bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elderly Patients Are at Higher Risk for Poor Outcomes After Intra-Arterial Therapy
Authors: Chandra Ronil V. , Leslie-Mazwi Thabele M. , Oh Daniel C. , Chaudhry Zeshan A. , Mehta Brijesh P. , Rost Natalia S. , Rabinov James D. , Hirsch Joshua A. , González R. Gilberto , Schwamm Lee H. , Yoo Albert J. 
Published: June 2012

Background and Purpose—
Conflicting data exist regarding outcomes after intra-arterial therapy (IAT) in elderly stroke patients. We compare safety and clinical outcomes of multimodal IAT in elderly versus nonelderly patients and investigate differences in baseline health and disability as possible explanatory factors.

Methods—
Data from a prospectively collected institutional IAT database were analyzed comparing elderly (80 years or older) versus nonelderly patients. Baseline demographics, angiographic reperfusion (Thrombolysis in Cerebral Infarction scale score 2–3), rate of parenchymal hematoma type 2, and 90-day modified Rankin Scale scores were compared in univariate and multivariate analyses.

Results—

There were 49 elderly and 130 nonelderly patients treated between 2005 and 2010. Between the 2 cohorts, there was no significant difference in Thrombolysis in Cerebral Infarction 2 to 3 reperfusion (71% vs 75%;
P
=0.57), time to reperfusion (
P
=0.77), or rate of parenchymal hematoma type 2 (4% vs 7%;
P
=0.73) after IAT. However, elderly patients had significantly lower rates of good outcome (modified Rankin Scale score 0–2: 2% vs 33%;
P
<0.0001) and higher mortality (59% vs 24%;
P
<0.0001) at 90 days. Atrial fibrillation, coronary artery disease, hypertension, hyperlipidema, and baseline disability were significantly more common in elderly patients. Adjusting for baseline disability, stroke severity, and reperfusion, elderly patients were 29-times more likely to be dependent or dead at 90 days (odds ratio, 28.7; 95% confidence interval, 3.2–255.7;
P
=0.003).

Conclusions—
Despite comparable rates of reperfusion and significant hemorrhage, elderly patients had worse clinical outcomes after IAT, which may relate, in part, to worse baseline health and disability. The use of IAT in the elderly should be performed after a careful analysis of the potential risks and benefits.
A Systematic Review of Laryngomalacia and Acid Reflux
Authors: Hartl Trevor T. , Chadha Neil K. 
Published: June 2012

ObjectiveTo identify and appraise the evidence for an association between laryngomalacia (LM) and acid reflux through a systematic review of the existing literature.Data SourcesMEDLINE, EMBASE, the Cochrane Library, Google Scholar, and collected additional publications cited in bibliographies.Review MethodsLiterature search by both authors with structured criteria to select studies evaluated for systematic review. The Oxford Centre for Evidence‐Based Medicine (CEBM) guidelines were applied to assess study quality of evidence.ResultsTwenty‐seven studies, representing 1295 neonates with LM, were included. Levels of evidence varied from CEBM level 2a (n = 1) to 4 (n = 23). Although reflux definitions were diverse, overall reflux prevalence in this group was 59% (pooled odds ratio [OR] of 4 controlled studies = 1.15, P =. 67). Further evidence supporting an association between reflux and LM included the ubiquity of acid reflux using dual‐probe pH monitoring in children with LM (2 studies; n = 84), the increased prevalence of reflux in severe as compared with mild LM (3 studies; n = 237; pooled OR = 9.86, P <. 0001), case series and reports of LM improvement with antireflux therapy (6 studies; n = 275), and histological evidence of reflux‐related laryngeal inflammation in children with LM (2 studies; n = 18).ConclusionThe literature shows a coexistence between acid reflux and LM, but the evidence for a causal association is limited. In view of the widespread use of antireflux treatment in LM, a randomized controlled trial of antireflux medication vs placebo appears justified.
Critical Care Nurses’ Perception of Barriers and Supportive Behaviors in End-of-Life Care
Authors: Attia Amal Kadry , Abd-Elaziz Wafaa Wahdan , Kandeel Nahed Attia 
Published: June 2012

Aim: To investigate critical care nurses' perceptions of barriers and supportive behaviors in providing end of life (EOL) care to dying patients and their families. Methods: The study involved a convenient sample of 70 nurses who were involved in caring for critically ill patients. Data were collected using a structured interview sheet. Results: Barriers to providing EOL care were related to intensive care environment, family members, nurses' knowledge and skills, physicians' attitudes and treatment policy. Possible help to providing EOL care involved nurses' support to each other, patient and family-centered care, and families' support. Conclusions: There is a need to allow the family unlimited access to the dying patient, involve them in patient care and provide them with a private place for grieving.
Collagen Gene Variants Previously Associated With Anterior Cruciate Ligament Injury Risk Are Also Associated With Joint Laxity
Authors: Bell Richard D. , Shultz Sandra J. , Wideman Laurie , Henrich Vincent C. 
Published: June 2012

Background: Genetic association studies demonstrate a relationship between several collagen gene variants and anterior cruciate ligament (ACL) injury, yet the mechanism of these relationships is still unclear. Joint laxity is a heritable trait; increased magnitudes of anterior knee laxity (AKL), genu recurvatum (GR), and general joint laxity (GJL) have been consistently associated with a greater risk of ACL injury. Joint laxity may constitute an important intermediate phenotype for the genetic association with ACL injury that can be measured clinically. Hypothesis: To determine if genetic variants within the COL1A1, COL5A1, and COL12A1 genes, previously associated with ACL injury, were also associated with greater magnitudes of AKL, GR, and GJL. Study Design: Descriptive laboratory study. Methods: Blood samples and measures of AKL, GR, and GJL were obtained from 124 (50 male, 74 female) healthy, recreationally active subjects. Genomic DNA was extracted from the blood samples and genotyped for single-nucleotide polymorphisms previously examined relative to ACL injury. Univariate analyses of variance compared the magnitude of each laxity variable across the 3 genotypes for each single-nucleotide polymorphism in both sex-combined and sex-specific models. Results: Specific genotypes were associated with greater GR in all subjects. Some genotypes were associated with greater magnitudes of GR, AKL, and GJL in females only. Conclusions: Gene variants previously associated with ACL injury risk were in large part also associated with joint laxity. Sex-specific genetic associations with joint laxity were consistent with those previously reported for ACL injury. Clinical Relevance: These data provide insight into potential pathways through which genotypic variants in collagen genes have the potential to alter ligament structure and behavior and, thus, ACL injury risk.
Identification of a 3-gene model as a powerful diagnostic tool for the recognition of ALK-negative anaplastic large-cell lymphoma
Authors: Agnelli Luca , Mereu Elisabetta , Pellegrino Elisa , Limongi Tania , Kwee Ivo , Bergaggio Elisa , Ponzoni Maurilio , Zamò Alberto , Iqbal Javeed , Piccaluga Pier Paolo , Neri Antonino , Chan Wing C. , Pileri Stefano , Bertoni Francesco , Inghirami Giorgio , Piva Roberto 
Published: June 2012

Abstract
Anaplastic large-cell lymphomas (ALCLs) are a group of clinically and biologically heterogeneous diseases including the ALK+ and ALK− systemic forms. Whereas ALK+ ALCLs are molecularly characterized and can be readily diagnosed, specific immunophenotypic or genetic features to define ALK− ALCL are missing, and their distinction from other T-cell non-Hodgkin lymphomas (T-NHLs) remains controversial. In the present study, we undertook a transcriptional profiling meta-analysis of 309 cases, including ALCL and other primary T-NHL samples. Pathway discovery and prediction analyses defined a minimum set of genes capable of recognizing ALK− ALCL. Application of quantitative RT-PCR in independent datasets from cryopreserved and formalin-fixed paraffin-embedded samples validated a 3-gene model (TNFRSF8, BATF3, and TMOD1) able to successfully separate ALK− ALCL from peripheral T-cell lymphoma not otherwise specified, with overall accuracy near 97%. In conclusion, our data justify the possibility of translating quantitative RT-PCR protocols to routine clinical settings as a new approach to objectively dissect T-NHL and to select more appropriate therapeutic protocols.
Single nucleotide polymorphisms and inherited risk of chronic lymphocytic leukemia among African Americans
Authors: Coombs Catherine C. , Rassenti Laura Z. , Falchi Lorenzo , Slager Susan L. , Strom Sara S. , Ferrajoli Alessandra , Weinberg J. Brice , Kipps Thomas J. , Lanasa Mark C. 
Published: June 2012

AbstractThe incidence of chronic lymphocytic leukemia (CLL) is significantly lower in African Americans than whites, but overall survival is inferior. The biologic basis for these observations remains unexplored. We hypothesized that germline genetic predispositions differ between African Americans and whites with CLL and yield inferior clinical outcomes among African Americans. We examined a discovery cohort of 42 African American CLL patients ascertained at Duke University and found that the risk allele frequency of most single nucleotide polymorphisms known to confer risk of development for CLL is significantly lower among African Americans than whites. We then confirmed our results in a distinct cohort of 68 African American patients ascertained by the CLL Research Consortium. These results provide the first evidence supporting differential genetic risk for CLL between African Americans compared with whites. A fuller understanding of differential genetic risk may improve prognostication and therapeutic decision making for all CLL patients.
Consensus properties for the deep coalescence problem and their application for scalable tree search
Authors: Lin Harris T , Burleigh J Gordon , Eulenstein Oliver 
Published: June 2012

Abstract

Background
To infer a species phylogeny from unlinked genes, phylogenetic inference methods must confront the biological processes that create incongruence between gene trees and the species phylogeny. Intra-specific gene variation in ancestral species can result in deep coalescence, also known as incomplete lineage sorting, which creates incongruence between gene trees and the species tree. One approach to account for deep coalescence in phylogenetic analyses is the deep coalescence problem, which takes a collection of gene trees and seeks the species tree that implies the fewest deep coalescence events. Although this approach is promising for phylogenetics, the consensus properties of this problem are mostly unknown and analyses of large data sets may be computationally prohibitive.

Results
We prove that the deep coalescence consensus tree problem satisfies the highly desirable Pareto property for clusters (clades). That is, in all instances, each cluster that is present in all of the input gene trees, called a consensus cluster, will also be found in every optimal solution. Moreover, we introduce a new divide and conquer method for the deep coalescence problem based on the Pareto property. This method refines the strict consensus of the input gene trees, thereby, in practice, often greatly reducing the complexity of the tree search and guaranteeing that the estimated species tree will satisfy the Pareto property.

Conclusions
Analyses of both simulated and empirical data sets demonstrate that the divide and conquer method can greatly improve upon the speed of heuristics that do not consider the Pareto consensus property, while also guaranteeing that the proposed solution fulfills the Pareto property. The divide and conquer method extends the utility of the deep coalescence problem to data sets with enormous numbers of taxa.
The maximum clique enumeration problem: algorithms, applications, and implementations
Authors: Eblen John D , Phillips Charles A , Rogers Gary L , Langston Michael A 
Published: June 2012

Abstract

Background
The maximum clique enumeration (MCE) problem asks that we identify all maximum cliques in a finite, simple graph. MCE is closely related to two other well-known and widely-studied problems: the maximum clique optimization problem, which asks us to determine the size of a largest clique, and the maximal clique enumeration problem, which asks that we compile a listing of all maximal cliques. Naturally, these three problems are

N
P

-hard, given that they subsume the classic version of the

N
P

-complete clique decision problem. MCE can be solved in principle with standard enumeration methods due to Bron, Kerbosch, Kose and others. Unfortunately, these techniques are ill-suited to graphs encountered in our applications. We must solve MCE on instances deeply seeded in data mining and computational biology, where high-throughput data capture often creates graphs of extreme size and density. MCE can also be solved in principle using more modern algorithms based in part on vertex cover and the theory of fixed-parameter tractability (FPT). While FPT is an improvement, these algorithms too can fail to scale sufficiently well as the sizes and densities of our datasets grow.

Results
An extensive testbed of benchmark graphs are created using publicly available transcriptomic datasets from the Gene Expression Omnibus (GEO). Empirical testing reveals crucial but latent features of such high-throughput biological data. In turn, it is shown that these features distinguish real data from random data intended to reproduce salient topological features. In particular, with real data there tends to be an unusually high degree of maximum clique overlap. Armed with this knowledge, novel decomposition strategies are tuned to the data and coupled with the best FPT MCE implementations.

Conclusions
Several algorithmic improvements to MCE are made which progressively decrease the run time on graphs in the testbed. Frequently the final runtime improvement is several orders of magnitude. As a result, instances which were once prohibitively time-consuming to solve are brought into the domain of realistic feasibility.
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis
Authors: Cornman R Scott , Bennett Anna K , Murray K Daniel , Evans Jay D , Elsik Christine G , Aronstein Kate 
Published: June 2012

Abstract

Background
We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture.

Results
We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website.

Conclusions
This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.
Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis
Authors: Song Yuepeng , Wang Zeliang , Bo Wenhao , Ren Yuanyuan , Zhang Zhiyi , Zhang Deqiang 
Published: June 2012

Abstract

Background
Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.

Results
Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.

Conclusion
The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.
Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species
Authors: Nishimura Osamu , Hirao Yukako , Tarui Hiroshi , Agata Kiyokazu 
Published: June 2012

Abstract

Background
Planarians are considered to be among the extant animals close to one of the earliest groups of organisms that acquired a central nervous system (CNS) during evolution. Planarians have a bilobed brain with nine lateral branches from which a variety of external signals are projected into different portions of the main lobes. Various interneurons process different signals to regulate behavior and learning/memory. Furthermore, planarians have robust regenerative ability and are attracting attention as a new model organism for the study of regeneration. Here we conducted large-scale EST analysis of the head region of the planarian Dugesia japonica to construct a database of the head-region transcriptome, and then performed comparative analyses among related species.

Results
A total of 54,752 high-quality EST reads were obtained from a head library of the planarian Dugesia japonica, and 13,167 unigene sequences were produced by de novo assembly. A new method devised here revealed that proteins related to metabolism and defense mechanisms have high flexibility of amino-acid substitutions within the planarian family. Eight-two CNS-development genes were found in the planarian (cf. C. elegans 3; chicken 129). Comparative analysis revealed that 91% of the planarian CNS-development genes could be mapped onto the schistosome genome, but one-third of these shared genes were not expressed in the schistosome.

Conclusions
We constructed a database that is a useful resource for comparative planarian transcriptome studies. Analysis comparing homologous genes between two planarian species showed that the potential of genes is important for accumulation of amino-acid substitutions. The presence of many CNS-development genes in our database supports the notion that the planarian has a fundamental brain with regard to evolution and development at not only the morphological/functional, but also the genomic, level. In addition, our results indicate that the planarian CNS-development genes already existed before the divergence of planarians and schistosomes from their common ancestor.
Reprogramming of gene expression during compression wood formation in pine: Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
Authors: Villalobos David P , Díaz-Moreno Sara M , Said El-Sayed S , Cañas Rafael A , Osuna Daniel , Van Kerckhoven Sonia H E , Bautista Rocío , Claros Manuel Gonzalo , Cánovas Francisco M , Cantón Francisco R 
Published: June 2012

AbstractBackgroundTranscript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified.ResultsBy combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesisin vivoandin vitro.ConclusionsThe comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification.