bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomechanical Comparison of the Bioabsorbable RetroScrew System, BioScrew XtraLok with Stress Equalization Tensioner, and 35-mm Delta Screws for Tibialis Anterior Graft-Tibial Tunnel Fixation in Porcine Tibiae
Authors: Chang Haw Chong , Nyland John , Nawab Akbar , Burden Robert , Caborn David N. M. 
Published: May 2005

Background Achieving effective soft tissue graft-tibial tunnel fixation remains problematic. Hypothesis No differences would exist for tibialis anterior graft-tibial tunnel fixation when comparing the RetroScrew System (20-mm retrograde screw, 17-mm antegrade screw), the 35-mm tapered Delta Screw (manual tensioning), and the 35-mm BioScrew XtraLok (applied using an instrumented tensioner). Study Design Controlled laboratory study. Methods Porcine tibiae (apparent bone mineral density, 1.3 g/cm2) and human tendon allografts were divided into 3 matched groups of 6 specimens each before cyclic (500 cycles, 50-250 N, 1 Hz) and load-to-failure (20 mm/min) tests. Results The BioScrew XtraLok (210.9 ± 54.9 N/mm) and the 35-mm Delta Screw (224.3 ± 43.7 N/mm) displayed superior stiffness to the RetroScrew System (114.1 ± 23.3 N/mm) (P =. 0004) during cyclic testing. The BioScrew XtraLok (1.0 ± 0.2 mm) and the Delta Screw (0.9 ± 0.2 mm) also displayed less displacement during cyclic testing than the RetroScrew System (1.8 ± 0.5 mm) (P =. 001). During load-to-failure testing, the BioScrew XtraLok withstood greater loads (1436.3 ± 331.3 N) (P =. 001) and displayed greater stiffness (323.6 ± 56.8 N/mm) (P =. 002) than the 35-mm Delta Screw (load, 1042.2 ± 214.4 N; stiffness, 257.2 ± 22.2 N/mm) and the RetroScrew System (load, 778.7 ± 177.5 N; stiffness, 204.4 ± 52.9 N/mm). Conclusion The BioScrew XtraLok with instrumented tensioning displayed superior fixation to the RetroScrew System and the 35-mm Delta Screw applied with manual tensioning. Clinical Relevance The BioScrew XtraLok may provide superior soft tissue graft-tibial tunnel fixation. Further in vitro studies using human tissue and in vivo clinical studies are needed.
A Biomechanical Comparison of Posterior Cruciate Ligament Reconstructions Using Single- and Double-Bundle Tibial Inlay Techniques
Authors: Bergfeld John A. , Graham Scott M. , Parker Richard D. , Valdevit Antonio D. C. , Kambic Helen E. 
Published: May 2005

Background The efficacy of using a double-bundle versus single-bundle graft for posterior cruciate ligament reconstruction has not been demonstrated. Hypothesis A double-bundle graft restores knee kinematics better than a single-bundle graft does in tibial inlay PCL reconstructions. Study Design Controlled laboratory study. Methods Eight cadaveric knees were subjected to 6 cycles from a 40-N anterior reference point to a 100-N posterior translational force at 10°, 30°, 60°, and 90° of flexion. Testing was performed for the intact and posterior cruciate deficient knee as well as for both reconstructed conditions. Achilles tendons, divided into 2 equal sections, were prepared as both single-bundle and double-bundle grafts. Both grafts were employed in the same knee, and the order of graft reconstruction was randomized. Results There were no statistical differences in translation between the intact state and either of the reconstructions (P >. 05) or between either of the reconstructions at any flexion angle (P >. 05). Conclusion No differences in translation between the 2 graft options were identified. Clinical Relevance The use of a double-bundle graft may not offer any advantages over a single-bundle graft for tibial inlay posterior cruciate reconstructions.
Conditional overexpression of transgenes in megakaryocytes and platelets in vivo
Authors: Nguyen Hao G. , Yu Guangyao , Makitalo Maria , Yang Dan , Xie Hou-Xiang , Jones Matthew R. , Ravid Katya 
Published: May 2005

Abstract
Megakaryocyte (MK)–specific transgene expression has proved valuable in studying thrombotic and hemostatic processes. Constitutive expression of genes, however, could result in altered phenotypes due to compensatory mechanisms or lethality. To circumvent these limitations, we used the tetracycline/doxycycline (Tet)–off system to conditionally over-express genes in megakaryocytes and platelets in vivo. We generated 3 transactivator transgenic lines expressing the Tet transactivator element (tTA), under the control of the MK-specific platelet factor 4 promoter (PF4-tTA-VP16). Responder lines were simultaneously generated, each with a bidirectional minimal cytomegalovirus (CMV)–tTA responsive promoter driving prokaryotic β-galactosidase gene, as a cellular reporter, and a gene of interest (in this case, the mitotic regulator Aurora-B). A transactivator founder line that strongly expressed PF4-driven tTA–viral protein 16 (VP16) was crossbred to a responder line. The homozygous double-transgenic mouse line exhibited doxycycline-dependent transgene overexpression in MKs and platelets. Using this line, platelets were conveniently indicated at sites of induced stress by β-galactosidase staining. In addition, we confirmed our earlier report on effects of constitutive expression of Aurora-B, indicating a tight regulation at protein level and a modest effect on MK ploidy. Hence, we generated a new line, PF4-tTA-VP16, that is available for conditionally overexpressing genes of interest in the MK/platelet lineage in vivo.
Integration of the Gene Ontology into an object-oriented architecture
Authors: Shegogue Daniel , Zheng W Jim 
Published: May 2005

Abstract
Background
To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model.

Results
Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181).

Conclusion
We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes.
CAGER: classification analysis of gene expression regulation using multiple information sources
Authors: Ruan Jianhua , Zhang Weixiong 
Published: May 2005

Abstract
Background
Many classification approaches have been applied to analyzing transcriptional regulation of gene expressions. These methods build models that can explain a gene's expression level from the regulatory elements (features) on its promoter sequence. Different types of features, such as experimentally verified binding motifs, motifs discovered by computer programs, or transcription factor binding data measured with Chromatin Immunoprecipitation (ChIP) assays, have been used towards this goal. Each type of features has been shown successful in modeling gene transcriptional regulation under certain conditions. However, no comparison has been made to evaluate the relative merit of these features. Furthermore, most publicly available classification tools were not designed specifically for modeling transcriptional regulation, and do not allow the user to combine different types of features.

Results
In this study, we use a specific classification method, decision trees, to model transcriptional regulation in yeast with features based on predefined motifs, automatically identified motifs, ChlP-chip data, or their combinations. We compare the accuracies and stability of these models, and analyze their capabilities in identifying functionally related genes. Furthermore, we design and implement a user-friendly web server called CAGER (Classification Analysis of Gene Expression Regulation) that integrates several software components for automated analysis of transcriptional regulation using decision trees. Finally, we use CAGER to study the transcriptional regulation of Arabidopsis genes in response to abscisic acid, and report some interesting new results.

Conclusion
Models built with ChlP-chip data suffer from low accuracies when the condition under which gene expressions are measured is significantly different from the condition under which the ChIP experiment is conducted. Models built with automatically identified motifs can sometimes discover new features, but their modeling accuracies may have been over-estimated in previous studies. Furthermore, models built with automatically identified motifs are not stable with respect to noises. A combination of ChlP-chip data and predefined motifs can substantially improve modeling accuracies, and is effective in identifying true regulons. The CAGER web server, which is freely available at http://cic.cs.wustl.edu/CAGER/, allows the user to select combinations of different feature types for building decision trees, and interact with the models graphically. We believe that it will be a useful tool to facilitate the discovery of gene transcriptional regulatory networks.
An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays
Authors: Gadgil Mugdha , Lian Wei , Gadgil Chetan , Kapur Vivek , Hu Wei-Shou 
Published: May 2005

Abstract
Background
DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values.

Results
We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions.

Conclusion
Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray assays using genomic DNA as a reference. We conclude that the use of genomic DNA as reference DNA should greatly facilitate comparative transcriptome analysis.
Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes
Authors: Anderle Pascale , Sengstag Thierry , Mutch David M , Rumbo Martin , Praz Viviane , Mansourian Robert , Delorenzi Mauro , Williamson Gary , Roberts Matthew-Alan 
Published: May 2005

Abstract

Background
The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing whole gut tissue rather than purified epithelial cells to examine regional variations in gene expression.

Results
We have characterized the mRNA expression profiles of 76 % of all currently known transporters along the anterior-posterior axis of the gut. This is the first study to describe the expression profiles of the majority of all known transporters in the intestine. The expression profiles of transporters, as defined according to the Gene Ontology consortium, were measured in whole tissue of the murine duodenum, jejunum, ileum and colon using high-density microarrays. For nine transporters (Abca1, Abcc1, Abcc3, Abcg8, Slc10a2, Slc28a2, Slc2a1, Slc34a2 and Slc5a8), the mRNA profiles were further measured by RT-PCR in laser micro-dissected crypt and villus epithelial cells corresponding to the aforementioned intestinal regions. With respect to differentially regulated transporters, the colon had a distinct expression profile from small intestinal segments. The majority (59 % for p cutoff ≤ 0.05) of transporter mRNA levels were constant across the intestinal sections studied. For the transporter subclass "carrier activity", which contains the majority of known carriers for biologically active compounds, a significant change (p ≤ 0.05) along the anterior-posterior axis was observed.

Conclusion
All nine transporters examined in laser-dissected material demonstrated good replication of the region-specific profiles revealed by microarray. Furthermore, we suggest that the distribution characteristics of Slc5a8 along the intestinal tract render it a suitable candidate carrier for monocarboxylate drugs in the posterior portion of the intestine. Our findings also predict that there is a significant difference in the absorption of carrier-mediated compounds in the different intestinal segments. The most pronounced differences can be expected between the adjoining segments ileum and colon, but the differences between the other adjoining segments are not negligible. Finally, for the examined genes, profiles measured in whole intestinal tissue extracts are representative of epithelial cell-only gene expression.
Hyperspectral microarray scanning: impact on the accuracy and reliability of gene expression data
Authors: Timlin Jerilyn A , Haaland David M , Sinclair Michael B , Aragon Anthony D , Martinez M Juanita , Werner-Washburne Margaret 
Published: May 2005

Abstract

Background
Commercial microarray scanners and software cannot distinguish between spectrally overlapping emission sources, and hence cannot accurately identify or correct for emissions not originating from the labeled cDNA. We employed our hyperspectral microarray scanner coupled with multivariate data analysis algorithms that independently identify and quantitate emissions from all sources to investigate three artifacts that reduce the accuracy and reliability of microarray data: skew toward the green channel, dye separation, and variable background emissions.

Results
Here we demonstrate that several common microarray artifacts resulted from the presence of emission sources other than the labeled cDNA that can dramatically alter the accuracy and reliability of the array data. The microarrays utilized in this study were representative of a wide cross-section of the microarrays currently employed in genomic research. These findings reinforce the need for careful attention to detail to recognize and subsequently eliminate or quantify the presence of extraneous emissions in microarray images.

Conclusion
Hyperspectral scanning together with multivariate analysis offers a unique and detailed understanding of the sources of microarray emissions after hybridization. This opportunity to simultaneously identify and quantitate contaminant and background emissions in microarrays markedly improves the reliability and accuracy of the data and permits a level of quality control of microarray emissions previously unachievable. Using these tools, we can not only quantify the extent and contribution of extraneous emission sources to the signal, but also determine the consequences of failing to account for them and gain the insight necessary to adjust preparation protocols to prevent such problems from occurring.
The antimicrobial susceptibility of Stenotrophomonas maltophilia isolates using three different methods and their genetic relatedness
Authors: Tatman-Otkun Müşerref , Gürcan Şaban , Özer Burçin , Aydoslu Bayram , Bukavaz Şebnem 
Published: May 2005

Abstract
Background
Stenotrophomonas maltophilia is inherently resistant to many antimicrobials. So far, antimicrobial susceptibility tests for S. maltophilia have not been fully standardized. The purpose of the study was to compare the susceptibility of S. maltophilia isolates against seven different antimicrobials using three different methods and to investigate their genetic relatedness.

Results
Although trimethoprim/sulfamethoxazole (SXT) and ciprofloxacin have the lowest MIC values, SXT (98.1%) and ticarcillin/clavulanate (TLc) (73.1%) were found to be the most effective antimicrobials by agar dilution method, which was in accordance with the breakpoints established by NCCLS. Disc diffusion and E-test was in agreement with agar dilution method for SXT. When the isolation dates, clinics, antibiotyping, and AP-PCR data were investigated, two small outbreaks consisting of five and three cases were determined.

Conclusion
By using the NCCLS criteria, disc diffusion and E-test were unreliable alternative methods for S. maltophilia, except for SXT. However, the significance of these data should be confirmed by further experimental and clinical studies.
Protection of cortical cells by equine estrogens against glutamate-induced excitotoxicity is mediated through a calcium independent mechanism
Authors: Perrella Joel , Bhavnani Bhagu R 
Published: May 2005

Abstract
Background
High concentrations of glutamate can accumulate in the brain and may be involved in the pathogenesis of neurodegenerative disorders such as Alzheimer's disease. This form of neurotoxicity involves changes in the regulation of cellular calcium (Ca2+) and generation of free radicals such as peroxynitrite (ONOO-). Estrogen may protect against glutamate-induced cell death by reducing the excitotoxic Ca2+ influx associated with glutamate excitotoxicity. In this study, the inhibition of N-methyl-D-aspartate (NMDA) receptor and nitric oxide synthase (NOS) along with the effect of 17β-estradiol (17β-E2) and a more potent antioxidant Δ8, 17β-estradiol (Δ8, 17β-E2) on cell viability and intracellular Ca2+ ([Ca2+]i), following treatment of rat cortical cells with glutamate, was investigated.

Results
Primary rat cortical cells were cultured for 7–12 days in Neurobasal medium containing B27 supplements. Addition of glutamate (200 μM) decreased cell viability to 51.3 ± 0.7% compared to control. Treatment with the noncompetitive NMDAR antagonist, MK-801, and the NOS inhibitor, L-NAME, completely prevented cell death. Pretreatment (24 hrs) with 17β-E2 and Δ8, 17β-E2 (0.01 to 10 μM) significantly reduced cell death. 17β-E2 was more potent than Δ8, 17β-E2. Glutamate caused a rapid 2.5 fold increase in [Ca2+]i. Treatment with 0.001 to 10 μM MK-801 reduced the initial Ca2+ influx by 14–41% and increased cell viability significantly. Pretreatment with 17β-E2 and Δ8, 17β-E2 had no effect on Ca2+ influx but protected the cortical cells against glutamate-induced cell death.

Conclusion
Glutamate-induced cell death in cortical cultures can occur through NMDAR and NOS-linked mechanisms by increasing nitric oxide and ONOO-. Equine estrogens: 17β-E2 and Δ8, 17β-E2, significantly protected cortical cells against glutamate-induced excitotoxicity by a mechanism that appears to be independent of Ca2+ influx. To our knowledge, this is a first such observation. Whether the decrease in NOS related products such as ONOO-, is a mechanism by which estrogens protect against glutamate toxicity, remains to be investigated. Estrogen replacement therapy in healthy and young postmenopausal women may protect against neurodegenerative diseases by these mechanisms.
Failure of a patient-centered intervention to substantially increase the identification and referral for-treatment of ambulatory emergency department patients with occult psychiatric conditions: a randomized trial [ISRCTN61514736]
Authors: Schriger David L , Gibbons Patrick S , Nezami Wais A , Langone Carol A 
Published: May 2005

Abstract
Background
We previously demonstrated that a computerized psychiatric screening interview (the PRIME-MD) can be used in the Emergency Department (ED) waiting room to identify patients with mental illness. In that trial, however, informing the ED physician of the PRIME-MD results did not increase the frequency of psychiatric diagnosis, consultation or referral. We conducted this study to determine whether telling the patient and physician the PRIME-MD result would result in the majority of PRIME-MD-diagnosed patients being directed toward treatment for their mental illness.

Methods
In this single-site RCT, consenting patients with non-specific somatic chief complaints (e.g., fatigue, back pain, etc.) completed the computerized PRIME-MD in the waiting room and were randomly assigned to one of three groups: patient and physician told PRIME-MD results, patient told PRIME-MD results, and neither told PRIME-MD results.
The main outcome measure was the percentage of patients with a PRIME-MD diagnosis who received a psychiatric consultation or referral from the ED.

Results
183 (5% of all ED patients) were approached. 123 eligible patients consented to participate, completed the PRIME-MD and were randomized. 95 patients had outcomes recorded. 51 (54%) had a PRIME-MD diagnosis and 8 (16%) of them were given a psychiatric consultation or referral in the ED. While the frequency of consultation or referral increased as the intervention's intensity increased (tell neither = 11% (1/9), tell patient 15% (3/20), tell patient and physician 18% (4/22)), no group came close to the 50% threshold we sought. For this reason, we stopped the trial after an interim analysis.

Conclusion
Patients willingly completed the PRIME-MD and 54% had a PRIME-MD diagnosis. Unfortunately, at our institution, informing the patient (and physician) of the PRIME-MD results infrequently led to the patient being directed toward care for their psychiatric condition.