bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing Northern Hemisphere Snow Seasons
Authors: Choi Gwangyong , Robinson David A. , Kang Sinkyu 
Published: May 2010

Abstract
Spatial and temporal patterns in the onset, offset, and length of the snow season across Northern Hemisphere continents are examined for the period from 1967 to 2008. Full snow seasons (FSS) and core snow seasons (CSS) are defined based on the consistency of snow cover within a location over the course of the cold season. Climatologically, the seasonal onsets of FSS and CSS progress more rapidly across the continents than the slower spring northward offset. Average Northern Hemisphere FSS duration has decreased at a rate of 0.8 week decade−1 (5.3 days decade−1) between the winters of 1972/73 and 2007/08, while there is no significant hemispheric change in CSS duration. Changes in the FSS duration are attributed primarily to a progressively earlier offset, which has advanced poleward at a rate of 5.5 days decade−1. A major change in the trends of FSS offset and duration occurred in the late 1980s. Earlier FSS offsets, ranging from 5 to 25 days, and resultant abbreviated durations are observed in western Europe, central and East Asia, and the mountainous western United States. Where regional changes in CSS were observed, most commonly there were shifts in both onset and offset dates toward earlier dates. Results indicate that it is important to pay close attention to spring snowmelt as an indicator of hemispheric climate variability and change.
Observation and Parameterization of Ablation at the Base of Ronne Ice Shelf, Antarctica
Authors: Jenkins Adrian , Nicholls Keith W. , Corr Hugh F. J. 
Published: May 2010

Abstract
Parameterizations of turbulent transfer through the oceanic boundary layer beneath an ice shelf are tested using direct measurements of basal ablation. Observations were made in the southwestern part of Ronne Ice Shelf, about 500 km from open water. The mean basal ablation rate was measured over a month-long and a year-long period using phase-sensitive radar to record the thinning of the ice shelf. Ocean temperatures were observed within about 25 m of the ice shelf base over the period of the radar observations, while the tidally dominated ocean currents were estimated from tidal analysis of collocated current observations from an earlier period. Ablation rates derived using these ocean data and a number of bulk parameterizations of turbulent transfer within the boundary layer are compared with the direct measurements. The ablation rates derived using a parameterization that explicitly includes the impact of ocean currents on the turbulent transfer of heat and salt match the observations to within 40%; with suitable tuning of the drag coefficient, the mismatch can be reduced below the level of the observational errors. Equally good agreement can be obtained with two slightly simpler, current-dependent parameterizations that use constant turbulent transfer coefficients, and the optimal values for the coefficients at this particular location on Ronne Ice Shelf are given.
An Examination of the Incremental Balance in a Global Ensemble-Based 3D-Var Data Assimilation System
Authors: Caron Jean-François , Fillion Luc 
Published: May 2010

Abstract
This study examines the modification to the balance properties of the analysis increments in a global three-dimensional variational data assimilation scheme when using flow-dependent background-error covariances derived from an operational ensemble Kalman filter instead of static homogenous and isotropic background-error covariances based on lagged forecast differences. It is shown that the degree of balance in the analysis increments is degraded when the former method is used. This change can be attributed in part to the reduced degree of rotational balance found in short-term ensemble Kalman filter perturbations as compared to lagged forecast differences based on longer-range forecasts. However, the use of a horizontal and vertical localization technique to increase the rank of the ensemble-based covariances are found to have a significant deleterious effect on the rotational balance with the largest detrimental impact coming from the vertical localization and affecting particularly the upper levels. The examination of the vertical motion part of the analysis increments revealed that the spatial covariance localization technique also produces unrealistic vertical structure of vertical motion increments with abnormally large increments near the surface. A comparison between the analysis increments from the ensemble Kalman filter and from the ensemble-based three-dimensional variational data assimilation (3D-Var) scheme showed that the balance characteristics of the analysis increments resulting from the two systems are very similar.
Impact of Resolution Degradation of the Initial Condition on Typhoon Track Forecasts
Authors: Miyoshi Takemasa , Komori Takuya , Yonehara Hitoshi , Sakai Ryota , Yamaguchi Munenhiko 
Published: May 2010

Abstract
The operational numerical weather prediction (NWP) systems at the Japan Meteorological Agency (JMA) indicated that the typhoon track forecasts made by the control member of the ensemble prediction system (EPS) tended to be worse than those made by the high-resolution global NWP. The control forecast of the EPS with horizontal triangular truncation at 319 wavenumbers and 60 vertical levels (T319/L60 resolution) was initialized by eliminating the higher-wavenumber components of the global analysis at T959/L60 resolution. When the data assimilation cycle was performed at the lower T319/L60 resolution, the forecast gave typhoon track forecasts closer to the high-resolution global NWP. Therefore, it stands to reason that the resolution transform of the initial condition must be responsible for the degradation of the typhoon track forecasts at least to considerable extent. To improve the low-resolution forecast, two approaches are tested in this study: 1) applying a smoother spectral truncation for the resolution transform and 2) performing noncycled lower-resolution data assimilation during preprocessing. Results from the single case study of Typhoon Nuri (2008) indicate almost no impact from the former approach, but a significant positive impact when using the latter approach. The results of this study illuminate the importance of considering a model’s resolving capability during data assimilation. Namely, if the initial conditions contain features caused by unresolved scales, degraded forecasts may result.
The relationship between initial trunk control or postural balance and inpatient rehabilitation outcome after stroke: a prospective comparative study
Authors: Di Monaco Marco , Trucco Marco , Di Monaco Roberto , Tappero Rosa , Cavanna Alberto 
Published: May 2010

Objective: To compare the predictive validity of trunk control in sitting position assessed by Trunk Impairment Scale and balance in lying, sitting and standing posture assessed by Postural Assessment Scale for Stroke patients on functional outcome in stroke survivors. Design: Prospective observational study. Setting: A single rehabilitation hospital in Italy. Subjects: Sixty of 68 consecutive subjects admitted to a rehabilitation hospital after stroke. Main measures: We performed Trunk Impairment Scale and Postural Assessment Scale for Stroke patients at admission to inpatient rehabilitation. Outcome measures at discharge were Functional Independence Measure score and destination (classified as either home or institution). Results: After adjustment for 14 potential confounders, including Functional Independence Measure score at admission to rehabilitation, both Trunk Impairment Scale and Postural Assessment Scale for Stroke patients scores were significantly associated with the Functional Independence Measure score at discharge (P = 0.010 and P =0.04, respectively), change in the Functional Independence Measure score during rehabilitation (P = 0.003 and P<0.001, respectively), Functional Independence Measure effectiveness (P = 0.024 and P =0.017, respectively) and destination at discharge (P = 0.040 and P =0.032, respectively). The panel of prognostic variables predicted 64—65% of the variance in the final Functional Independence Measure score, 30—35% of the variance in the change of the Functional Independence Measure score during rehabilitation, and 45—46% of the variance in the Functional Independence Measure effectiveness depending on the inclusion of either Trunk Impairment Scale or Postural Assessment Scale for Stroke patients score among the predictors.
Benefits arising from lay involvement in community-based public health initiatives: The experience from community nutrition
Authors: Kennedy Lynne 
Published: May 2010

Aims: To explore the experiences of lay food and health workers (LFHW) and professionals involved in delivering local food and health initiatives, to improve understanding of the perceived benefits associated with their involvement and wider opportunities for promoting health. Study design: An interpretive qualitative inquiry. Setting: Community-based NHS LFHW programmes in 16 locations serving less-affluent neighbourhoods across England, UK. Subjects: Twenty nine (29) food and health professionals, 53 LFHW employed by and associated with the management or day-to-day implementation of 16 LFHW initiatives in the study. Findings: Salient benefits identified at service, individual lay worker and community levels were: increased service coverage and ability to reach the ‘hard to reach’; personal development; and enhanced social support. Conclusions: This study highlights previously unreported benefits related to the direct experiences of lay people used in community nutrition in the UK, which go beyond those associated with professional-led initiatives, suggesting the need to adopt a broader view of lay involvement in the UK public health workforce.
Validation of the high-dose heparin confirmatory step for the diagnosis of heparin-induced thrombocytopenia
Authors: Whitlatch Nicole L. , Kong David F. , Metjian Ara D. , Arepally Gowthami M. , Ortel Thomas L. 
Published: May 2010

Abstract
The diagnosis of heparin-induced thrombocytopenia (HIT) requires detection of antibodies to the heparin/platelet factor 4 (PF4) complexes via enzyme-linked immunosorbent assay. Addition of excess heparin to the sample decreases the optical density by 50% or more and confirms the presence of these antibodies. One hundred fifteen patients with anti-heparin/PF4 antibodies detected by enzyme-linked immunosorbent assay were classified as clinically HIT-positive or HIT-negative, followed by confirmation with excess heparin. A multivariate logistic regression model was fitted to estimate relationships between patient characteristics, laboratory findings, and clinical HIT status. This model was validated on an independent sample of 97 patients with anti-heparin/PF4 antibodies. No relationship between age, race, or sex and clinical HIT status was found. Maximal optical density and confirmatory positive status independently predicted HIT in multivariate analysis. Predictive accuracy on the training set (c-index 0.78, Brier score 0.17) was maintained when the algorithm was applied to the independent validation population (c-index 0.80, Brier score 0.20). This study quantifies the clinical utility of the confirmatory test to diagnose HIT. On the basis of data from the heparin/PF4 enzyme-linked immunosorbent assay and confirmatory assays, a predictive computer algorithm could distinguish patients likely to have HIT from those who do not.
Revealing and avoiding bias in semantic similarity scores for protein pairs
Authors: Wang Jing , Zhou Xianxiao , Zhu Jing , Zhou Chenggui , Guo Zheng 
Published: May 2010

AbstractBackgroundSemantic similarity scores for protein pairs are widely applied in functional genomic researches for finding functional clusters of proteins, predicting protein functions and protein-protein interactions, and for identifying putative disease genes. However, because some proteins, such as those related to diseases, tend to be studied more intensively, annotations are likely to be biased, which may affect applications based on semantic similarity measures. Thus, it is necessary to evaluate the effects of the bias on semantic similarity scores between proteins and then find a method to avoid them.ResultsFirst, we evaluated 14 commonly used semantic similarity scores for protein pairs and demonstrated that they significantly correlated with the numbers of annotation terms for the proteins (also known as the protein annotation length). These results suggested that current applications of the semantic similarity scores between proteins might be unreliable. Then, to reduce this annotation bias effect, we proposed normalizing the semantic similarity scores between proteins using the power transformation of the scores. We provide evidence that this improves performance in some applications.ConclusionsCurrent semantic similarity measures for protein pairs are highly dependent on protein annotation lengths, which are subject to biological research bias. This affects applications that are based on these semantic similarity scores, especially in clustering studies that rely on score magnitudes. The normalized scores proposed in this paper can reduce the effects of this bias to some extent.
Duplicability of self-interacting human genes
Authors: Pérez-Bercoff Åsa , Makino Takashi , McLysaght Aoife 
Published: May 2010

Abstract

Background
There is increasing interest in the evolution of protein-protein interactions because this should ultimately be informative of the patterns of evolution of new protein functions within the cell. One model proposes that the evolution of new protein-protein interactions and protein complexes proceeds through the duplication of self-interacting genes. This model is supported by data from yeast. We examined the relationship between gene duplication and self-interaction in the human genome.

Results
We investigated the patterns of self-interaction and duplication among 34808 interactions encoded by 8881 human genes, and show that self-interacting proteins are encoded by genes with higher duplicability than genes whose proteins lack this type of interaction. We show that this result is robust against the system used to define duplicate genes. Finally we compared the presence of self-interactions amongst proteins whose genes have duplicated either through whole-genome duplication (WGD) or small-scale duplication (SSD), and show that the former tend to have more interactions in general. After controlling for age differences between the two sets of duplicates this result can be explained by the time since the gene duplication.

Conclusions
Genes encoding self-interacting proteins tend to have higher duplicability than proteins lacking self-interactions. Moreover these duplicate genes have more often arisen through whole-genome rather than small-scale duplication. Finally, self-interacting WGD genes tend to have more interaction partners in general in the PIN, which can be explained by their overall greater age. This work adds to our growing knowledge of the importance of contextual factors in gene duplicability.
Generation of a BAC-based physical map of the melon genome
Authors: González Víctor M , Garcia-Mas Jordi , Arús Pere , Puigdomènech Pere 
Published: May 2010

Abstract

Background

Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity and a small genome size (450 Mb), which make this species suitable for a great variety of molecular and genetic studies that can lead to the development of tools for breeding varieties of the species. A number of genetic and genomic resources have already been developed, such as several genetic maps and BAC genomic libraries. These tools are essential for the construction of a physical map, a valuable resource for map-based cloning, comparative genomics and assembly of whole genome sequencing data. However, no physical map of any Cucurbitaceae has yet been developed. A project has recently been started to sequence the complete melon genome following a whole-genome shotgun strategy, which makes use of massive sequencing data. A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced.

Results
A melon physical map was constructed using a 5.7 × BAC library and a genetic map previously developed in our laboratories. High-information-content fingerprinting (HICF) was carried out on 23,040 BAC clones, digesting with five restriction enzymes and SNaPshot labeling, followed by contig assembly with FPC software. The physical map has 1,355 contigs and 441 singletons, with an estimated physical length of 407 Mb (0.9 × coverage of the genome) and the longest contig being 3.2 Mb. The anchoring of 845 BAC clones to 178 genetic markers (100 RFLPs, 76 SNPs and 2 SSRs) also allowed the genetic positioning of 183 physical map contigs/singletons, representing 55 Mb (12%) of the melon genome, to individual chromosomal loci. The melon FPC database is available for download at http://melonomics.upv.es/static/files/public/physical_map/.

Conclusions
Here we report the construction of the first physical map of a Cucurbitaceae species described so far. The physical map was integrated with the genetic map so that a number of physical contigs, representing 12% of the melon genome, could be anchored to known genetic positions. The data presented is already helping to improve the quality of the melon genomic sequence available as a result of a project currently being carried out in Spain, adopting a whole genome shotgun approach based on 454 sequencing data.
Bioinformatic identification and characterization of human endothelial cell-restricted genes
Authors: Bhasin Manoj , Yuan Lei , Keskin Derin B , Otu Hasan H , Libermann Towia A , Oettgen Peter 
Published: May 2010

Abstract

Background
In this study, we used a systematic bioinformatics analysis approach to elucidate genes that exhibit an endothelial cell (EC) restricted expression pattern, and began to define their regulation, tissue distribution, and potential biological role.

Results
Using a high throughput microarray platform, a primary set of 1,191 transcripts that are enriched in different primary ECs compared to non-ECs was identified (LCB >3, FDR <2%). Further refinement of this initial subset of transcripts, using published data, yielded 152 transcripts (representing 109 genes) with different degrees of EC-specificity. Several interesting patterns emerged among these genes: some were expressed in all ECs and several were restricted to microvascular ECs. Pathway analysis and gene ontology demonstrated that several of the identified genes are known to be involved in vasculature development, angiogenesis, and endothelial function (P < 0.01). These genes are enriched in cardiovascular diseases, hemorrhage and ischemia gene sets (P < 0.001). Most of the identified genes are ubiquitously expressed in many different tissues. Analysis of the proximal promoter revealed the enrichment of conserved binding sites for 26 different transcription factors and analysis of the untranslated regions suggests that a subset of the EC-restricted genes are targets of 15 microRNAs. While many of the identified genes are known for their regulatory role in ECs, we have also identified several novel EC-restricted genes, the function of which have yet to be fully defined.

Conclusion
The study provides an initial catalogue of EC-restricted genes most of which are ubiquitously expressed in different endothelial cells.
Infrequent detection of Pneumocystis jirovecii by PCR in oral wash specimens from TB patients with or without HIV and healthy contacts in Tanzania
Authors: Jensen Lotte , Jensen Andreas V , Praygod George , Kidola Jeremiah , Faurholt-Jepsen Daniel , Changalucha John , Range Nyagosya , Friis Henrik , Helweg-Larsen Jannik , Jensen Jorgen S , Andersen Aase B 
Published: May 2010

Abstract

Background
In tuberculosis (TB) endemic parts of the world, patients with pulmonary symptoms are managed as "smear-negative TB patients" if they do not improve on a two-week presumptive, broad-spectrum course of antibiotic treatment even if they are TB microscopy smear negative. These patients are frequently HIV positive and have a higher mortality than smear-positive TB patients. Lack of access to diagnose Pneumocystis jirovecii pneumonia might be a contributing reason. We therefore assessed the prevalence of P. jirovecii by PCR in oral wash specimens among TB patients and healthy individuals in an HIV- and TB-endemic area of sub-Saharan Africa.

Methods
A prospective study of 384 patients initiating treatment for sputum smear-positive and smear-negative TB and 100 healthy household contacts and neighbourhood controls.
DNA from oral wash specimens was examined by PCR for P. jirovecii. All patients delivered sputum for TB microscopy and culture. Healthy contacts and community controls were clinically assessed and all study subjects were HIV tested and had CD4 cell counts determined. Clinical status and mortality was assessed after a follow-up period of 5 months.

Results
384 patients and 100 controls were included, 53% and 8% HIV positive respectively. A total number of 65 patients and controls (13.6%) were at definitive risk for PCP based on CD4 counts <200 cells per mm3 and no specific PCP prophylaxis. Only a single patient (0.3% of the patients) was PCR positive for P. jirovecii. None of the healthy household contacts or neighbourhood controls had PCR-detectable P. jirovecii DNA in their oral wash specimens regardless of HIV-status.

Conclusions
The prevalence of P. jirovecii as detected by PCR on oral wash specimens was very low among TB patients with or without HIV and healthy individuals in Tanzania. Colonisation by P. jirovecii was not detected among healthy controls. The present findings may encourage diagnostic use of this non-invasive method.