bluuebunny/crossref_metadata_2025_split huggingface dataset:
Undifilum, a new genus for endophyticEmbellisia oxytropisand parasiticHelminthosporium bornmuellerion legumes
Authors: Pryor B. M. , Creamer R. , Shoemaker R. A. , McLain-Romero J. , Hambleton S. 
Published: March 2009

Fungal endophytes of Oxytropis kansuensis Bunge from China, previously described as Embellisia oxytropis Q. Wang, Nagao & Kakish, and endophytes of Oxytropis sericea Nutt. and Oxytropis lambertii Pursh from the United States were compared and are reported here as conspecific members of a new genus in the Pleosporaceae, Undifilum, based on morphological and molecular analyses. Morphological comparisons revealed characters that are similar to those of the genus Embellisia including conidia ovate to obclavate to long ellipsoid, straight or slightly to decidedly inequilateral with occasionally one or two cells distinctly swollen, and transepta occasionally thickened, dark, and rigid in comparison with the exterior conidium wall. However, upon germination, conidia produced unique and diagnostic germ tubes that were wavy or undulating in their growth until branching. Moreover, all isolates were found to produce the toxic alkaloid swainsonine. Parsimony analysis of sequences from ITS1–5.8S–ITS2, glyceraldehyde-3-phosphate dehydrogenase gene, and mitochondrial small subunit rDNA data sets revealed that the Oxytropis endophytes formed a clade distinct from other Embellisia species and species in the genera Alternaria , Ulocladium , Nimbya , and Crivellia . A second taxon, Helminthosporium bornmuelleri P. Magnus, was reexamined and found to possess similar morphological features to those of the Oxytropis isolates, but lacked swainsonine production. Sequence analysis placed this second taxon in the same clade with high bootstrap support. The distinct morphology and genetics of these taxa demonstrates that these fungi, both recovered from legumes, represent a new genus, hereinafter described as Undifilum . The two species now placed in this genus are redescribed as Undifilium oxytropis and Undifilium bornmuelleri .
On the Proper Use of Satellite-Derived Leaf Area Index in Climate Modeling
Authors: Ge Jianjun 
Published: March 2009

Abstract
Satellite-observed leaf area index (LAI) is increasingly being used in climate modeling. In common land surface models, LAI is specified for the vegetated part only. In contrast, satellite LAI is defined for the total area including both vegetated and nonvegetated fractions. Some recent modeling studies and model developments have not noticed this difference, which resulted in improper use of satellite LAI. This paper clarified this issue. A sensitivity test was carried out using a regional model to investigate the impacts of LAI definitions on simulated climates. This study showed that use of satellite LAI without considering the inconsistency in definition caused much smaller LAI values in the model. As a result, partitioning of surface energy into latent and sensible heat fluxes, as well as the model-simulated precipitation, was affected substantially. Overall, improper use of satellite LAI increased the model biases in simulated precipitation.
The Diabatic Contour-Advective Semi-Lagrangian Algorithms for the Spherical Shallow Water Equations
Authors: Mohebalhojeh Ali R. , Dritschel David G. 
Published: March 2009

Abstract
The diabatic contour-advective semi-Lagrangian (DCASL) algorithm is extended to the thermally forced shallow water equations on the sphere. DCASL rests on the partitioning of potential vorticity (PV) to adiabatic and diabatic parts solved, respectively, by contour advection and a grid-based conventional algorithm. The presence of PV in the source term for diabatic PV makes the shallow water equations distinct from the quasigeostrophic model previously studied. To address the more rapid generation of finescale structures in diabatic PV, two new features are added to DCASL: (i) the use of multiple sets of contours with successively finer contour intervals and (ii) the application of the underlying method of DCASL at a higher level to diabatic PV. That is, the diabatic PV is allowed to have both contour and grid parts. The added features make it possible to make the grid part of diabatic PV arbitrarily small and thus pave the way for a fully Lagrangian DCASL in the presence of forcing.
The DCASL algorithms are constructed using a standard semi-Lagrangian (SL) algorithm to solve for the grid-based part of diabatic PV. The 25-day time evolution of an unstable midlatitude jet triggered by the action of thermal forcing is used as a test case to examine and compare the properties of the DCASL algorithms with a pure SL algorithm for PV. Diagnostic measures of vortical and unbalanced activity as well as of the relative strength of the grid and contour parts of the solution for PV indicate that the superiority of contour advection can be maintained even in the presence of strong, nonsmooth forcing.
Accounting for Model Errors in Ensemble Data Assimilation
Authors: Li Hong , Kalnay Eugenia , Miyoshi Takemasa , Danforth Christopher M. 
Published: March 2009

Abstract
This study addresses the issue of model errors with the ensemble Kalman filter. Observations generated from the NCEP–NCAR reanalysis fields are assimilated into a low-resolution AGCM. Without an effort to account for model errors, the performance of the local ensemble transform Kalman filter (LETKF) is seriously degraded when compared with the perfect-model scenario. Several methods to account for model errors, including model bias and system noise, are investigated. The results suggest that the two pure bias removal methods considered [Dee and Da Silva (DdSM) and low dimensional (LDM)] are not able to beat the multiplicative or additive inflation schemes used to account for the effects of total model errors. In contrast, when the bias removal methods are augmented by additive noise representing random errors (DdSM+ and LDM+), they outperform the pure inflation schemes. Of these augmented methods, the LDM+, where the constant bias, diurnal bias, and state-dependent errors are estimated from a large sample of 6-h forecast errors, gives the best results. The advantage of the LDM+ over other methods is larger in data-sparse regions than in data-dense regions.
Influence of cytogenetics in patients with relapsed or refractory multiple myeloma treated with lenalidomide plus dexamethasone: adverse effect of deletion 17p13
Authors: Reece Donna , Song Kevin W. , Fu Tommy , Roland Birgitte , Chang Hong , Horsman Douglas E. , Mansoor Adnan , Chen Christine , Masih-Khan Esther , Trieu Young , Bruyere Helene , Stewart Douglas A. , Bahlis Nizar J. 
Published: March 2009

AbstractAlthough the combination of lenalidomide and dexamethasone is effective therapy for patients with relapsed/refractory multiple myeloma, the influence of high-risk cytogenetic abnormalities on outcomes is unknown. This subanalysis of a large, open-label study investigated the effects of the most common unfavorable cytogenetic abnormalities detected by fluorescence in situ hybridization, del(13q), t(4;14), and del(17p13), in 130 evaluable patients treated with this regimen. Whereas patients with either del(13q) or t(4;14) experienced a median time to progression and overall survival comparable with those without these cytogenetic abnormalities, patients with del(17p13) had a significantly worse outcome, with a median time to progression of 2.22 months (hazard ratio, 2.82; P < .001) and median overall survival of 4.67 months (hazard ratio, 3.23; P < .001). Improved therapeutic strategies are required for this subgroup of patients. This study was registered at www.ClinicalTrials.gov as #NCT00179647.
131I anti-CD45 radioimmunotherapy effectively targets and treats T-cell non-Hodgkin lymphoma
Authors: Gopal Ajay K. , Pagel John M. , Fromm Jonathan R. , Wilbur Shani , Press Oliver W. 
Published: March 2009

AbstractRadioimmunotherapy (RIT) options for T-cell non-Hodgkin lymphomas (T-NHLs) are limited. We evaluated anti-CD45-RIT in human (h) and murine (m) T-NHL. CD45 was highly expressed on hT-NHL patient samples (median, 2.3 × 105 antigen-binding capacity units/cell) and hT-NHL cell lines (3.4 × 105 CD45 antigen-binding capacity units/cell). Biodistribution studies in hTNHL xenografts showed that 131I-labeled BC8 (anti-hCD45) delivered 154% (P = .01) and 237% (P = .002) more radioiodine to tumor sites over control antibodies at 24 hours and 48 hours, respectively. Importantly, tumor sites targeted with 131I-BC8 exhibited 2.5-fold (P = .05), 3.0-fold (P = .007), and 3.6-fold (P = .07) higher 131I retention over the nontarget organs of lungs, liver, and kidneys, respectively (24 hours). Because the clinical use of anti-hCD45 would target both T-NHL and other hematolymphoid tissues, we evaluated the ability of anti-mCD45 to target mT-NHL. mT-NHL grafts targeted with anti-mCD45 correspondingly retained 5.3 (P < .001), 5.4 (P < .001), and 8.7 (P < .001) times the radioactivity in tumor sites compared with nontarget organs of lung, liver, and kidney. 131I-labeled BC8 therapy yielded improved complete remission rates (75% vs 0%, P < .001) and progression-free survivals (median, 23 days vs 4.5 days, P < .001) compared with controls. These data indicate that the high CD45 expression of T-NHL allows reliable tumor targeting and disease control supporting anti-CD45 RIT for T-NHL patients.
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy
Authors: Alexopoulou Dimitra , Andreopoulos Bill , Dietze Heiko , Doms Andreas , Gandon Fabien , Hakenberg Jörg , Khelif Khaled , Schroeder Michael , Wächter Thomas 
Published: March 2009

Abstract

Background
Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.

Results
The 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate.

Conclusion
Metadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90% success given a consistently modelled ontology. Overall, the results show that well structured ontologies can play a very important role to improve disambiguation.

Availability
The three benchmark datasets created for the purpose of disambiguation are available in Additional file 1.
Genetic clusters and sex-biased gene flow in a unicolonial Formica ant
Authors: Holzer Barbara , Keller Laurent , Chapuisat Michel 
Published: March 2009

AbstractBackgroundAnimal societies are diverse, ranging from small family-based groups to extraordinarily large social networks in which many unrelated individuals interact. At the extreme of this continuum, some ant species form unicolonial populations in which workers and queens can move among multiple interconnected nests without eliciting aggression. Although unicoloniality has been mostly studied in invasive ants, it also occurs in some native non-invasive species. Unicoloniality is commonly associated with very high queen number, which may result in levels of relatedness among nestmates being so low as to raise the question of the maintenance of altruism by kin selection in such systems. However, the actual relatedness among cooperating individuals critically depends on effective dispersal and the ensuing pattern of genetic structuring. In order to better understand the evolution of unicoloniality in native non-invasive ants, we investigated the fine-scale population genetic structure and gene flow in three unicolonial populations of the wood antF. paralugubris.ResultsThe analysis of geo-referenced microsatellite genotypes and mitochondrial haplotypes revealed the presence of cryptic clusters of genetically-differentiated nests in the three populations ofF. paralugubris. Because of this spatial genetic heterogeneity, members of the same clusters were moderately but significantly related. The comparison of nuclear (microsatellite) and mitochondrial differentiation indicated that effective gene flow was male-biased in all populations.ConclusionThe three unicolonial populations exhibited male-biased and mostly local gene flow. The high number of queens per nest, exchanges among neighbouring nests and restricted long-distance gene flow resulted in large clusters of genetically similar nests. The positive relatedness among clustermates suggests that kin selection may still contribute to the maintenance of altruism in unicolonial populations if competition occurs among clusters.
Determination of enriched histone modifications in non-genic portions of the human genome
Authors: Rosenfeld Jeffrey A , Wang Zhibin , Schones Dustin E , Zhao Keji , DeSalle Rob , Zhang Michael Q 
Published: March 2009

Abstract

Background
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) has recently been used to identify the modification patterns for the methylation and acetylation of many different histone tails in genes and enhancers.

Results
We have extended the analysis of histone modifications to gene deserts, pericentromeres and subtelomeres. Using data from human CD4+ T cells, we have found that each of these non-genic regions has a particular profile of histone modifications that distinguish it from the other non-coding regions. Different methylation states of H4K20, H3K9 and H3K27 were found to be enriched in each region relative to the other regions. These findings indicate that non-genic regions of the genome are variable with respect to histone modification patterns, rather than being monolithic. We furthermore used consensus sequences for unassembled centromeres and telomeres to identify the significant histone modifications in these regions. Finally, we compared the modification patterns in non-genic regions to those at silent genes and genes with higher levels of expression. For all tested methylations with the exception of H3K27me3, the enrichment level of each modification state for silent genes is between that of non-genic regions and expressed genes. For H3K27me3, the highest levels are found in silent genes.

Conclusion
In addition to the histone modification pattern difference between euchromatin and heterochromatin regions, as is illustrated by the enrichment of H3K9me2/3 in non-genic regions while H3K9me1 is enriched at active genes; the chromatin modifications within non-genic (heterochromatin-like) regions (e.g. subtelomeres, pericentromeres and gene deserts) are also quite different.
Regulation of HSP27 on NF-κB pathway activation may be involved in metastatic hepatocellular carcinoma cells apoptosis
Authors: Guo Kun , Kang Nan Xiao , Li Yan , Sun Lu , Gan Lin , Cui Feng Jie , Gao Mei Dong , Liu Kun Yin 
Published: March 2009

Abstract

Background
During the process of metastasis, cells are subjected to various apoptotic stimuli. Aberrant expression of apoptotic regulators often contribute to cell metastasis. Heat shock protein 27(HSP27) is confirmed as an apoptosis regulator, but its antiapoptotic mechanism in metastatic hepatocellular carcinoma (HCC) cells remains unclear.

Methods
Levels of HSP27 protein and its phosphorylation in Hep3B, MHCC97L to MHCC97H cells with different metastatic potentials were determined by western blot analysis. MHCC97H cells were transfected with specific small interference RNA (siRNA) against HSP27. The in vitro migration and invasion potentials of cells were evaluated by Transwell assay. The apoptosis ratio of MHCC97H cells was analyzed by TUNEL staining and Flow Cytometry. Alteration of signal transduction pathway after HSP27 knockdown in MHCC97H cells was evaluated through a Human Q Series Signal Transduction in Cancer Gene Array analysis. Nuclear NF-κB contentration and endogenous IKK activity were demonstrated by ELISA assay. The association of IKKα, IKKβ, IκBα with HSP27 and the association between IKKβ and IKKα in MHCC97H cells were determined by co-immunoprecipitation assay followed by western blot analysis.

Results
HSP27 protein and its phosphorylation increased in parallel with enhanced metastatic potentials of HCC cells. siRNA-mediated HSP27 knockdown in MHCC97H significantly suppressed cells migration and invasion in vitro and induced cell apoptosis; the prominently altered signal transduction pathway was NF-κB pathway after HSP27 knockdown in MHCC97H cells. Furthermore, inhibition of HSP27 expression led to a significant decrease of nuclear NF-κB contentration and endogenous IKK activity. In addition, HSP27 was associated with IKKα, IKKβ, IκBα in three HCC cells above. ELISA assay and western blot analysis also showed a decrease of the association between IKKβ and IKKα, the association between phosphor-HSP27 and IKK complex, and an increase of total IκBα but reducing tendency of phosphor-IκBα when HSP27 expression was efficiently knocked down in MHCC97H cells.

Conclusion
Altogether, these findings revealed a possible effect of HSP27 on apoptosis in metastatic HCC cells, in which HSP27 may regulate NF-kB pathway activation.
Timeliness of national notifiable diseases surveillance system in Korea: a cross-sectional study
Authors: Yoo Hyo-Soon , Park Ok , Park Hye-Kyung , Lee Eun-Gyu , Jeong Eun-Kyeong , Lee Jong-Koo , Cho Sung-Il 
Published: March 2009

AbstractBackgroundWith the increase of international travels, infectious disease control is gaining a greater importance across regional borders. Adequate surveillance system function is crucial to prevent a global spread of infectious disease at the earliest stage. There have been limited reports on the characteristics of infectious disease surveillance in Asia. The authors studied the timeliness of the Korean National Notifiable Disease Surveillance System with regard to major notifiable diseases from 2001 to 2006.MethodsSix notifiable infectious diseases reported relatively frequently were included in this study. Five diseases were selected by the criteria of reported cases > 100 per year: typhoid fever, shigellosis, mumps, scrub typhus, and hemorrhagic fever with renal syndrome. In addition, dengue fever was also included to represent an emerging disease, despite its low number of cases. The diseases were compared for the proportion notified within the recommended time limits, median time lags, and for the cumulative distribution of time lags at each surveillance step between symptom onset and date of notification to the Korea Centers for Disease Control and Prevention (KCDC).ResultsThe proportion of cases reported in time was lower for disease groups with a recommended time limit of 1 day compared with 7 days (60%–70% vs. > 80%). The median time from disease onset to notification to KCDC ranged between 6 and 20 days. The median time from onset to registration at the local level ranged between 2 and 15 days. Distribution of time lags showed that main delays arose in the time from onset to diagnosis. There were variations in timeliness by disease categories and surveillance steps.ConclusionTime from disease onset to diagnosis generally contributed most to the delay in reporting. It is needed to promote public education and to improve clinical guidelines. Rapid reporting by doctors should be encouraged, and unification of recommended reporting time limit can be helpful. Our study also demonstrates the utility of the overall assessment of time-lag distributions for disease-specific strategies to improve surveillance.
Rates of asthma attacks in patients with previously inadequately controlled mild asthma treated in clinical practice with combination drug therapy: an exploratory post-hoc analysis
Authors: Dal Negro Robert W , Borderias Luis , Zhang Qiaoyi , Fan Tao , Sazonov Vasilisa , Guilera Magda , Taylor Stephanie D 
Published: March 2009

Abstract

Background
Differences could exist in the likelihood of asthma attacks in patients treated with inhaled corticosteroid (ICS), long-acting beta-agonist (LABA), and montelukast (MON) (ICS/LABA/MON) and patients treated with an inhaled corticosteroid (ICS) and montelukast (MON) (ICS/MON).

Methods
This was a post-hoc analysis of a pretest-posttest retrospective cohort study. Patients with mild persistent asthma and allergic rhinitis, who were taking an ICS either alone or in combination with a LABA, started concomitant MON treatment as part of their routine care. Rates of asthma- and allergic rhinitis-related medical resource use in the 12-months after the initial (index) MON prescription were compared in the ICS/MON and ICS/LABA/MON groups. An asthma attack was defined as an asthma-related hospitalization, ER visit, or use of an oral corticosteroid.

Results
Of the total of 344 patients, 181 (53%) received ICS/MON and 163 (47%) received ICS/LABA/MON in the post-index period for means of 10.5 and 11.4 months, respectively, (P < 0.05). Short-acting beta-agonists were used by 74.6% in the ICS/MON and 71.8% in the ICS/LABA/MON groups (P > 0.05). An asthma attack occurred in 4.4% of the ICS/MON group and 6.8% of the ICS/LABA/MON group (P > 0.05). The adjusted odds of an asthma attack in the post-index period in the ICS/LABA/MON group relative to the ICS/MON group was 1.24, 95% confidence interval 0.35–4.44.

Conclusion
In this observational study of combination drug treatment of mild persistent asthma and allergic rhinitis, no difference was observed between LABA/ICS/MON combination therapy and the ICS/MON combination without LABA use, for the rate of asthma attacks over one year.