bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of plasminogen activator inhibitor-1 deficiency on nutritionally-induced obesity in mice
Authors: Lijnen Roger 
Published: April 2005

SummaryPlasminogen activator inhibitor-1 (PAI-1) is the main physiological inhibitor of tissue-type (t-PA) and urokinase-type (u-PA) plasminogen activator. Recent studies in murine models have yielded apparently conflicting data on a potential role of PAI-1 in adipose tissue development and obesity. To reinvestigate this issue, we have rederived PAI-1 deficient (PAI-1-/-) and wild-type (WT) mice and generated true littermates in a 81.25% C57Bl/6: 18.75% 129 SV genetic background. Male 5-week-old PAI-1-/- and WT mice were kept on a high fat diet (20.1 kJ/g) for 15 weeks. Body weight gain was comparable for both genotypes, and at the time of sacrifice total body weights (39 ± 1.1 versus 41 ± 1.2 g) as well as the weights of subcutaneous (SC, 1,520 ± 110 versus 1,480 ± 110 mg) adipose tissue were not significantly different. In contrast, the gonadal (GON, 1,900 ± 43 versus 1,510 ± 86 mg, p < 0.005) tissue mass was larger in PAI-1-/- mice. Plasma levels of insulin, leptin, glucose, triglycerides, total, HDL and LDL cholesterol were comparable for both genotypes. Immunohisto-chemical analysis of SC and GON adipose tissues did not reveal differences in adipocyte size or number between both genotypes, whereas blood vessel density was also comparable for GON fat but lower in SC fat of WT mice. Thus, this study in littermate mice on high fat diet did not reveal an effect of PAI-1 deficiency on body weight, and a differential effect on SC and GON adipose tissue.
Drift Characteristics of a Moored Conductivity–Temperature–Depth Sensor and Correction of Salinity Data
Authors: Ando Kentaro , Matsumoto Takeo , Nagahama Tetsuya , Ueki Iwao , Takatsuki Yasushi , Kuroda Yoshifumi 
Published: April 2005

Abstract
The temperature and conductivity drift (time change of the characteristics) of moored SBE37IM conductivity and temperature (CT) sensors was investigated by pre- and postdeployment calibration of the Triangle TransOcean Buoy Network (TRITON). This buoy network comprises the western portion of the basinwide (Tropical Atmosphere Ocean) TAO/TRITON buoy array, which monitors phenomena such as El Niño and contributes to forecasting climate change. Over the time of deployment the drift of the temperature sensors was very small, within 3 mK of the postdeployment calibration data. The drift of the conductivity sensors was more significant. After 1 yr of mooring, conductivity drift observed in the shallowest layer (1.5–100 m) was positive and 0.010 S m−1 [equivalent to 0.065 (PSS-78) at 30°C and 6 S m−1; here, 1 S is 1 Ω−1] at 6 S m −1 on average. Drift observed in the thermocline layer (125–200 m) was also positive and 0.0053 S m−1 [0.034 (PSS-78)] at 6 S m−1 on average. Conversely, the drift of conductivity in the deepest layer (250–750 m) was 0.00002 S m−1 with a standard deviation of 0.001 S m−1 [0.0065 (PSS-78)].
Assuming a linear trend of conductivity drift with time, the authors attempted to correct the conductivity data using the postdeployment calibration data. The corrected data for about 80% of the sensors exhibited smaller differences than the uncorrected data when compared with the in situ conductivity–temperature–depth (CTD) data. However, the corrected salinity data became worse than the uncorrected data for about 20% of the sensors. The reasons for these errors are also discussed in this paper.
Sport-Dependent Variations in arm Position during Single-Limb Landing Influence Knee Loading
Authors: Chaudhari Ajit M. , Hearn Brenna K. , Andriacchi Thomas P. 
Published: April 2005

Background Increased valgus loading at the knee has been previously identified as a possible risk factor for noncontact anterior cruciate ligament injuries, which are common in sports. Arm position variation may affect risk of injury by altering valgus knee loading. Hypothesis Sport-dependent variations in arm position increase valgus loading of the knee during run-to-cut maneuvers. Study Design Controlled laboratory study. Methods Eleven subjects performed a sidestep cutting maneuver, first with no arm constraints and then with 3 sports-related arm positions in random order (holding a lacrosse stick, holding a football on the plant side, and holding a football on the cut side). The analysis focused on the knee valgus moment relative to the arm positions during the landing phase of the activity. Results Arm position significantly influenced the valgus moment with an increase in the lacrosse trials and in the plant-side football trials but not in the cut-side football trials (α =. 05). Conclusions Constraining the plant-side arm results in increased valgus loading at the knee during run-to-cut maneuvers, which suggests the possibility of greater risk of anterior cruciate ligament injury during these conditions. Clinical Relevance These results suggest that training methods that consider arm position as a risk factor could help reduce the risk of anterior cruciate ligament noncontact injury.
Variations in Mortise Anatomy
Authors: LeBrun Christopher T. , Krause John O. 
Published: April 2005

Background Variations in ankle mortise anatomy may be a predisposing factor to ankle instability. Hypothesis A posteriorly positioned fibula associated with ankle instability may not be a true pathologic entity but rather the result of measuring off an internally rotated talus. Study Design Cohort study (diagnosis); Level of evidence, 2. Methods The authors reviewed 60 ankle computed tomography scans performed on patients from their institution for reasons unrelated to ankle instability. They also reviewed ankle computed tomography scans on 21 patients surgically treated for clinical ankle instability. The position of the fibula in relation to the talar articular surface was calculated and expressed as the axial malleolar index, as described by Scranton et al. They also calculated the intermalleolar index, a new method that references the medial malleolus, not the talus. Results Using the method of Scranton et al, the axial malleolar index in the control and instability patients was similar to values previously described, and there was a significant difference between control and instability patients (P <. 01). However, using the intermalleolar index method referencing the medial malleolus, there was not a significant difference between control and instability patients (P =. 43). Conclusion The new method of referencing the medial malleolus assesses fibular position independent of talar rotation. The data, when referencing the medial malleolus, do not show significant variation in fibular position in patients with and without ankle instability.
The Posterolateral Corner of the Knee
Authors: Stannard James P. , Brown Stephen L. , Farris Rory C. , McGwin Gerald , Volgas David A. 
Published: April 2005

Background Injuries to the posterolateral corner of the knee are disabling. Despite improved understanding of this group of tendons and ligaments, the best surgical treatment of an unstable corner is not clear. Hypothesis Surgical repair of acute tears of the posterolateral corner has outcomes that are as good as those from reconstruction combined with an early motion rehabilitation protocol. Study Design Cohort study; Level of evidence, 2. Methods Sixty-three patients with 64 posterolateral corner tears were included in this study, with 39 posterolateral corner repairs and 25 reconstructions using the modified 2-tailed technique. Patients were evaluated with clinical and KT-2000 arthrometer examinations, as well as with Lysholm, International Knee Documentation Committee, and Short Form-36 scores. Results Fifty-six patients with 57 corner tears had minimum clinical follow-up of 24 months (range, 24-59 months). Acute primary repairs were performed on 35 patients, with 22 successful outcomes and 13 (37%) failures. Primary reconstructions were performed on 22 patients, with 20 successful outcomes and 2 (9%) failures. The difference in stability on clinical examination between repairs and reconstructions was significant (P <. 05). Fourteen of 15 patients with failures of the primary posterolateral corner repair or reconstruction underwent successful revision reconstruction. The final patient with failure of the primary repair elected not to have a revision reconstruction. The final mean Lysholm knee score for both repair and reconstruction patients was 88.7 (range, 53-100). Final International Knee Documentation Committee objective scores yielded 14 (26%) normal, 28 (52%) near-normal, 9 (17%) abnormal, and 3 (6%) severely abnormal knees; the mean score was 60 at the most recent clinical evaluation. Conclusion Results with repair followed by early motion rehabilitation have been significantly inferior when compared with results from reconstruction using the modified 2-tailed technique. The authors now use reconstruction rather than repair in the majority of patients who sustain posterolateral corner tears after high-energy injuries.
Instruction of Jump-Landing Technique Using Videotape Feedback
Authors: Oñate James A. , Guskiewicz Kevin M. , Marshall Stephen W. , Giuliani Carol , Yu Bing , Garrett William E. 
Published: April 2005

Background Anterior cruciate ligament injury prevention programs have used videotapes of jump-landing technique as a key instructional component to improve landing performance. Hypothesis All videotape feedback model groups will increase knee flexion angles at initial contact and overall knee flexion motion and decrease peak vertical ground reaction forces and peak proximal anterior tibial shear forces to a greater extent than will a nonfeedback group. The secondary hypothesis is that the videotape feedback using the combination of the expert and self models will create the greatest change in each variable. Study Design Controlled laboratory study. Methods Knee kinematics and kinetics of college-aged recreational athletes randomly placed in 3 different videotape feedback model groups (expert only, self only, combination of expert and self) and a nonfeedback group were collected while participants performed a basketball jump-landing task on 3 testing occasions. Results All feedback groups significantly increased knee angular displacement flexion angles [F(6,70) = 8.03, P =. 001] and decreased peak vertical ground reaction forces [F(6,78) = 2.68, P =. 021] during performance and retention tests. The self and combination groups significantly increased knee angular displacement flexion angles more than the control group did; the expert model group did not change significantly more than the control group did. All feedback groups and the nonfeedback group significantly reduced peak vertical forces across performance and retention tests. There were no statistically significant changes in knee flexion angle at initial ground contact (P =. 111) and peak proximal anterior tibial shear forces (P =. 509) for both testing sessions for each group. Conclusion The use of self or combination videotape feedback is most useful for increasing knee angular displacement flexion angles and reducing peak vertical forces during landing. Clinical Relevance The use of self or combination modeling is more effective than is expert-only modeling for the implementation of instructional programs aimed at reducing the risk of jump-landing anterior cruciate ligament injuries.
Location of the Glenoid Defect in Shoulders with Recurrent Anterior Dislocation
Authors: Saito Hidetomo , Itoi Eiji , Sugaya Hiroyuki , Minagawa Hiroshi , Yamamoto Nobuyuki , Tuoheti Yilihamu 
Published: April 2005

Background In patients with recurrent anterior dislocations of the shoulder, it is well known that the glenoid rim is often deficient (8%-95%). However, little is known regarding the precise location of the bony defect of the glenoid. Hypothesis The bony defect is anterior rather than anteroinferior to the glenoid Study Design Cohort study (symptom prevalence); Level of evidence, 2. Methods The authors studied 3-dimensional images of the glenoid reconstructed from computed tomography to determine the location of the glenoid defect in 123 shoulders of 123 patients with recurrent anterior dislocations of the shoulder. They measured the location, extent, and orientation of the defect based on the clock face of the glenoid. Results The defects were located between 12:08 and 6:32, with the range between 2:30 and 4:20 being the most frequent. The extent of the glenoid defect was 106.7°± 27.1° (mean ± standard deviation). The mean orientation of the defect was pointing toward 3:01 on the clock face of the glenoid, at a mean angle of 90.5°± 10.4° from the 12-o'clock direction. Conclusion The glenoid defect is located almost anterior to the glenoid.
Mutant-specific gene programs in the zebrafish
Authors: Weber Gerhard J. , Choe Sung E. , Dooley Kimberly A. , Paffett-Lugassy Noëlle N. , Zhou Yi , Zon Leonard I. 
Published: April 2005

AbstractHematopoiesis involves the production of stem cells, followed by the orchestrated differentiation of the blood lineages. Genetic screens in zebrafish have identified mutants with defects that disrupt specific stages of hematopoiesis and vasculogenesis, including the cloche, spadetail (tbx16), moonshine (tif1g), bloodless, and vlad tepes (gata1) mutants. To better characterize the blood program, gene expression profiling was carried out in these mutants and in scl-morphants (sclmo). Distinct gene clusters were demarcated by stage-specific and mutant-specific gene regulation. These were found to correlate with the transcriptional program of hematopoietic progenitor cells, as well as of the erythroid, myeloid, and vascular lineages. Among these, several novel hematopoietic and vascular genes were detected, for instance, the erythroid transcription factors znfl2 and ncoa4. A specific regulation was found for myeloid genes, as they were more strongly expressed in vlt mutants compared with other erythroid mutants. A unique gene expression pattern of up-regulated isoprenoid synthesis genes was found in cloche and sclmo, possibly in migrating cells. In conjunction with the high conservation of vertebrate hematopoiesis, the comparison of transcriptional profiles in zebrafish blood mutants represents a versatile and powerful tool to elucidate the genetic regulation of blood and blood vessel development.
Conservation of unique cell-surface CD antigen mosaics in HIV-1–infected individuals
Authors: Woolfson Adrian , Stebbing Justin , Tom Brian D. M. , Stoner Kerryn J. , Gilks Walter R. , Kreil David P. , Mulligan Stephen P. , Belov Larissa , Chrisp Jeremy S. , Errington Will , Wildfire Adrian , Erber Wendy N. , Bower Mark , Gazzard Brian , Christopherson Richard I. , Scott Mike A. 
Published: April 2005

AbstractCluster of differentiation (CD) antigens are expressed on cells of myeloid and lymphoid lineages. As most disease processes involve immune system activation or suppression, these antigens offer unique opportunities for monitoring host responses. Immunophenotyping using limited numbers of CD antigens enables differentiation states of immune system cells to be determined. Extended phenotyping involving parallel measurement of multiple CD antigens may help identify expression pattern signatures associated with specific disease states. To explore this possibility we have made a CD monoclonal antibody array and scanner, enabling the parallel immunophenotyping of leukocyte cell suspensions in a single and rapid analysis. To demonstrate this approach, we used the specific example of patients infected with human immunodeficiency virus type-1 (HIV-1). An invariant HIV-induced CD antigen signature has been defined that is both robust and independent of clinical outcome, composed of a unique profile of CD antigen expression levels that are both increased and decreased relative to internal controls. The results indicate that HIV-induced changes in CD antigen expression are disease specific and independent of outcome. Their invariant nature indicates an irreversible component to retroviral infection and suggests the utility of CD antigen expression patterns in other disease settings.
'PACLIMS': A component LIM system for high-throughput functional genomic analysis
Authors: Donofrio Nicole , Rajagopalon Ravi , Brown Douglas , Diener Stephen , Windham Donald , Nolin Shelly , Floyd Anna , Mitchell Thomas , Galadima Natalia , Tucker Sara , Orbach Marc J , Patel Gayatri , Farman Mark , Pampanwar Vishal , Soderlund Cari , Lee Yong-Hwan , Dean Ralph A 
Published: April 2005

Abstract
Background
Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the ~11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

Results
The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.

Conclusion
Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
Authors: Stenger Judith E , Xu Hong , Haynes Carol , Hauser Elizabeth R , Pericak-Vance Margaret , Goldschmidt-Clermont Pascal J , Vance Jeffery M 
Published: April 2005

Abstract
Background
To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis.

Results
Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath.

Conclusion
Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks. Statistic View is a novel and powerful visual feature that enhances Ensembl's utility as valuable resource for integrative genomic-based approaches to the identification of candidate disease susceptibility genes. At present there are no other tools that provide for the visualization of 2-dimensional plots of quantitative data scores against genomic coordinates in the context of a primary public genome annotation browser.
Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery
Authors: Grate Leslie R 
Published: April 2005

Abstract
Background
Molecular profiling generates abundance measurements for thousands of gene transcripts in biological samples such as normal and tumor tissues (data points). Given such two-class high-dimensional data, many methods have been proposed for classifying data points into one of the two classes. However, finding very small sets of features able to correctly classify the data is problematic as the fundamental mathematical proposition is hard. Existing methods can find "small" feature sets, but give no hint how close this is to the true minimum size. Without fundamental mathematical advances, finding true minimum-size sets will remain elusive, and more importantly for the microarray community there will be no methods for finding them.

Results
We use the brute force approach of exhaustive search through all genes, gene pairs (and for some data sets gene triples). Each unique gene combination is analyzed with a few-parameter linear-hyperplane classification method looking for those combinations that form training error-free classifiers. All 10 published data sets studied are found to contain predictive small feature sets. Four contain thousands of gene pairs and 6 have single genes that perfectly discriminate.

Conclusion
This technique discovered small sets of genes (3 or less) in published data that form accurate classifiers, yet were not reported in the prior publications. This could be a common characteristic of microarray data, thus making looking for them worth the computational cost. Such small gene sets could indicate biomarkers and portend simple medical diagnostic tests. We recommend checking for small gene sets routinely. We find 4 gene pairs and many gene triples in the large hepatocellular carcinoma (HCC, Liver cancer) data set of Chen et al. The key component of these is the "placental gene of unknown function", PLAC8. Our HMM modeling indicates PLAC8 might have a domain like part of lP59's crystal structure (a Non-Covalent Endonuclease lii-Dna Complex). The previously identified HCC biomarker gene, glypican 3 (GPC3), is part of an accurate gene triple involving MT1E and ARHE. We also find small gene sets that distinguish leukemia subtypes in the large pediatric acute lymphoblastic leukemia cancer set of Yeoh et al.