria. Here, we examined whether iron transport mechanisms were conserved throughout the evolution of photosynthetic organisms. Comparison of the sequences of putative plastid transporters from Arabidopsis thaliana with those involved in cyanobacterial Fe transport identified two orthologs of the FutC protein, AtNAP11 and AtNAP14. To study their function, we analysed insertional mutants in the genes coding for these proteins. Both nap11/nap11 and nap14/nap14 plants exhibited severe growth defects. Significant changes in transition metal homeostasis were detected only in nap14/nap14. This mutant was found to contain ∼18 times more Fe in the shoot tissue than in wild‐type plants. The increased shoot transition metal content was accompanied by a specific loss of chloroplast structures and by a reduction in transcript levels of Fe homeostasis‐related genes. Based on these results, we propose that AtNAP14 plays an important role in plastid transition metal homeostasis. One possibility is that AtNAP14 is part of a chloroplast transporter complex. Alternatively, AtNAP14 function may be in regulating transition metal homeostasis.
How to read a nephrology systematic review
Authors: PALMER SUETONIA C , NAVANEETHAN SANKAR D , STRIPPOLI GIOVANNI FM 
Published: January 2010

ABSTRACT:A systematic review provides the best summary of evidence for clinical decision‐making in nephrology by summarizing all the primary studies that evaluate a specific clinical question. By using rigorous and pre‐specified methods, conclusions about the overall effect of an intervention can be more reliable, precise and comprehensive in a systematic review than those derived from individual studies. In this article, we describe the key components of a systematic review and meta‐analysis. We summarize the features of a systematic review that should be looked for when considering the accuracy and validity of its results – particularly when applying the outcomes of a systematic review to a clinical question.
The depth of the prostatic apex is an independent predictor of positive apical margins at radical prostatectomy
Authors: Matikainen Mika P. , Von Bodman Christian J. , Secin Fernando P. , Yunis Luis Herran , Vora Kinjal , Guillonneau Bertrand , Laudone Vincent , Eastham James A. , Scardino Peter T. , Akin Oguz , Rabbani Farhang 
Published: January 2010

Study Type – Therapy (case series) Level of Evidence 4OBJECTIVETo determine the effect of a deep and narrow pelvis on apical positive surgical margins (PSM) at radical prostatectomy (RP), controlling for other clinical and pathological variables and surgical approach, i.e. open retropubic (RRP) vs laparoscopic (LRP), as apical dissection is expected to be more challenging at RP with a prostate situated deep in a narrow pelvis.PATIENTS AND METHODSFrom July 2003 to January 2005, 512 consecutive patients with preoperative prostate magnetic resonance imaging (MRI) underwent RRP or LRP with no previous radio‐ or hormonal therapy. An additional 74 patients with preoperative MRI undergoing RP from December 2001 to June 2007 who had an apical PSM were also included, with 586 patients comprising the study population. Bony and soft‐tissue pelvic dimensions, including interspinous distance (ISD), bony (BFW) and soft tissue (SW) pelvic width, apical prostate depth (AD) and symphysis pubis angle, were measured on preoperative MRI. The pelvic dimension index (PDI), bony width index (BWI) and soft‐tissue width index (SWI) were defined as ISD/AD, BFW/AD and SW/AD, respectively. Multivariate logistic regression was used to assess the effect of pelvic dimensions on apical PSM, controlling for surgical approach and clinical and pathological variables.RESULTSThere was no significant difference in ISD, BFW, SW or symphysis angle between patients with and without apical PSM. The AD was significantly greater in men with an apical PSM and consequently PDI, BWI and SWI were significantly lower in men with an apical PSM. Each of PDI, AD, BWI and SWI was a significant independent predictor of apical PSM, independent of surgical approach, and other clinicopathological variables. The main limitations of the study were that it was retrospective, and the relatively few patients with apical PSM.CONCLUSIONSApical prostate depth is an independent risk factor for apical PSM at RP. MRI pelvimetry might allow for preoperative planning of the approach to RP.