bluuebunny/crossref_metadata_2025_split huggingface dataset:
Goal attainment scaling: a direct comparison of alternative rating methods
Authors: Turner-Stokes Lynne , Williams Heather 
Published: December 2009

Purpose: To compare two alternative rating systems for goal attainment scaling (GAS) intended to improve capture of goal underachievement. Setting: A tertiary inpatient neurorehabilitation unit. Design: Secondary comparative analysis of prospective cohort data. Participants: A total of 243 patients were included, with 977 goals between them; M:F ratio 146:97, mean age 44.8 (SD 14.2) years. Diagnosis: 200 (82%) acquired brain injury, 21 (9%) spinal cord injury, 22 (9%) other neurological conditions. Methods: Goal attainment scaling-rated achievement of 1—6 patient-selected goals was collected using the standard 5-point scale (—2 to +2) and formula to derive aggregated T-scores, as recommended by its originators. Two alternative 6-point rating systems were applied retrospectively. Version 1 set all baseline scores at ‘—2’ and added ‘—3’ to denote ‘worsening’. Version 2 added a ‘—0.5’ score to denote ‘partial achievement’ for goals starting at ‘—1’, without change to range or baseline scores. Results: Baseline scores were identical for standard rating and version 2 (median 34.9, interquartile range (IQR) 31.9—35.5), but lower for version 1 (median 21.0, IQR 19.8—22.6), which was reflected in the change scores. While median achieved T-scores were 50.0 for all three methods, version 2 marginally overestimated goal attainment (Wilcoxon z —6.8, P<0.001), while version 1 underestimated it (Wilcoxon z —7.2, P<0.001), in comparison with standard goal rating. Conclusion: Different goal rating methods may have significant impact on goal attainment scaling results. Version 2 provided the closest match to standard rating, supporting documentation of partial goal achievement without affecting score range. For analysis and reporting, ‘0.5’ scores should be converted to ‘—1’, to maintain parity with standard rating systems.
Mislocalization of SLP-76 leads to aberrant inflammatory cytokine and autoantibody production
Authors: Sonnenberg Gregory F. , Mangan Paul R. , Bezman Natalie A. , Sekiguchi Debora R. , Luning Prak Eline T. , Erikson Jan , Maltzman Jonathan S. , Jordan Martha S. , Koretzky Gary A. 
Published: December 2009

Abstract
Central and peripheral tolerance is required to prevent immune responses to self-antigens. We now present a mouse model in which wild-type (WT) SH2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76) has been constitutively targeted to the membrane, where CD4+ T cells become spontaneously dysregulated and develop an inflammatory phenotype. Mice bearing membrane-targeted SLP-76 (MTS) have a partial T-cell lymphopenia and impaired signaling though the mature T-cell receptor. The CD4+ T cells that develop in these mice possess an activated-like phenotype and are skewed toward the inflammatory TH1 and TH17 lineages. MTS mice also spontaneously develop autoantibodies at an early age. To rule out abnormal thymic selection as the sole cause of the MTS phenotype, we expressed WT SLP-76 along with the MTS followed by deletion of the WT allele in peripheral T cells. The peripheral MTS-expressing T cells demonstrate skewed cytokine responses when transferred into lymphopenic hosts. Thus, the abnormal effector T-cell phenotype still occurs in the presence of preserved central and peripheral tolerance, suggesting that diminished T-cell receptor signaling can promote skewed T-cell responses.
In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana
Authors: Nero Damion , Katari Manpreet S , Kelfer Jonathan , Tranchina Daniel , Coruzzi Gloria M 
Published: December 2009

Abstract

Background
Prediction of transcriptional regulatory mechanisms in Arabidopsis has become increasingly critical with the explosion of genomic data now available for both gene expression and gene sequence composition. We have shown in previous work [1], that a combination of correlation measurements and cis-regulatory element (CRE) detection methods are effective in predicting targets for candidate transcription factors for specific case studies which were validated. However, to date there has been no quantitative assessment as to which correlation measures or CRE detection methods used alone or in combination are most effective in predicting TF→target relationships on a genome-wide scale.

Results
We tested several widely used methods, based on correlation (Pearson and Spearman Rank correlation) and cis- regulatory element (CRE) detection (≥1 CRE or CRE over-representation), to determine which of these methods individually or in combination is the most effective by various measures for making regulatory predictions. To predict the regulatory targets of a transcription factor (TF) of interest, we applied these methods to microarray expression data for genes that were regulated over treatment and control conditions in wild type (WT) plants. Because the chosen data sets included identical experimental conditions used on TF over-expressor or T-DNA knockout plants, we were able to test the TF→target predictions made using microarray data from WT plants, with microarray data from mutant/transgenic plants. For each method, or combination of methods, we computed sensitivity, specificity, positive and negative predictive value and the F-measure of balance between sensitivity and positive predictive value (precision). This analysis revealed that the ≥1 CRE and Spearman correlation (used alone or in combination) were the most balanced CRE detection and correlation methods, respectively with regard to their power to accurately predict regulatory-target interactions.

Conclusion
These findings provide an approach and guidance for researchers interested in predicting transcriptional regulatory mechanisms using microarray data that they generate (or microarray data that is publically available) combined with CRE detection in promoter sequence data.
Functional diversity of human protein kinase splice variants marks significant expansion of human kinome
Authors: Anamika Krishanpal , Garnier Nicolas , Srinivasan Narayanaswamy 
Published: December 2009

Abstract

Background
Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants.

Results
Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways.

Conclusions
Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.
IL-15 Prevents Apoptosis, Reverses Innate and Adaptive Immune Dysfunction, and Improves Survival in Sepsis
Authors: Inoue Shigeaki , Unsinger Jacqueline , Davis Christopher G. , Muenzer Jared T. , Ferguson Thomas A. , Chang Katherine , Osborne Dale F. , Clark Andrew T. , Coopersmith Craig M. , McDunn Jonathan E. , Hotchkiss Richard S. 
Published: December 2009

Abstract
IL-15 is a pluripotent antiapoptotic cytokine that signals to cells of both the innate and adaptive immune system and is regarded as a highly promising immunomodulatory agent in cancer therapy. Sepsis is a lethal condition in which apoptosis-induced depletion of immune cells and subsequent immunosuppression are thought to contribute to morbidity and mortality. This study tested the ability of IL-15 to block apoptosis, prevent immunosuppression, and improve survival in sepsis. Mice were made septic using cecal ligation and puncture or Pseudomonas aeruginosa pneumonia. The experiments comprised a 2 × 2 full factorial design with surgical sepsis versus sham and IL-15 versus vehicle. In addition to survival studies, splenic cellularity, canonical markers of activation and proliferation, intracellular pro- and antiapoptotic Bcl-2 family protein expression, and markers of immune cell apoptosis were evaluated by flow cytometry. Cytokine production was examined both in plasma of treated mice and splenocytes that were stimulated ex vivo. IL-15 blocked sepsis-induced apoptosis of NK cells, dendritic cells, and CD8 T cells. IL-15 also decreased sepsis-induced gut epithelial apoptosis. IL-15 therapy increased the abundance of antiapoptotic Bcl-2 while decreasing proapoptotic Bim and PUMA. IL-15 increased both circulating IFN-γ, as well as the percentage of NK cells that produced IFN-γ. Finally, IL-15 increased survival in both cecal ligation and puncture and P. aeruginosa pneumonia. In conclusion, IL-15 prevents two immunopathologic hallmarks of sepsis, namely, apoptosis and immunosuppression, and improves survival in two different models of sepsis. IL-15 represents a potentially novel therapy of this highly lethal disorder.
IL-8 Dictates Glycosaminoglycan Binding and Stability of IL-18 in Cystic Fibrosis
Authors: Reeves Emer P. , Williamson Michael , Byrne Barry , Bergin David A. , Smith Stephen G. J. , Greally Peter , O’Kennedy Richard , O’Neill Shane J. , McElvaney Noel G. 
Published: December 2009

Abstract
Dysregulation of airway inflammation contributes to lung disease in cystic fibrosis (CF). Inflammation is mediated by inflammatory cytokines, including IL-8, which illustrates an increase in biological half-life and proinflammatory activity when bound to glycosaminoglycans (GAGs). The aim of this project was to compare IL-8 and IL-18 for their relative stability, activity, and interaction with GAGs, including chondroitin sulfate, hyaluronic acid, and heparan sulfate, present in high quantities in the lungs of patients with CF. Bronchoalveolar lavage fluid was collected from patients with CF (n = 28), non-CF controls (n = 14), and patients with chronic obstructive pulmonary disease (n = 12). Increased levels of IL-8 and reduced concentrations of IL-18 were detected in bronchial samples obtained from CF individuals. The low level of IL-18 was not a defect in IL-18 production, as the pro- and mature forms of the molecule were expressed and produced by CF epithelial cells and monocytes. There was, however, a marked competition between IL-8 and IL-18 for binding to GAGs. A pronounced loss of IL-18 binding capacity occurred in the presence of IL-8, which displaced IL-18 from these anionic-matrices, rendering the cytokine susceptible to proteolytic degradation by neutrophil elastase. As a biological consequence of IL-18 degradation, reduced levels of IL-2 were secreted by Jurkat T lymphocytes. In conclusion, a novel mechanism has been identified highlighting the potential of IL-8 to determine the fate of other inflammatory molecules, such as IL-18, within the inflammatory milieu of the CF lung.
Cutting Edge: Bortezomib-Treated Tumors Sensitized to NK Cell Apoptosis Paradoxically Acquire Resistance to Antigen-Specific T Cells
Authors: Lundqvist Andreas , Su Su , Rao Sheila , Childs Richard 
Published: December 2009

Abstract
Bortezomib augments caspase-8 activity, rendering tumors susceptible to NK cell lysis. We hypothesized this effect would likewise sensitize tumors to Ag-specific CTLs. Instead, bortezomib-treated tumors that acquired sensitivity to NK cells simultaneously became resistant to killing by Ag-specific CTLs. Reduction in CTL killing persisted for days, was not due to changes in tumor expression of MHC class I, and was overcome by pulsing tumors with peptides recognized by tumor-reactive CTLs. Tumor-outgrowth experiments showed tumors grew faster in SCID mice when cocultures of tumor-reactive CTLs and bortezomib-treated tumors were injected compared with untreated tumors (tumor doubling time 3.1 and 10.6 d, respectively; p &lt; 0.01), whereas tumors grew slower in mice receiving cocultures of NK cells and bortezomib-treated tumors compared with untreated tumors (11.8 d and 5.0 d, respectively; p &lt; 0.01). These findings demonstrate bortezomib-treated tumors sensitized to NK cell apoptosis paradoxically acquire resistance to CTLs as a consequence of bortezomib altering proteasomal processing and presentation of tumor Ags.
Mutually Aposyndetic Decomposition of Homogeneous Continua
Authors: Prajs Janusz R. 
Published: December 2009

AbstractA new decomposition, the mutually aposyndetic decomposition of homogeneous continua into closed, homogeneous sets is introduced. This decomposition is respected by homeomorphisms and topologically unique. Its quotient is a mutually aposyndetic homogeneous continuum, and in all known examples, as well as in some general cases, the members of the decomposition are semiindecomposable continua. As applications, we show that hereditarily decomposable homogeneous continua and path connected homogeneous continua are mutually aposyndetic. A class of new examples of homogeneous continua is defined. The mutually aposyndetic decomposition of each of these continua is non-trivial and different from Jones’ aposyndetic decomposition.
A Highly Diastereoselective Tertiary Amine‐Catalyzed Cascade Michael–Michael–Henry Reaction between Nitromethane, Activated Alkenes and α,β‐Unsaturated Carbonyl Compounds
Authors: Zhang Bo , Cai Lingchao , Song Haibin , Wang Zhihong , He Zhengjie 
Published: December 2009

AbstractA new tertiary amine‐catalyzed cascade Michael–Michael–Henry reaction between nitromethane, a doubly activated alkene and an α,β‐unsaturated carbonyl compound is described, which provides a convenient and efficient synthesis for densely functionalized cyclohexanes and some bicyclic compounds in moderate to excellent yields with high diastereoselectivity.
Fluid‐particle drag in inertial polydisperse gas–solid suspensions
Authors: Holloway William , Yin Xiaolong , Sundaresan Sankaran 
Published: December 2009

AbstractIn this article, we extend the low Reynolds number fluid‐particle drag relation proposed by Yin and Sundaresan for polydisperse systems to include the effect of moderate fluid inertia. The proposed model captures the fluid‐particle drag results obtained from lattice‐Boltzmann simulations of bidisperse and ternary suspensions at particle mixture Reynolds numbers ranging from 0 ≤ Remix ≤ 40, over a particle volume fraction range of 0.2 ≤ ϕ ≤ 0.4, volume fraction ratios of 1 ≤ ϕi/ϕj ≤ 3, and particle diameter ratios of 1 ≤ di/dj ≤ 2.5. © 2009 American Institute of Chemical Engineers AIChE J, 2010
Additive‐Multiplicative Regression Models for Spatio‐Temporal Epidemics
Authors: Höhle Michael 
Published: December 2009

AbstractAn extension of the stochastic susceptible–infectious–recovered (SIR) model is proposed in order to accommodate a regression context for modelling infectious disease data. The proposal is based on a multivariate counting process specified by conditional intensities, which contain an additive epidemic component and a multiplicative endemic component. This allows the analysis of endemic infectious diseases by quantifying risk factors for infection by external sources in addition to infective contacts. Inference can be performed by considering the full likelihood of the stochastic process with additional parameter restrictions to ensure non‐negative conditional intensities. Simulation from the model can be performed by Ogata's modified thinning algorithm. As an illustrative example, we analyse data provided by the Federal Research Centre for Virus Diseases of Animals, Wusterhausen, Germany, on the incidence of the classical swine fever virus in Germany during 1993–2004.
Decrease of adenosine deaminase activity and increase of the lipid peroxidation after acute methotrexate treatment in young rats: protective effects of grape seed extract
Authors: Pinheiro F. V. , Pimentel V. C. , De Bona K. S. , Scola G. , Salvador M. , Funchal C. , Moretto M. B. 
Published: December 2009

AbstractThe methotrexate (MTX) is an anti‐folate used to treat cancer and some inflammatory diseases. The efficacy of MTX is often limited by its severe toxicity. The present study was undertaken to determine whether Grape seed (Cabernet Sauvignon) extract (GSE) could ameliorate the MTX‐induced oxidative injury and the effect on adenosine deaminase activity (ADA) in rats. The rats were pretreated with 50 mg/kg of GSE, i.p., prior to MTX administration (10 mg/kg, i.p.) with a second dose given 4 h and a third dose 16 h after MTX administration. Biochemical parameters were investigated 48 h after the last MTX administration. The administration of MTX increased thiobarbituric acid reactive species (TBARS) levels in hippocampus, kidney and liver, whereas induced a significant decreased in the ADA activity in the cerebral cortex, kidney and liver tissues. MTX administration significantly increased the activity of ALT(alanine aminotransferase) and urea levels and decreased uric acid levels in the serum. Urinary uric acid levels decreased in the MTX group when compared to those of the control group. The GSE along with MTX‐administration significantly reversed these parameters toward to near normal. These results indicated that GSE could reduce hepatic and nephritic damage induced by MTX‐treatment in young rats therefore having free radical scavenging. Copyright © 2009 John Wiley & Sons, Ltd.
A diagonal measure and a local distance matrix to display relations between objects and variables
Authors: Tóth Gergely , Szepesváry Pál 
Published: December 2009

AbstractProper permutation of data matrix rows and columns may result in plots showing striking information on the objects and variables under investigation. To control the permutation first, a diagonal matrix measure D was defined expressing the size relations of the matrix elements. D is essentially the absolute norm of a matrix where the matrix elements are weighted by their distance to the matrix diagonal. Changing the order of rows and columns increases or decreases D. Monte Carlo technique was used to achieve maximum D in the case of the object distance matrix or even minimal D in the case of the variable correlation matrix to get similar objects or variables close together. Secondly, a local distance matrix was defined, where an element reflects the distances of neighboring objects in a limited subspace of the variables. Due to the maximization of D in the local distance matrix by row and column changes of the original data matrix, the similar objects were arranged close to each other and simultaneously the variables responsible for their similarity were collected close to the diagonal part defined by these objects. This combination of the diagonal measure and the local distance matrix seems to be an efficient tool in the exploration of hidden similarities of a data matrix. Copyright © 2009 John Wiley & Sons, Ltd.
Sandwich Compounds of Transition Metals with Cyclopolyenes and Isolobal Boron Analogues
Authors: Gribanova Tatyana N. , Starikov Andrey G. , Minyaev Ruslan M. , Minkin Vladimir I. , Siebert Matthew R. , Tantillo Dean J. 
Published: December 2009

AbstractA series of sandwich compounds of transition metals (M=Ni, Fe, Cr) with cyclic hydrocarbon (M(CH)n) and borane (M(BH2)n), ligands (including mixed hydrocarbon/borane sandwiches) has been studied using density functional theory (B3LYP/6‐311+G(df,p)). Multicenter bonding between the central metal atom and basal cycloborane rings provides stabilization to planar cycloborane species. Large negative NICS values allude to aromatic character in the cycloboranes similar to the analogous cyclic hydrocarbons. The ability of cycloborane sandwiches to stabilize attached carbocations, radicals and carbanions is also assessed.
A Singularity Model for Chemical Reactivity
Authors: Menger Fredric M. , Karaman Rafik 
Published: December 2009

AbstractThis article proposes a model for chemical reactivity that involves singularities (“catastrophes”) in the timing of bond‐making and bond‐breaking events. The common stapler is a good mechanical analogy: As hand‐pressure is increased on the machine, the staple hardly changes its configuration until the staple suddenly bends. This is viewed as a singularity or catastrophe, defined classically as an abrupt change resulting from a smooth increase or decrease in external conditions (pressure in the case of a stapler, distance in the case of reactivity). Although experimental observations are provided to support the singularity effect, the model remains a heterodox notion at the present time.
Cervical cancer incidence among 6 Asian ethnic groups in the United States, 1996 through 2004
Authors: Wang Sophia S. , Carreon J. Daniel , Gomez Scarlett L. , Devesa Susan S. 
Published: December 2009

AbstractBACKGROUND:Cervical cancer incidence was evaluated by histologic type, age at diagnosis, and disease stage for 6 Asian ethnic groups residing in the United States.METHODS:Incidence rates were estimated for cervical squamous cell carcinoma (SCC) and adenocarcinoma by age and stage for 6 Asian ethnic groups—Asian Indian/Pakistani, Chinese, Filipino, Japanese, Korean, and Vietnamese—in 5 US cancer registry areas during 1996 through 2004. For comparison, rates among non‐Hispanic whites, non‐Hispanic blacks, and Hispanics were also calculated.RESULTS:During 1996 through 2004, Vietnamese women had the highest (18.9 per 100,000) and Asian Indian/Pakistani women had the lowest (4.5) incidence of cervical cancer; this pattern was consistent by histologic type. Vietnamese women also had the highest incidence for localized (7.3) and regional (5.7) SCC and for localized (2.4) adenocarcinoma. Contrary to the plateau of SCC incidence apparent among white women by age 45 years, SCC rates continued to rise with age among Chinese, Filipina, Korean, and Vietnamese women.CONCLUSIONS:There exists large variation in invasive cervical cancer incidence patterns among Asian ethnic groups in the United States and in comparison with rates for blacks, Hispanics, and whites. Early detection and prevention strategies for cervical cancer among Asians require targeted strategies by ethnic group. Cancer 2010. Published 2010 by the American Cancer Society.
Angiogenesis and vascular targeting in Ewing sarcoma
Authors: DuBois Steven G. , Marina Neyssa , Glade‐Bender Julia 
Published: December 2009

AbstractEwing sarcoma is the second most common type of bone cancer in children and young adults. In recent years, the mechanisms by which these tumors develop and maintain their vascular supply have been elucidated. Additional work has demonstrated that inhibition of angiogenic pathways or disruption of established vasculature can attenuate the growth of Ewing sarcoma mouse xenografts. Early clinical data suggest that these results also may extend to patients with Ewing sarcoma who are treated with antiangiogenic or antivascular therapies. For the current review, the authors summarized the available data supporting this approach. Cancer 2010. © 2009 American Cancer Society.