bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Report of Squash leaf curl Philippines virus Infecting Chayote (Sechium edule) in Taiwan
Authors: Tsai W. S. , Hu C. J. , Shung D. P. , Lee L. M. , Wang J. T. , Kenyon L. 
Published: May 2011

Young shoots and leaves of chayote (Sechium edule (Jacq.) Sw.) are commonly consumed as a vegetable in Taiwan. In Hualien County, the major chayote-production area of Taiwan, as much as 15% of chayote plants were not marketable between September and October 2010 because of mosaic symptoms on the leaves. Three symptomatic leaves were collected from each of three fields in Hualien. All nine samples tested positive for a begomovirus by PCR using general primer pair PAL1v1978B/PAR1c715H (3) and negative for Zucchini yellow mosaic virus, Cucumber mosaic virus, Cucumber green mottle mosaic virus, Melon yellow spot virus, Papaya ringspot virus - type W, Watermelon mosaic virus, and Watermelon silver mottle virus by ELISA (2). On the basis of the high nucleotide sequence identity (97.7 to 99.6%) of the 1.5-kb begomoviral DNA-A fragments, all nine samples were considered infected by the same begomovirus species. The 1.5-kb sequences had greatest nucleotide sequence identity (96.6 to 97.8%) with Squash leaf curl Philippines virus (SLCPHV) pumpkin isolate from Taiwan (1) (GenBank Accession No. DQ866135; SLCPHV-TW[TW:Pum:05]). One sample was selected to complete viral genomic DNA analysis. Abutting primer pairs PKA-V/C (PKA-V: 5′-AACGGATCCACTTATGCACGATTTCCCT-3′; PKA-C: 5′-TAAGGATCCCACATGTTGTGGAGCA-3′) and PKB-V/C (PKB-V: 5′-TGTCCATGGATTGATGCGTTATCGGA-3′; PKB-C: 5′-TGACCATGGCATTTCCGAGATCTCCCA-3′') were used to amplify the complete DNA-A and DNA-B, respectively. The sequences of DNA-A (GenBank Accession No. JF146795) and DNA-B (GenBank Accession No. JF146796) contain 2,734 and 2,715 nucleotides, respectively. The geminivirus conserved sequence TAATATTAC was found in both DNA-A and -B. The DNA-A has two open reading frames (ORFs) in the virus sense (V1 and V2) and four in the complementary sense (C1 to C4). The DNA-B also had one ORF each in the virus sense (BV1) and the complementary sense (BC1). When compared by BLASTn in GenBank and analyzed by MEGALIGN software (DNASTAR, Madison, WI), they were found to have greatest nucleotide identity (98.0 to 99.0% of DNA-A and 96.7% of DNA-B) with SLCPHV isolates from Taiwan. In addition, SLCPHV caused similar symptoms on leaves when transmitted to healthy chayote by viruliferous whitefly. In Taiwan, SLCPHV has been detected and sequenced from naturally infected melon (GenBank Accession No. EU479710), pumpkin (GenBank Accession No. DQ866135), and wax gourd (GenBank Accession No. EU310406). To our knowledge, this is the first report of SLCPHV infecting chayote plants in Taiwan. The prevalence of SLCPHV infection on different cucurbit crops should be taken into consideration for managing viral diseases in Taiwan. References: (1) W. S. Tsai et al. Plant Dis. 91:907, 2007. (2) W. S. Tsai et al. Plant Dis. 94:923, 2010. (3) W. S. Tsai et al. Online publication. doi: 10.1111/j.1365-3059.2011.02424.x. Plant Pathol., 2011.
Tissue rinse liquid‐based cytology: a feasible tool for the intraoperative pathological evaluation of sentinel lymph nodes in breast cancer patients
Authors: Yamashiro K. , Taira K. , Nakajima M. , Okuyama D. , Azuma M. , Takeda H. , Suzuki H. , Jotoku H. , Watanabe K. , Takahashi M. , Taguchi K. , Tamura M. 
Published: May 2011

K. Yamashiro, K. Taira, M. Nakajima, D. Okuyama, M. Azuma, H. Takeda, H. Suzuki, H. Jotoku, K. Watanabe, M. Takahashi, K. Taguchi and M. Tamura  Tissue rinse liquid‐based cytology: a feasible tool for the intraoperative pathological evaluation of sentinel lymph nodes in breast cancer patientsObjectives:  A unique diagnostic method was designed for the intraoperative pathological evaluation of sentinel lymph nodes (SLNs) in breast cancer patients, and the results were verified with 2 years of experience.Methods:  Excised lymph nodes were cut into 2‐mm‐thick slices and rinsed thoroughly in CytoRich Red®. The sliced tissues were embedded in a paraffin block. Three cytological glass slides of the cells exfoliated in CytoRich Red® were prepared by the SurePath® liquid‐based cytology (LBC) technique. Two slides were stained by the Papanicolaou method, and the remaining slide was immunostained with an anti‐keratin antibody. This process is called tissue rinse liquid‐based cytology (TRLBC). The results of TRLBC were compared with those of the final pathological diagnoses, including immunostaining with an anti‐keratin antibody on paraffin blocks (PB).Results:  This study analysed 444 SLNs from 247 consecutive breast cancer patients. It required 35 minutes to complete the intraoperative diagnosis on a single node, and it took an additional 5 minutes per node if more than one node was submitted. When the results of PB were assumed to be the gold standard, the sensitivity and specificity of TRLBC were 81.9% and 96.1%, respectively. TRLBC detected all nodes with macrometastasis and 23 of 24 nodes with micrometastasis. Fifteen false‐negative TRLBC results were ‘isolated tumour cell clusters’ on PB, but there was one with micrometastasis histologically. Four of 14 false‐positive TRLBC results were proven to be true positive by supplementary examination using step sectioning of the paraffin blocks of the nodes.Conclusion:  TRLBC is a feasible and promising intraoperative cytopathological tool showing a comparable efficacy to PB while still allowing the conventional postoperative histological examination.
Asthma: a simple concept but in reality a complex disease
Authors: Holgate Stephen T. 
Published: May 2011

Eur J Clin Invest 2011; 41 (12): 1339–1352AbstractBackground  Asthma is a disorder of the conducting airways that contract too easily and too much to cause variable airflow obstruction with symptoms of wheeze, cough, chest tightness and shortness of breath. Based on this knowledge, initial treatments were directed to dilating the contracted airways with anticholinergic and adrenergic drugs. The recognition that allergic‐type inflammation underlay the hyperresponsive airways in asthma led to the introduction of anti‐inflammatory drugs such as sodium cromoglicate and corticosteroids. Over the 2 decades that followed, these drugs have been progressively improved by increasing their therapeutic index and duration of action.Methods  A review of the recent literature indicates that since the 1980s, the explosive increase in knowledge of the cell and mediator mechanisms of asthma has only led to modest improvements in therapy including the introduction of leukotriene modifiers and a blocking monoclonal antibody against IgE. Indeed, biologics targeting allergic cytokines and effector cells have on the whole proven disappointing despite initial promise being shown in animal models.Results  Part of the difficulty lies in the oversimplified concept that asthma is only driven by allergic processes when in reality there are many environmental causes and triggers and the view that it is a homogeneous disorder only varying in severity.Conclusions  The more recent views that asthma is a complex disorder made up of different subtypes with differing causes, treatment responses and natural histories creates a new opportunity for stratified medicine in which therapies acting upstream selectively target specific disease subtypes identified by specific diagnostic biomarkers.
Adhesion molecules and high‐sensitivity C‐reactive protein levels in patients with sickle cell beta‐thalassaemia
Authors: Kanavaki Ino , Makrythanasis Periklis , Lazaropoulou Christina , Kattamis Antonis , Tzanetea Revekka , Kalotychou Vassiliki , Rombos Ioannis , Papassotiriou Ioannis 
Published: May 2011

Eur J Clin Invest 2012; 42 (1): 27–33AbstractBackground and aim  The primary symptoms of sickle cell disease (SCD) arise from vaso‐occlusive crises. The pathogenesis of these crises is complex phenomenon where endothelial activation and damage has a major role. Chronic inflammation also plays an important role in the pathophysiology of SCD. We aimed to investigate endothelial activation in Caucasian Greek patients with SCD by means of measuring adhesion molecules and markers of inflammation.Subjects and methods  Twenty‐eight patients with SCD aged 5–63 years were included in the study. Most of the patients (23/28) were double heterozygotes for sickle cell/beta‐thalassaemia, while five patients (5/28) were sickle cell homozygotes. Patients were treated with one/or more of hydroxyurea, therapeutic phlebotomies, blood transfusion or splenectomy. Twenty apparently healthy individuals matched for age and sex formed the control group. Measurements of soluble intercellular adhesion molecule‐1, (sICAM‐1), soluble vascular cell adhesion molecule‐1 (sVCAM‐1), P‐selectin, E‐selectin, soluble thrombomodulin (sTM) and high‐sensitivity C‐reactive protein (hs‐CRP) levels were performed using immunoassays in both patients and healthy individuals.Results  We found that all endothelial adhesion molecules and hs‐CRP were significantly increased (P < 0·001) in patients with SCD compared with controls, while sTM levels did not differ significantly (P > 0·05) and this increase was not influenced by the treatment.Conclusion  Our findings demonstrate the high degree of endothelial activation and damage seen in sickle cell patients even in steady‐state condition, as well as the important chronic inflammation underlying the pathophysiology of this widespread disease.
Bioinformatics meets parasitology
Authors: CANTACESSI C. , CAMPBELL B. E. , JEX A. R. , YOUNG N. D. , HALL R. S. , RANGANATHAN S. , GASSER R. B. 
Published: May 2011

SummaryThe advent and integration of high‐throughput ‘‐omics’ technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next‐generation sequencing technologies and bioinformatic tools to large‐scale investigations of the transcriptomes of parasitic nematodes of socio‐economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention.
Social exposure to an antiretroviral treatment programme in rural KwaZulu‐Natal
Authors: Bor Jacob , Bärnighausen Till , Newell Colin , Tanser Frank , Newell Marie‐Louise 
Published: May 2011

SummaryObjective  To investigate the prevalence of social exposure to a large, government‐run ART programme in rural South Africa.Method  Clinical data on 6681 patients were matched with demographic data on a nearly complete cohort of 102 359 people residing in the programme catchment area. We calculated the proportion of residents in the demographic surveillance area that were members of a household, or resided in a compound where someone had initiated ART or received pre‐ART care.Results  By January 2010, 3% of the population had initiated ART. However, 25% of the population shared household membership or resided in a compound with someone who had initiated ART; 40% shared household or living arrangements with people who had either initiated ART or were enrolled in pre‐ART care.Conclusion  Such high rates of social exposure suggest that ART programmes in HIV endemic areas are likely to have significant population‐level effects on social norms and economic welfare. These results also point to the opportunity to reach large numbers of people with health and social services through existing ART programmes.
Estimation of seed production by Myosotis arvensis, Veronica hederifolia, Veronica persica and Viola arvensis under different competitive conditions
Authors: LUTMAN P J W , WRIGHT K J , BERRY K , FREEMAN S E , TATNELL L 
Published: May 2011

Lutman PJW, Wright KJ, Berry K, Freeman SE & Tatnell L (2011). Estimation of seed production by Myosotis arvensis, Veronica hederifolia, Veronica persica and Viola arvensis under different competitive conditions. Weed Research51, 499–507.SummarySeed production by Myosotis arvensis, Viola arvensis, Veronica persica and Veronica hederifolia was estimated in a series of 12 experiments. These species were grown in the field either on their own or in competition with a range of arable crops, though mainly winter wheat. Plants were harvested in summer, as they approached maturity and capsule and flower head numbers and dry weights were recorded. Seeds produced by each capsule (flower head) were also assessed in all experiments. Seed numbers were regressed with plant weight on a log/log basis, and high correlations were achieved in all cases (percentage variance accounted for >91%). Slopes of the overall regression lines were slightly <1.0 for all species (0.77–0.92). In the absence of crop competition, M. arvensis was estimated to produce c. 100 000, V. arvensis 3714, V. persica 4100 and V. hederifolia 980 seeds per plant. Competition from winter wheat reduced seed production of three of the species by more than 70%, but only reduced V. hederifolia production by 56%. These data on seed production form a key building block for the construction of population dynamics models to predict the likely consequences of the lower input weed management that is being promoted to reduce the environmental impact of weed control.
Strategies for exome and genome sequence data analysis in disease‐gene discovery projects
Authors: Robinson PN , Krawitz P , Mundlos S 
Published: May 2011

Robinson PN, Krawitz P, Mundlos S. Strategies for exome and genome sequence data analysis in disease‐gene discovery projects.In whole‐exome sequencing (WES), target capture methods are used to enrich the sequences of the coding regions of genes from fragmented total genomic DNA, followed by massively parallel, ‘next‐generation’ sequencing of the captured fragments. Since its introduction in 2009, WES has been successfully used in several disease‐gene discovery projects, but the analysis of whole‐exome sequence data can be challenging. In this overview, we present a summary of the main computational strategies that have been applied to identify novel disease genes in whole‐exome data, including intersect filters, the search for de novo mutations, and the application of linkage mapping or inference of identity‐by‐descent (IBD) in family studies.
Optimization of Glycerol Concentration and Freezing Rate in the Cryopreservation of Ejaculate From Brown Bear (Ursus arctos)
Authors: de Paz P , Alvarez‐Rodriguez M , Nicolas M , Alvarez M , Chamorro CA , Borragán S , Martinez‐Pastor F , Anel L 
Published: May 2011

ContentsIn order to establish a semen bank for the endangered Cantabrian brown bear, we tested five glycerol concentrations and three freezing rates for electroejaculated semen. Electroejaculation was performed on nine males. Semen was diluted in TES–Tris–Fructose (20% egg yolk, 2% EDTA, 1% Equex) with 2%, 4%, 6%, 8% or 10% glycerol and frozen at −10, −20 or −40°C/min. Before and after cryopreservation, samples were analysed for motility (CASA), viability and acrosomal status (flow cytometry). Pre‐freezing results showed that glycerol concentration had no significant effect on total motility or progressive motility, but it significantly decreased VCL, ALH, viability and acrosomal status (p < 0.05). After thawing, sperm motility was higher at extender with 4%, 6% and 8% glycerol, but only at 4% and 6% glycerol for viability and acrosomal status. For 4% and 6% glycerol, freezing rates did not have significant effects. The curve fitting gave an estimate of the optimal glycerol concentration, with all the optimal values for every parameter between 6% and 7% glycerol falling. We propose using 6% glycerol and a freezing velocity of −20°C/min for freezing brown bear ejaculated spermatozoa.
Impact of urethral ultrasonography on decision‐making in anterior urethroplasty
Authors: Buckley Jill C. , Wu Alex K. , McAninch Jack W. 
Published: May 2011

Study Type – Diagnostic (Exploratory cohort)Level of Evidence 2bWhat’s known on the subject? and What does the study add?Standard plain film evaluation of an anterior urethral strictures is inaccurate and can be misleading. A useful adjunctive imaging study that adds objective, precise anatomical information that helps guide surgical planning.OBJECTIVE• To assess the impact of urethral ultrasonography on decision‐making in complex anterior urethral reconstructions.PATIENTS AND METHODS• This was an institutional review board approved retrospective review of 500 patients receiving anterior urethroplasty from 1985 to 2007.• In all, 232 patients met the inclusion criteria of documented preoperative clinical assessment, retrograde urethrogram (RUG), urethral ultrasonogram, and measured operative stricture length and dimensions.• At the time of surgery, intraoperative urethral ultrasonography was performed.• A preoperative planned reconstructive approach was compared with the reconstructive procedure performed to determine how often urethral ultrasonography impacted operative decision‐making.RESULTS• Of the 232 patients in our review, 115 (50%), 88 (38%) and 16 (7%) received respectively anastomotic, buccal mucosa graft and fasciocutaneous flap urethroplasties.• Intraoperative ultrasonography changed surgical approach in 44 patients (19%), and was integral in deciding between two equally possible approaches in an additional 61 patients (26%).• In patients whose approach was changed from anastomotic urethroplasty to an onlay urethroplasty, mean RUG length was 2.0 cm while mean ultrasound length was significantly longer at 3.4 cm (P= 0.02).• When the surgical approach was changed from an onlay urethroplasty to an anastomotic urethroplasty, mean RUG length was 2.7 cm compared with a significantly shorter intraoperative ultrasonography length of 1.9 cm (P < 0.005).CONCLUSIONS• Ultrasonography of the anterior urethra directly influenced our reconstructive operative approach in 45% of patients.• It is a simple, reliable procedure that adds valuable clinical insight and objective radiographic data to help select the optimal anterior urethral reconstructive approach.
Properties of Preliminary Test Estimators and Shrinkage Estimators for Evaluating Multiple Exposures—Application to Questionnaire Data from the ‘Study of Nevi in Children’
Authors: Satagopan Jaya M. , Zhou Qin , Oliveria Susan A. , Dusza Stephen W. , Weinstock Martin A. , Berwick Marianne , Halpern Allan C. 
Published: May 2011

SummaryEpidemiology studies increasingly examine multiple exposures in relation to disease by selecting the exposures of interest in a thematic manner. For example, sun exposure, sunburn and sun protection behaviour could be themes for an investigation of sun-related exposures. Several studies now use predefined linear combinations of the exposures pertaining to the themes to estimate the effects of the individual exposures. Such analyses may improve the precision of the exposure effects, but they can lead to inflated bias and type I errors when the linear combinations are inaccurate. We investigate preliminary test estimators and empirical Bayes-type shrinkage estimators as alternative approaches when it is desirable to exploit the thematic choice of exposures, but the accuracy of the predefined linear combinations is unknown. We show that the two types of estimator are intimately related under certain assumptions. The shrinkage estimator that is derived under the assumption of an exchangeable prior distribution gives precise estimates and is robust to misspecifications of the user-defined linear combinations. The precision gains and robustness of the shrinkage estimation approach are illustrated by using data from the ‘Study of nevi in children’, where the exposures are the individual questionnaire items and the outcome is log(total back naevus count).
Workload Portfolio Optimization for Virtualized Computer Systems Based on Semiparametric Quantile Function Estimation
Authors: Li Ta-Hsin 
Published: May 2011

SummaryThe latest technologies of server virtualization allow multiple computer workloads to share the same physical system dynamically while protecting them from interference from each other. Consolidation of workloads from stand-alone systems into virtualized systems requires accurate capacity sizing and optimal portfolio design to maximize the benefit of virtualization. This requirement often translates into a demand for accurate estimation of high quantiles from a limited amount of data for hundreds of workloads with diverse statistical characteristics. To deal with the problem, a semiparametric method of quantile function estimation is considered. The method employs the generalized Pareto distribution to model the high quantiles that exceed a certain threshold and retains the sample quantiles below the threshold. An automatic procedure is proposed for adaptive threshold and estimator selection and for adaptive data trimming. A simulation study shows that the procedure proposed is superior to the non-parametric sample quantile method for a variety of distributions. The procedure is applied to a portfolio optimization problem for computer workload consolidation with real data.
Bayesian Estimation of Extent of Recovery for Aspects of Verbal Memory in Women Undergoing Adjuvant Chemotherapy Treatment for Breast Cancer
Authors: Rolfe Margaret I. , Mengersen Kerrie L. , Vearncombe Katharine J. , Andrew Brooke , Beadle Geoffrey F. 
Published: May 2011

SummaryDecline in cognitive function can be experienced by up to 50% of women while undergoing adjuvant chemotherapy with a subset of patients experiencing long-term effects. Bayesian latent basis longitudinal random-effects and latent class growth models were used to assess the degree of verbal memory recovery for learning, immediate retention and delayed recall in women undergoing chemotherapy for early stage breast cancer and who were assessed before, and at 1, 6 and 18 months post chemotherapy. The latent basis model, with the initial time point fixed to 1 and the second to 0, enabled the estimation of the degree of recovery at times 3 and 4. In the single-class model, three prior distributions for the random effects were used, resulting in minimal differences in parameter estimation. These models resulted in a near complete recovery for learning, and 57–60% for immediate retention and delayed recall at 18 months post chemotherapy. A range of two- to five-class Bayesian mixture models were fitted, with classes differing for baseline and degree of recovery. In the three-class model, the ‘Low’ class indicated 29.0%, 11.0% and 9.6% recovery at 18 months post treatment for the three outcome measures respectively, indicating an extended time of reduced verbal memory function.