bluuebunny/crossref_metadata_2025_split huggingface dataset:
Percutaneous Closure of Left Ventricular Pseudoaneurysm
Authors: Dudiy Yuriy , Jelnin Vladimir , Einhorn Bryce N. , Kronzon Itzhak , Cohen Howard A. , Ruiz Carlos E. 
Published: July 2011

Background—
Left ventricular pseudoaneurysm is a rare but serious complication from myocardial infarction and cardiac surgery. Although standard treatment is surgical intervention, percutaneous closure of left ventricular pseudoaneurysm has become an option for high-risk surgical candidates. Experience with percutaneous treatment is limited to a few single case reports. This is the first series of percutaneous treatment of the left ventricular pseudoaneurysms.

Methods and Results—
This is a retrospective analysis of 9 procedures of percutaneous repair of left ventricular pseudoaneurysm in 7 consecutive patients (ages 51 to 83 years, 6 men) completed in our Structural Heart Disease center from June 2008 to December 2010. All patients were considered as a high risk for surgery because of multiple comorbidities. Multiple imaging modalities were used before, during, and after the procedures to improve success and efficacy. The left ventricular pseudoaneurysms of all 7 patients were successfully repaired. Fluoroscopy time on average was 36.5±24.0 minutes (range, 12.4 to 75.7 minutes). All patients were followed up for a period ranging from 3 to 32 months after the procedure. Each patient improved by at least 1 New York Heart Association functional class, and 4 patients improved by 2 classes.

Conclusions—
Transcatheter closure of the left ventricular pseudoaneurysm is a feasible alternative for high-risk surgical candidates. The use of multiple imaging modalities is required for a detail planning and execution of the procedure.
Climatological Variations in North Atlantic Tropical Cyclone Tracks
Authors: Colbert Angela J. , Soden Brian J. 
Published: July 2011

Abstract
This study investigates the relationship between tropical cyclone (TC) tracks and climatological variations in large-scale environmental parameters associated with the TC steering flow. By using the Atlantic Ocean hurricane database for 1950–2010, TCs that form in the main development region (MDR) are categorized into one of three track types: straight moving, recurving landfall, or recurving ocean. As expected, the straight-moving storms are associated with a westward extension and strengthening of the subtropical high, whereas the recurving ocean storms are associated with a weakening of the high. The presence of El Niño conditions in the tropical Pacific Ocean is shown to be associated with a weakening of the high, an increase in the percentage of recurving ocean TCs, and a decrease in the percentage of recurving landfall TCs. Positive phases of the Atlantic Meridional Mode are associated with an increase in the percentage of recurving ocean TCs and a decrease in the percentage of straight-moving TCs. Synthetic tracks are simulated for each storm using a beta and advection model. Sensitivity experiments using both observed and uniformly seeded genesis locations indicate that the path of straight-moving TCs is largely a reflection of their tendency to form in the southwestern portion of the MDR rather than of differences in steering flow. These experiments also suggest that the shift in TC tracks associated with El Niño/La Niña conditions is largely attributable to changes in the steering flow, whereas the track changes associated with variations in the Atlantic Meridional Mode are due to a systematic shift in genesis location.
Tornado Maintenance Investigated with High-Resolution Dual-Doppler and EnKF Analysis
Authors: Marquis James , Richardson Yvette , Markowski Paul , Dowell David , Wurman Joshua 
Published: July 2011

AbstractDual-Doppler wind synthesis and ensemble Kalman filter analyses produced by assimilating Doppler-on-Wheels velocity data collected in four tornadic supercells are examined in order to further understand the maintenance of tornadoes. Although tornado-scale features are not resolved in these analyses, larger-scale processes involved with tornado maintenance are well represented.The longest-lived tornado is maintained underneath the midlevel updraft within a zone of low-level horizontal convergence along a rear-flank gust front for a considerable time, and dissipates when horizontally displaced from the midlevel updraft. The shortest-lived tornado resides in a similar zone of low-level convergence briefly, but dissipates underneath the location of the midlevel updraft when the updraft becomes tilted and low-level convergence is displaced several kilometers from the tornado. This suggests that a location beneath the midlevel updraft is not always a sufficient condition for tornado maintenance, particularly in the presence of strongly surging outflow. Tornadoes in two other storms persist within a band of low-level convergence in the outflow air (a possible secondary rear-flank gust front), suggesting that tornado maintenance can occur away from the main boundary separating the outflow air and the ambient environment.In at least one case, tilting of horizontal vorticity occurs near the tornado along the secondary gust front, as evidenced by three-dimensional vortex line arching. This observation suggests that a relatively cold secondary rear-flank downdraft may assist with tornado maintenance through the baroclinic generation and tilting of horizontal vorticity, despite the fact that parcels composing them would be more negatively buoyant than the preceding outflow air.
Responsiveness of Goal Attainment Scaling in comparison to two standardized measures in outcome evaluation of children with cerebral palsy
Authors: Steenbeek Duco , Gorter Jan Willem , Ketelaar Marjolijn , Galama Krys , Lindeman Eline 
Published: July 2011

Objectives: To assess the responsiveness of Goal Attainment Scaling compared with the Pediatric Evaluation of Disability Inventory (PEDI) and the 66-item Gross Motor Function Measure (GMFM-66) in multidisciplinary rehabilitation practice. Design: Observational study. Pretest–posttest design. Subjects/patients: Twenty-three children with cerebral palsy, aged 2–13 years. Methods: Goal Attainment Scaling, PEDI and GMFM-66 assessments were performed before and after six months of treatment. Physical, occupational and speech therapists constructed and scored 6-point Goal Attainment Scaling scales meeting predetermined criteria, describing the main functional goal per discipline. The contents of the three measures were compared using International Classification of Functioning, Disability and Health child and youth version (ICF-CY) codes. Spearman’s rho correlations between Goal Attainment Scaling change scores per discipline and change scores obtained with the PEDI functional skills scales and GMFM-66 were calculated. Complete goal attainment was compared with significant change in terms of the standardized measures. Results: Twenty per cent of the Goal Attainment Scaling items were not covered by items of the PEDI or the GMFM-66. Inconclusive correlations were found between Goal Attainment Scaling and PEDI change scores ( r 0.28–0.64). Even after exclusion of the non-corresponding items, correlations were moderate ( r 0.57–0.73). Of 39/64 Goal Attainment Scaling scales scored as complete goal attainment, 16 individual PEDI scores did not show change on the corresponding scale. Low correlation was found between Goal Attainment Scaling change scores and GMFM-66 change scores. Conclusion: Goal Attainment Scaling, PEDI and GMFM-66 were complementary in their ability to measure individual change over time in children with cerebral palsy. Using only the standardized instruments could have caused many individual rehabilitation goals actually attained being missed in the outcome evaluation.
Stromal pleiotrophin regulates repopulation behavior of hematopoietic stem cells
Authors: Istvanffy Rouzanna , Kröger Monika , Eckl Christina , Gitzelmann Sylke , Vilne Baiba , Bock Franziska , Graf Steffi , Schiemann Matthias , Keller Ulrich B. , Peschel Christian , Oostendorp Robert A. J. 
Published: July 2011

AbstractPleiotrophin (Ptn) is strongly expressed by stromal cells which maintain HSCs. However, in vivo, Ptn deficiency does not alter steady-state hematopoiesis. However, knockdown of Ptn (PtnKD) in stromal cells increases production of hematopoietic progenitors as well as HSC activity in cocultures, suggesting that Ptn may have a role in HSC activation. Indeed, transplantations of wild-type (Ptn+/+) HSCs into Ptn−/− mice show increased donor cell production in serial transplantations and dominant myeloid regeneration caused by Ptn-dependent regulation of HSC repopulation behavior. This regulation of Lin−Kit+Sca1+ function is associated with increased proliferation and, on a molecular level, with up-regulated expression of cyclin D1 (Ccnd1) and C/EBPα (Cepba), but reduced of PPARγ. The known HSC regulator β-catenin is, however, not altered in the absence of Ptn. In conclusion, our results point to different Ptn-mediated regulatory mechanisms in normal hemostasis and in hematopoietic regeneration and in maintaining the balance of myeloid and lymphoid regeneration. Moreover, our results support the idea that microenvironmental Ptn regulates hematopoietic regeneration through β-catenin–independent regulation of Ccnd1 and Cebpa.
How I treat extramedullary acute myeloid leukemia
Authors: Bakst Richard L. , Tallman Martin S. , Douer Dan , Yahalom Joachim 
Published: July 2011

AbstractExtramedullary (EM) manifestations of acute leukemia include a wide variety of clinically significant phenomena that often pose therapeutic dilemmas. Myeloid sarcoma (MS) and leukemia cutis (LC) represent 2 well-known EM manifestations with a range of clinical presentations. MS (also known as granulocytic sarcoma or chloroma) is a rare EM tumor of immature myeloid cells. LC specifically refers to the infiltration of the epidermis, dermis, or subcutis by neoplastic leukocytes (leukemia cells), resulting in clinically identifiable cutaneous lesions. The molecular mechanisms underlying EM involvement are not well defined, but recent immunophenotyping, cytogenetic, and molecular analysis are beginning to provide some understanding. Certain cytogenetic abnormalities are associated with increased risk of EM involvement, potentially through altering tissue-homing pathways. The prognostic significance of EM involvement is not fully understood. Therefore, it has been difficult to define the optimal treatment of patients with MS or LC. The timing of EM development at presentation versus relapse, involvement of the marrow, and AML risk classification help to determine our approach to treatment of EM disease.
Surface-retained tPA is essential for effective fibrinolysis on vascular endothelial cells
Authors: Suzuki Yuko , Yasui Hideki , Brzoska Tomasz , Mogami Hideo , Urano Tetsumei 
Published: July 2011

Abstract
In a previous study, we demonstrated unique secretory dynamics of tissue plasminogen activator (tPA) in which tPA was retained on the cell surface in a heavy chain–dependent manner after exocytosis from secretory granules in vascular endothelial cells. Here, we examined how retained tPA expresses its enzymatic activity. Retained tPA effectively increased the lysine binding site–dependent binding of plasminogen on the cell surface and pericellular area; this was abolished by inhibition of enzymatic activity of either tPA or plasmin, which suggests that de novo generation of carboxyl-terminal lysine as a consequence of degradation of surface/pericellular proteins by plasmin is essential. Retained tPA initiated zonal clot lysis of a fibrin network that had been formed on vascular endothelial cells, which was preceded by the binding of plasminogen to the lysis front. Our results provide evidence that secreted and retained tPA is essential for maintaining both high fibrinolytic activity and effective clot lysis on the vascular endothelial cell surface.
Risk of acute myeloid leukemia and myelodysplastic syndromes after multiple myeloma and its precursor disease (MGUS)
Authors: Mailankody Sham , Pfeiffer Ruth M. , Kristinsson Sigurdur Y. , Korde Neha , Bjorkholm Magnus , Goldin Lynn R. , Turesson Ingemar , Landgren Ola 
Published: July 2011

Abstract
Using population-based data from Sweden, we identified all multiple myeloma (MM) patients (n = 8740) and 5652 monoclonal gammopathy of undetermined significance (MGUS) patients diagnosed between 1986 and 2005. We calculated standardized incidence rates (SIRs) for all subsequent hematologic and nonhematologic malignancies for MM patients diagnosed before/after 1995 (introduction of high-dose melphalan/autologous stem cell transplantation [HDM-ASCT]) and 2000 (introduction of immunomodulatory drugs [IMiDs]), respectively. MM patients had an 11.51-fold (95% confidence interval: 8.19-15.74) increased risk of acute myeloid leukemia (AML)/myelodysplastic syndromes (MDS); risk was very similar before/after 1995 and 2000, respectively. MGUS patients had an 8.01-fold (5.40-11.43) increased risk of AML/MDS. Risk was confined to IgG/IgA, while no IgM MGUS patients developed AML/MDS; patients with monoclonal-protein (M-protein) concentrations &gt; 1.5 g/dL (SIR = 11.12; 3.61-25.96) had higher risk than those &lt; 1.5 g/dL (SIR = 4.67; 1.71-10.16). An excess risk of nonmelanoma skin cancer was observed subsequent to both MM (SIR = 2.22; 1.74-2.80) and MGUS (SIR = 3.30; 2.76-3.90). Our novel observations of an excess risk for AML/MDS following IgG/IgA (but not IgM) MGUS, and the highest risk associated with M-protein concentrations &gt; 1.5 g/dL, support a role for nontreatment-related factors in plasma cell dyscrasias. AML/MDS risk following MM was the same before/after the introduction of HDM-ASCT. Longer follow-up is needed to characterize second tumor risks in the IMiD era.
miRTar: an integrated system for identifying miRNA-target interactions in human
Authors: Hsu Justin Bo-Kai , Chiu Chih-Min , Hsu Sheng-Da , Huang Wei-Yun , Chien Chia-Hung , Lee Tzong-Yi , Huang Hsien-Da 
Published: July 2011

Abstract

Background
MicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis. Previous research has suggested that miRNAs regulate 30% or more of the human protein-coding genes. The aim of this work is to consider various analyzing scenarios in the identification of miRNA-target interactions, as well as to provide an integrated system that will aid in facilitating investigation on the influence of miRNA targets by alternative splicing and the biological function of miRNAs in biological pathways.

Results
This work presents an integrated system, miRTar, which adopts various analyzing scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in biological pathways. The system has three major features. First, the prediction system is able to consider various analyzing scenarios (1 miRNA:1 gene, 1:N, N:1, N:M, all miRNAs:N genes, and N miRNAs: genes involved in a pathway) to easily identify the regulatory relationships between interesting miRNAs and their targets, in 3'UTR, 5'UTR and coding regions. Second, miRTar can analyze and highlight a group of miRNA-regulated genes that participate in particular KEGG pathways to elucidate the biological roles of miRNAs in biological pathways. Third, miRTar can provide further information for elucidating the miRNA regulation, i.e., miRNA-target interactions, affected by alternative splicing.

Conclusions
In this work, we developed an integrated resource, miRTar, to enable biologists to easily identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. miRTar is now available at http://miRTar.mbc.nctu.edu.tw/.
IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
Authors: Kim Hyunsoo , Bi Yingtao , Pal Sharmistha , Gupta Ravi , Davuluri Ramana V 
Published: July 2011

Abstract

Background
mRNA-Seq technology has revolutionized the field of transcriptomics for identification and quantification of gene transcripts not only at gene level but also at isoform level. Estimating the expression levels of transcript isoforms from mRNA-Seq data is a challenging problem due to the presence of constitutive exons.

Results
We propose a novel algorithm (IsoformEx) that employs weighted non-negative least squares estimation method to estimate the expression levels of transcript isoforms. Validations based on in silico simulation of mRNA-Seq and qRT-PCR experiments with real mRNA-Seq data showed that IsoformEx could accurately estimate transcript expression levels. In comparisons with published methods, the transcript expression levels estimated by IsoformEx showed higher correlation with known transcript expression levels from simulated mRNA-Seq data, and higher agreement with qRT-PCR measurements of specific transcripts for real mRNA-Seq data.

Conclusions
IsoformEx is a fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. The software is available at http://bioinformatics.wistar.upenn.edu/isoformex.
Islands beneath islands: phylogeography of a groundwater amphipod crustacean in the Balearic archipelago
Authors: Bauzà-Ribot Maria M , Jaume Damià , Fornós Joan J , Juan Carlos , Pons Joan 
Published: July 2011

AbstractBackgroundMetacrangonyctidae (Amphipoda, Crustacea) is an enigmatic continental subterranean water family of marine origin (thalassoid). One of the species in the genus,Metacrangonyx longipes, is endemic to the Balearic islands of Mallorca and Menorca (W Mediterranean). It has been suggested that the origin and distribution of thalassoid crustaceans could be explained by one of two alternative hypotheses: (1) active colonization of inland freshwater aquifers by a marine ancestor, followed by an adaptative shift; or (2) passive colonization by stranding of ancestral marine populations in coastal aquifers during marine regressions. A comparison of phylogenies, phylogeographic patterns and age estimations of clades should discriminate in favour of one of these two proposals.ResultsPhylogenetic relationships withinM. longipesbased on three mitochondrial DNA (mtDNA) and one nuclear marker revealed five genetically divergent and geographically structured clades. Analyses of cytochrome oxidase subunit 1 (cox1) mtDNA data showed the occurrence of a high geographic population subdivision in both islands, with current gene flow occurring exclusively between sites located in close proximity. Molecular-clock estimations dated the origin ofM. longipesprevious to about 6 Ma, whereas major cladogenetic events within the species took place between 4.2 and 2.0 Ma.ConclusionsM. longipesdisplayed a surprisingly old and highly fragmented population structure, with major episodes of cladogenesis within the species roughly correlating with some of the major marine transgression-regression episodes that affected the region during the last 6 Ma. Eustatic changes (vicariant events) -not active range expansion of marine littoral ancestors colonizing desalinated habitats-explain the phylogeographic pattern observed inM. longipes.
Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci
Authors: Liu Jiang , Yu Li , Arnold Michael L , Wu Chun-Hua , Wu Shi-Fang , Lu Xin , Zhang Ya-Ping 
Published: July 2011

AbstractBackgroundInterspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species withinLepus, therefore it is possible that introgressive hybridization events also occur among ChineseLepusspecies and contribute to the current taxonomic confusion.ResultsData from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six ChineseLepusspecies. Remarkably, the mtDNA ofL. mandshuricuswas completely replaced by mtDNA fromL. timidusandL. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species.ConclusionThis study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.
QTLRel: an R Package for Genome-wide Association Studies in which Relatedness is a Concern
Authors: Cheng Riyan , Abney Mark , Palmer Abraham A , Skol Andrew D 
Published: July 2011

Abstract

Background
Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components.

Results
We have successfully used the package to analyze many datasets, including F34 body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU.

Conclusions
QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.