bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting and improving the protein sequence alignment quality by support vector regression
Authors: Lee Minho , Jeong Chan-seok , Kim Dongsup 
Published: December 2007

AbstractBackgroundFor successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significantly depending on our choice of various alignment parameters such as gap opening penalty and gap extension penalty. Because the accuracy of sequence alignment is typically measured by comparing it with its corresponding structure alignment, there is no good way of evaluating alignment accuracy without knowing the structure of a query protein, which is obviously not available at the time of structure prediction. Moreover, there is no universal alignment parameter option that would always yield the optimal alignment.ResultsIn this work, we develop a method to predict the quality of the alignment between a query and a template. We train the support vector regression (SVR) models to predict the MaxSub scores as a measure of alignment quality. The alignment between a query protein and a template of lengthnis transformed into a (n+ 1)-dimensional feature vector, then it is used as an input to predict the alignment quality by the trained SVR model. Performance of our work is evaluated by various measures including Pearson correlation coefficient between the observed and predicted MaxSub scores. Result shows high correlation coefficient of 0.945. For a pair of query and template, 48 alignments are generated by changing alignment options. Trained SVR models are then applied to predict the MaxSub scores of those and to select the best alignment option which is chosen specifically to the query-template pair. This adaptive selection procedure results in 7.4% improvement of MaxSub scores, compared to those when the single best parameter option is used for all query-template pairs.ConclusionThe present work demonstrates that the alignment quality can be predicted with reasonable accuracy. Our method is useful not only for selecting the optimal alignment parameters for a chosen template based on predicted alignment quality, but also for filtering out problematic templates that are not suitable for structure prediction due to poor alignment accuracy. This is implemented as a part in FORECAST, the server for fold-recognition and is freely available on the web athttp://pbil.kaist.ac.kr/forecast
Cerebellum morphogenesis: the foliation pattern is orchestrated by multi-cellular anchoring centers
Authors: Sudarov Anamaria , Joyner Alexandra L 
Published: December 2007

Abstract
Background
The cerebellum has a striking morphology consisting of folia separated by fissures of different lengths. Since folia in mammals likely serve as a broad platform on which the anterior-posterior organization of the sensory-motor circuits of the cerebellum are built, it is important to understand how such complex morphology arises.

Results
Using a combination of genetic inducible fate mapping, high-resolution cellular analysis and mutant studies in mouse, we demonstrate that a key event in initiation of foliation is the acquisition of a distinct cytoarchitecture in the regions that will become the base of each fissure. We term these regions 'anchoring centers'. We show that the first manifestation of anchoring centers when the cerebellar outer surface is smooth is an increase in proliferation and inward thickening of the granule cell precursors, which likely causes an associated slight invagination of the Purkinje cell layer. Thereafter, granule cell precursors within anchoring centers become distinctly elongated along the axis of the forming fissure. As the outer cerebellar surface begins to fold inwards, Bergmann glial fibers radiate in towards the base of the immature fissure in a fan shape. Once the anchoring center is formed, outgrowth of folia seems to proceed in a self-sustaining manner driven by granule cell migration along Bergmann glial fibers. Finally, by analyzing a cerebellum foliation mutant (Engrailed 2), we demonstrate that changing the timing of anchoring center formation leads to predictable changes in the shape and size of the surrounding folia.

Conclusion
We present a new cellular model of the initial formation of cerebellar fissures with granule cells providing the driving physical force. Both the precise timing of the appearance of anchoring centers at the prospective base of each fissure and the subsequent coordinated action of granule cells and Bergmann glial fibers within the anchoring centers dictates the shape of the folia.
Bioinformatics process management: information flow via a computational journal
Authors: Feagan Lance , Rohrer Justin , Garrett Alexander , Amthauer Heather , Komp Ed , Johnson David , Hock Adam , Clark Terry , Lushington Gerald , Minden Gary , Frost Victor 
Published: December 2007

AbstractThis paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hocscripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.
Hypercalcemia after transplant nephrectomy in a hemodialysis patient: a case report
Authors: Quack Ivo , Woznowski Magdalena , Schieren Gisela , Weiner Stefan M , Winnekendonk Guido , Tokmak Faruk , Rump Lars C , Rattensperger Dirk 
Published: December 2007

Abstract

Introduction
Hypercalcemia is a complication often seen in chronic hemodialysis patients. A rare cause of this condition is sarcoidosis. Its highly variable clinical presentation is challenging. Especially in patients suffering chronic kidney graft failure the nonspecific constitutional symptoms of sarcoidosis like fever, weight loss, arthralgia and fatigue may be easily misleading.

Case presentation
A 51 year old male developed hypercalcemia, arthralgia and B-symptoms after explantation of his kidney graft because of suspected acute rejection. The removed kidney showed vasculopathy and tubulointerstitial nephritis, which had not been overt in the biopsy taken half a year earlier. Despite explantation and withdrawal of the immunosuppression the patient's general condition deteriorated progressively. A rapid rise in serum calcium finally provoked us to check for sarcoidosis. CT scans of the lungs, broncho-alveolar-lavage and further lab tests confirmed the diagnosis.

Conclusion
This case demonstrates that withdrawal of immunosuppressive drugs sometimes unmasks sarcoidosis. It should be considered as differential diagnosis even in hemodialysis patients, in whom other reasons for hypercalcemia are much more common.
The IL-4Rα pathway in macrophages and its potential role in silica-induced pulmonary fibrosis
Authors: Migliaccio Christopher T , Buford Mary C , Jessop Forrest , Holian Andrij 
Published: December 2007

AbstractCrystalline silica exposure can result in pulmonary fibrosis, where the pulmonary macrophage is key as a result of its ability to react to silica particles. In the mouse silicosis model, there is initial Th1-type inflammation, characterized by TNF-α and IFN-γ. Previous studies determined that Th2 mediators (i.e., IL-13) are vital to development of pulmonary fibrosis. The present study, using in vivo and in vitro techniques, compares silica exposures between Balb/c and Th2-deficient mice in an effort to determine the link between Th2 immunity and silicosis. In long-term experiments, a significant increase in fibrosis and activated interstitial macrophages was observed in Balb/c but not IL-4Rα−/− mice. Additionally, a significant increase in Ym1 mRNA levels, a promoter of Th2 immunity, was determined in the interstitial leukocyte population of silica-exposed Balb/c mice. To elucidate the effects of silica on macrophage function, bone marrow-derived macrophages (BMdM) were exposed to particles and assayed for T cell (TC) stimulation activity. As a control, Ym1 mRNA expression in Balb/c BMdM was determined using IL-4 stimulation. In the in vitro assay, a significant increase in TC activation, as defined by surface markers and cytokines, was observed in the cultures containing the silica-exposed macrophages in wild-type and IL-4Rα−/− mice, with one exception: IL-4Rα−/− BMdM were unable to induce an increase in IL-13. These results suggest that crystalline silica alters cellular functions of macrophages, including activation of TC, and that the increase in Th2 immunity associated with silicosis is via the IL-4Rα-Ym1 pathway.
Heterodimerization of TLR2 with TLR1 or TLR6 expands the ligand spectrum but does not lead to differential signaling
Authors: Farhat Katja , Riekenberg Sabine , Heine Holger , Debarry Jennifer , Lang Roland , Mages Jörg , Buwitt-Beckmann Ute , Röschmann Kristina , Jung Günther , Wiesmüller Karl-Heinz , Ulmer Artur J 
Published: December 2007

AbstractTLR are primary triggers of the innate immune system by recognizing various microorganisms through conserved pathogen-associated molecular patterns. TLR2 is the receptor for a functional recognition of bacterial lipopeptides (LP) and is up-regulated during various disorders such as chronic obstructive pulmonary disease and sepsis. This receptor is unique in its ability to form heteromers with TLR1 or TLR6 to mediate intracellular signaling. According to the fatty acid pattern as well as the assembling of the polypeptide tail, LP can signal through TLR2 in a TLR1- or TLR6-dependent manner. There are also di- and triacylated LP, which stimulate TLR1-deficient cells and TLR6-deficient cells. In this study, we investigated whether heterodimerization evolutionarily developed to broaden the ligand spectrum or to induce different immune responses. We analyzed the signal transduction pathways activated through the different TLR2 dimers using the three LP, palmitic acid (Pam)octanoic acid (Oct)2C-(VPGVG)4VPGKG, fibroblast-stimulating LP-1, and Pam2C-SK4. Dominant-negative forms of signaling molecules, immunoblotting of MAPK, as well as microarray analysis indicate that all dimers use the same signaling cascade, leading to an identical pattern of gene activation. We conclude that heterodimerization of TLR2 with TLR1 or TLR6 evolutionarily developed to expand the ligand spectrum to enable the innate immune system to recognize the numerous, different structures of LP present in various pathogens. Thus, although mycoplasma and Gram-positive and Gram-negative bacteria may activate different TLR2 dimers, the development of different signal pathways in response to different LP does not seem to be of vital significance for the innate defense system.
Protein Biomarker Identification in the CSF of Patients With CNS Lymphoma
Authors: Roy Sushmita , Josephson S. Andrew , Fridlyand Jane , Karch Jon , Kadoch Cigall , Karrim Juliana , Damon Lloyd , Treseler Patrick , Kunwar Sandeep , Shuman Marc A. , Jones Ted , Becker Christopher H. , Schulman Howard , Rubenstein James L. 
Published: December 2007

Purpose Elucidation of the CSF proteome may yield insights into the pathogenesis of CNS disease. We tested the hypothesis that individual CSF proteins distinguish CNS lymphoma from benign focal brain lesions. Methods We used a liquid chromatography/mass spectrometry–based method to differentially quantify and identify several hundred CSF proteins in CNS lymphoma and control patients. We used enzyme-linked immunosorbent assay (ELISA) to confirm one of these markers in an additional validation set of 101 cases. Results Approximately 80 CSF proteins were identified and found to be present at significantly different concentrations, both higher and lower, in training and test studies, which were highly concordant. To further validate these observations, we defined in detail the expression of one of these candidate biomarkers, antithrombin III (ATIII). ATIII RNA transcripts were identified within CNS lymphomas, and ATIII protein was localized selectively to tumor neovasculature. Determination of ATIII concentration by ELISA was significantly more accurate (> 75% sensitivity; > 98% specificity) than cytology in the identification of cancer. Measurement of CSF ATIII levels was found to potentially enhance the ability to diagnose and predict outcome. Conclusion Our findings demonstrate for the first time that proteomic analysis of CSF yields individual biomarkers with greater sensitivity in the identification of cancer than does CSF cytology. We propose that the discovery of CSF protein biomarkers will facilitate early and noninvasive diagnosis in patients with lesions not amenable to brain biopsy, as well as provide improved surrogates of prognosis and treatment response in CNS lymphoma and brain metastasis.
Scatter Search for the Point-Matching Problem in 3D Image Registration
Authors: Cordón Oscar , Damas Sergio , Santamaría Jose , Martí Rafael 
Published: December 2007

Scatter search is a population-based method that has recently been shown to yield promising outcomes for solving combinatorial and nonlinear optimization problems. Based on formulations originally proposed in the 1960s for combining decision rules and problem constraints, such as the surrogate constraint method, scatter search uses strategies for combining solution vectors that have proved effective in a variety of problem settings. We present a scatter-search implementation designed to find high-quality solutions for the 3D image-registration problem, which has many practical applications. This problem arises in computer vision applications when finding a correspondence or transformation between two computer images obtained under different conditions. Our implementation goes beyond a simple exercise on applying scatter search, by incorporating innovative mechanisms to combine and improve solutions and to create a balance between intensification and diversification in the reference set. Furthermore, heuristic information taken from a preprocessing of the images is incorporated into the algorithm to improve its performance. Our computational experimentation tackling two different medical registration applications establishes the effectiveness of scatter search in relation to different approaches usually applied to solving the problem. We have considered both simulated magnetic resonance images and real-world computerized tomography images as data sets. To measure the robustness of our proposal, the image data sets are intentionally selected for addressing registration environments with the presence of noise, anatomical lesions, and occlusions between images.
Detection of Toxoplasma gondii-like oocysts in cat feces and estimates of the environmental oocyst burden
Authors: Dabritz Haydee A. , Miller Melissa A. , Atwill E. Robert , Gardner Ian A. , Leutenegger Christian M. , Melli Ann C. , Conrad Patricia A. 
Published: December 2007

Abstract
Objective—To estimate the analytic sensitivity of microscopic detection of Toxoplasma gondii oocysts and the environmental loading of T gondii oocysts on the basis of prevalence of shedding by owned and unowned cats.
Design—Cross-sectional survey.
Sample Population—326 fecal samples from cats.
Procedures—Fecal samples were collected from cat shelters, veterinary clinics, cat-owning households, and outdoor locations and tested via ZnSO4 fecal flotation.
Results—Only 3 (0.9%) samples of feces from 326 cats in the Morro Bay area of California contained T gondii–like oocysts. On the basis of the estimated tonnage of cat feces deposited outdoors in this area, the annual burden in the environment was estimated to be 94 to 4,671 oocysts/m2 (9 to 434 oocysts/ft2).
Conclusions and Clinical Relevance—Despite the low prevalence and short duration of T gondii oocyst shedding by cats detected in the present and former surveys, the sheer numbers of oocysts shed by cats during initial infection could lead to substantial environmental contamination. Veterinarians may wish to make cat owners aware of the potential threats to human and wildlife health posed by cats permitted to defecate outdoors.
Risk factors for excessive tibial plateau angle in large-breed dogs with cranial cruciate ligament disease
Authors: Duerr Felix M. , Duncan Colleen G. , Savicky Roman S. , Park Richard D. , Egger Erick L. , Palmer Ross H. 
Published: December 2007

Abstract
Objective—To identify risk factors for development of excessive tibial plateau angle (TPA) in large-breed dogs with cranial cruciate ligament disease (CCLD).
Design—Case-control study.
Animals—58 dogs with excessive TPAs (ie, TPA ≥ 35°; case dogs) and 58 dogs with normal TPAs (ie, TPA ≤ 30°; control dogs).
Procedures—Medical records and radiographs were reviewed and owners were interviewed to identify potential risk factors for excessive TPA.
Results—Case dogs were 3 times (95% confidence interval, 1.2 to 8.0) as likely to have been neutered before 6 months of age as were control dogs. Case dogs with TPA ≥ 35° in both limbs were 13.6 times (95% confidence interval, 2.72 to 68.1) as likely to have been neutered before 6 months of age as were control dogs with TPA ≤ 30° in both limbs. Case dogs were significantly younger at the onset of hind limb lameness than were control dogs.
Conclusions and Clinical Relevance—Results suggested that early neutering was a significant risk factor for development of excessive TPA in large-breed dogs with CCLD. Further research into the effects of early neutering on TPA and the pathophysiology of CCLD is warranted.
A field study of the effects of a monovalent Leptospira borgpetersenii serovar Hardjo strain hardjobovis vaccine administered with oxytetracycline on reproductive performance in beef cattle
Authors: Kasimanickam Ramanathan , Whittier William D. , Collins Jonathan C. , Currin John F. , Inman Bom , Hall John B. , Pelzer Kevin D. 
Published: December 2007

Abstract
Objective—To determine whether vaccination with a monovalent Leptospira borgpetersenii serovar Hardjo strain hardjobovis vaccine coupled with parenteral long-acting oxytetracycline treatment would improve the reproductive performance of beef cows.
Design—Randomized controlled field trial.
Animals—1,446 Angus-cross beef cows in 8 locations.
Procedures—Cows were given 2 doses, 4 weeks apart, of vaccine (treatment; n = 741) or placebo (control; 705). Cows in the treatment group were also given a single dose of a longacting oxytetracycline formulation (20 mg/kg [9.1 mg/lb], SC) at the time of booster vaccination. Estrus synchronization was performed, followed by fixed-time artificial insemination; bulls were introduced 14 days after insemination. Serum and urine samples were obtained on a random subset of cows (n = 194) for detection of serologic titers and leptospiruria, and locations were categorized as positive or negative for leptospirosis on the basis of detection of leptospiruric cows.
Results—No differences in pregnancy and calving rates between treatment and control groups were detected. Pregnancy rate following artificial insemination was lower among cows in locations positive for leptospirosis than among cows in locations negative for leptospirosis; however, overall pregnancy rate, calving rate following artificial insemination, and overall calving rate did not differ between groups when cows were grouped on the basis of location leptospirosis status.
Conclusions and Clinical Relevance—Results suggested that under the conditions of the present study, administration of a monovalent Leptospira vaccine in conjunction with systemic administration of oxytetracycline did not significantly improve reproductive performance of beef cows.
An outbreak of dictyocaulosis in lactating cows on a dairy farm
Authors: Wapenaar Wendela , Barkema Herman W. , Eysker Maarten , O'Handley Ryan M. 
Published: December 2007

Abstract
Case Description—The owner of a herd of 74 Holstein-Friesian cattle reported decreased milk production, weight loss, and coughing among lactating cows. Owner-initiated antimicrobial treatment was unsuccessful; 1 lactating cow died, and 50% of the lactating cows had clinical signs of respiratory distress, such as tachypnea and coughing.
Clinical Findings—On the basis of history, physical examination findings, and fecal examination results, affected animals were determined to have Dictyocaulus viviparus (lungworm) infestation. The disease history suggested that the herd contained cows with subclinical patent lungworm infestations; after introduction of susceptible heifers, the pastures had become heavily infested with D viviparus and clinical problems subsequently developed in both newly introduced and resident cows.
Treatment and Outcome—Affected and unaffected heifers and adult cows were treated with a pour-on formulation of eprinomectin (0.5 mg/kg [0.23 mg/lb]). One animal died, but 2 weeks after treatment, clinical signs among affected cattle were markedly improved. Ten weeks after treatment, milk production improved from 23 kg/cow/d (51 lb/cow/d) to 28 kg/cow/d (62 lb/cow/d).
Clinical Relevance—The outbreak provides additional evidence that dictyocaulosis is becoming more common among adult dairy cattle, rather than almost exclusively affecting young stock. This may be attributable to anthelmintic use and management practices on dairy farms. Combined with anecdotal reports of an increase in the incidence of dictyocaulosis among adult cattle in North America, D viviparus infestation should be included as a differential diagnosis for decreased milk production, weight loss, and coughing among adult dairy cattle.
Anatomy for biomedical engineers
Authors: Carmichael Stephen W. , Robb Richard A. 
Published: December 2007

AbstractThere is a perceived need for anatomy instruction for graduate students enrolled in a biomedical engineering program. This appeared especially important for students interested in and using medical images. These students typically did not have a strong background in biology. The authors arranged for students to dissect regions of the body that were of particular interest to them. Following completion of all the dissections, the students presented what they had learned to the entire class in the anatomy laboratory. This course has fulfilled an important need for our students. Anat Sci Ed 1:90–91, 2008. © 2007 American Association of Anatomists.