bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Authors: Haas Brian J , Salzberg Steven L , Zhu Wei , Pertea Mihaela , Allen Jonathan E , Orvis Joshua , White Owen , Buell C Robin , Wortman Jennifer R 
Published: February 2008

AbstractEVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
The role of educational track in adolescents' school burnout: A longitudinal study
Authors: Salmela‐Aro Katariina , Kiuru Noona , Nurmi Jari‐Erik 
Published: February 2008

BackgroundTransition from comprehensive school to later educational tracks is challenging for many adolescents. The present three‐wave longitudinal study conducted in Finland considers this issue from the perspective of school burnout.AimsThe study investigated the extent to which school‐related burnout (exhaustion, cynicism, and feelings of inadequacy) changes during the transition from comprehensive school to an academic or vocational track.SampleThe participants of the present study were 658 ninth graders, who filled in questionnaires twice during their final term of comprehensive school and once after the transition to post‐comprehensive schooling.MethodsThe participants filled in the school burnout inventory and supplied background information on gender and academic achievement. The data have analysed by latent growth curve modelling.ResultsThe results showed that adolescents on an academic track experienced more exhaustion at school than those on a vocational track. Moreover, among adolescents on an academic track both the level of cynicism and inadequacy at school increased across time. In turn, among adolescents on a vocational track inadequacy at school decreased across time while cynicism increased before the school transition and decreased thereafter. Girls experienced more overall school burnout than boys, and adolescents whose academic achievement was lower experienced a higher level of burnout than adolescents who did better at school.ConclusionsThe results support the stage‐environment fit theory according to which the nature of the environments in academic and vocational education are more important than the transitionper sefor changes in how adolescents think and feel about school (seeEccles & Midgley, 1989).
Bias in Sensitivity and Specificity Caused by Data-Driven Selection of Optimal Cutoff Values: Mechanisms, Magnitude, and Solutions
Authors: Leeflang Mariska M G , Moons Karel G M , Reitsma Johannes B , Zwinderman Aielko H 
Published: February 2008

Abstract
Background: Optimal cutoff values for tests results involving continuous variables are often derived in a data-driven way. This approach, however, may lead to overly optimistic measures of diagnostic accuracy. We evaluated the magnitude of the bias in sensitivity and specificity associated with data-driven selection of cutoff values and examined potential solutions to reduce this bias.
Methods: Different sample sizes, distributions, and prevalences were used in a simulation study. We compared data-driven estimates of accuracy based on the Youden index with the true values and calculated the median bias. Three alternative approaches (assuming a specific distribution, leave-one-out, smoothed ROC curve) were examined for their ability to reduce this bias.
Results: The magnitude of bias caused by data-driven optimization of cutoff values was inversely related to sample size. If the true values for sensitivity and specificity are both 84%, the estimates in studies with a sample size of 40 will be approximately 90%. If the sample size increases to 200, the estimates will be 86%. The distribution of the test results had little impact on the amount of bias when sample size was held constant. More robust methods of optimizing cutoff values were less prone to bias, but the performance deteriorated if the underlying assumptions were not met.
Conclusions: Data-driven selection of the optimal cutoff value can lead to overly optimistic estimates of sensitivity and specificity, especially in small studies. Alternative methods can reduce this bias, but finding robust estimates for cutoff values and accuracy requires considerable sample sizes.
Pervious Concrete Mixture Proportions for Improved Freeze-Thaw Durability
Authors: Kevern J. T. , Schaefer V. R. , Wang K. , Suleiman M. T. 
Published: February 2008

Abstract
Recent stormwater management regulations from the Environmental Protection Agency (EPA) and greater emphasis on sustainable development has increased interest in pervious pavement as a method for reducing stormwater runoff and improving stormwater quality. Pervious concrete is one of several pervious pavement systems that can be used to reduce stormwater runoff and treat stormwater on site. Pervious concrete systems have been used and are being proposed for all parts of the United States, including northern climates where severe freezing and thawing can occur. The purpose of the research is to develop pervious concrete mixtures that have sufficient porosity for stormwater infiltration along with desirable porosity, strength, and freeze-thaw durability. In this research, concrete mixtures were developed with single-sized river gravel aggregate (4.75 mm) and constant binder contents, together with high range water reducer. River sand was used as a replacement for up to 7 % coarse aggregate. Two different types of polypropylene fibers (a shorter fibrillated variable-length and a longer fibrillated single-length) were incorporated at several addition rates from 0 to 0.1 % by volume of concrete. The engineering properties of the aggregate were evaluated along with the porosity, permeability, strength, and freeze-thaw durability of selected concrete mixtures. The results indicate that the use of sand and fibers provided beneficial effects on pervious concrete properties, including increased strength, maintained or improved permeability, and enhanced freeze-thaw resistance.
Why Southern Gospel Music Matters
Authors: Harrison Douglas 
Published: February 2008

AbstractLong overlooked by scholars of culture and religion, southern (white) gospel music occupies a special place within evangelicalism. The dynamic interaction of lyrics, music, and religious experience in southern gospel music comprises a cultural discourse evangelicals use, not to diminish experience in this world as is commonly argued in southern gospel studies, but to understand better Protestant theological doctrines in, and to make useable meaning out of, the vicissitudes of conservative Christian life. This approach treats southern gospel as a network of interconnected rhetorics and signifying practices that serve a multitude of public and private needs among its performers and fans—needs that are not otherwise met in evangelical culture. Particularly, southern gospel music allows those who participate in it to explore a broader and deeper range of psychospiritual feelings and experiences. The study of southern gospel reveals the importance of private conflicts and tensions in defining the contours of conservative Protestant religious living, individually and collectively. For the millions of evangelicals today who turn regularly and eagerly to southern gospel, their identity as a covenanted elect emerges from within the struggle to manage and resolve spiritual disquietude through the experience of white gospel music.
Tumor Necrosis Factor-α Inhibition of Skeletal Muscle Regeneration Is Mediated by a Caspase-Dependent Stem Cell Response
Authors: Moresi Viviana , Pristerà Alessandro , Scicchitano Bianca M. , Molinaro Mario , Teodori Laura , Sassoon David , Adamo Sergio , Coletti Dario 
Published: February 2008

Abstract
Skeletal muscle is susceptible to injury following trauma, neurological dysfunction, and genetic diseases. Skeletal muscle homeostasis is maintained by a pronounced regenerative capacity, which includes the recruitment of stem cells. Chronic exposure to tumor necrosis factor-α (TNF) triggers a muscle wasting reminiscent of cachexia. To better understand the effects of TNF upon muscle homeostasis and stem cells, we exposed injured muscle to TNF at specific time points during regeneration. TNF exposure delayed the appearance of regenerating fibers, without exacerbating fiber death following the initial trauma. We observed modest cellular caspase activation during regeneration, which was markedly increased in response to TNF exposure concomitant with an inhibition in regeneration. Caspase activation did not lead to apoptosis and did not involve caspase-3. Inhibition of caspase activity improved muscle regeneration in either the absence or the presence of TNF, revealing a nonapoptotic role for this pathway in the myogenic program. Caspase activity was localized to the interstitial cells, which also express Sca-1, CD34, and PW1. Perturbation of PW1 activity blocked caspase activation and improved regeneration. The restricted localization of Sca-1+, CD34+, PW1+ cells to a subset of interstitial cells with caspase activity reveals a critical regulatory role for this population during myogenesis, which may directly contribute to resident muscle stem cells or indirectly regulate stem cells through cell-cell interactions.
Disclosure of potential conflicts of interest is found at the end of this article.
Sustained Endothelial Progenitor Cell Dysfunction After Chronic Hypoxia-Induced Pulmonary Hypertension
Authors: Marsboom Glenn , Pokreisz Peter , Gheysens Olivier , Vermeersch Pieter , Gillijns Hilde , Pellens Marijke , Liu Xiaoshun , Collen Désiré , Janssens Stefan 
Published: February 2008

Abstract
Circulating endothelial progenitor cells (EPCs) contribute to neovascularization of ischemic tissues and repair of injured endothelium. The role of bone marrow-derived progenitor cells in hypoxia-induced pulmonary vascular remodeling and their tissue-engineering potential in pulmonary hypertension (PH) remain largely unknown. We studied endogenous mobilization and homing of EPCs in green fluorescent protein bone marrow chimeric mice exposed to chronic hypoxia, a common hallmark of PH. Despite increased peripheral mobilization, as shown by flow cytometry and EPC culture, bone marrow-derived endothelial cell recruitment in remodeling lung vessels was limited. Moreover, transfer of vascular endothelial growth factor receptor-2+/Sca-1+/CXCR-4+-cultured early-outgrowth EPCs failed to reverse PH, suggesting hypoxia-induced functional impairment of transferred EPCs. Chronic hypoxia decreased migration to stromal cell-derived factor-1α, adhesion to fibronectin, incorporation into a vascular network, and nitric oxide production (−41%, −29%, −30%, and −32%, respectively, vs. normoxic EPCs; p &lt; .05 for all). The dysfunctional phenotype of hypoxic EPCs significantly impaired their neovascularization capacity in chronic hind limb ischemia, contrary to normoxic EPCs cultured in identical conditions. Mechanisms contributing to EPC dysfunction include reduced integrin αv and β1 expression, decreased mitochondrial membrane potential, and enhanced senescence. Novel insights from chronic hypoxia-induced EPC dysfunction may provide important cues for improved future cell repair strategies.
Disclosure of potential conflicts of interest is found at the end of this article.
Hedgehog Signaling Alters Adipocyte Maturation of Human Mesenchymal Stem Cells
Authors: Fontaine Coralie , Cousin Wendy , Plaisant Magali , Dani Christian , Peraldi Pascal 
Published: February 2008

Abstract
Human stem cells are powerful tools by which to investigate molecular mechanisms of cell growth and differentiation under normal and pathological conditions. Hedgehog signaling, the dysregulation of which causes several pathologies, such as congenital defects and cancer, is involved in several cell differentiation processes and interferes with adipocyte differentiation of rodent cells. The present study was aimed at investigating the effect of Hedgehog pathway modulation on adipocyte phenotype using different sources of human mesenchymal cells, such as bone marrow stromal cells and human multipotent adipose-derived stem cells. We bring evidence that Hedgehog signaling decreases during human adipocyte differentiation. Inhibition of this pathway is not sufficient to trigger adipogenesis, but activation of Hedgehog pathway alters adipocyte morphology as well as insulin sensitivity. Analysis of glycerol-3-phosphate dehydrogenase activity and expression of adipocyte marker genes indicate that activation of Hedgehog signaling by purmorphamine impairs adipogenesis. In sharp contrast to reports in rodent cells, the maturation process, but not the early steps of human mesenchymal stem cell differentiation, is affected by Hedgehog activation. Hedgehog interferes with adipocyte differentiation by targeting CCAAT enhancer-binding protein α and peroxisome proliferator-activated receptor (PPAR) γ2 expression, whereas PPARγ1 level remains unaffected. Although Hedgehog pathway stimulation does not modify the total number of adipocytes, adipogenesis appears dramatically impaired, with reduced lipid accumulation, a decrease in adipocyte-specific markers, and acquisition of an insulin-resistant phenotype. This study indicates that a decrease in Hedgehog signaling is necessary but not sufficient to trigger adipocyte differentiation and unveils a striking difference in the adipocyte differentiation process between rodent and human mesenchymal stem cells.
Disclosure of potential conflicts of interest is found at the end of this article.
Introduction
Authors: Bunn Paul A. , Thatcher Nick 
Published: February 2008

Abstract
Lung cancer is the most common cancer and a highly lethal disease, with improvements in survival rates being dependent on advances in early detection and improved systemic therapies applied to surgery and/or irradiation in early-stage disease. Non-small cell lung cancer (NSCLC) represents around 80% of all lung cancers, and unfortunately at diagnosis most patients have advanced unresectable disease with a very poor prognosis. Indeed, 30%–40% of patients treated with first-line therapy will subsequently be candidates for second-line treatment. Current U.S. Food and Drug Administration–approved second-line treatments are docetaxel (a taxane), pemetrexed (a folate antimetabolite), and erlotinib (an epidermal growth factor receptor [EGFR] tyrosine kinase inhibitor [TKI]). Gefitinib, another EGFR TKI, currently has only limited use in North America and is not available in Europe. These and other new molecular-target-specific agents may have the potential to maximize therapeutic benefit while minimizing toxicity to normal cells. Overexpression of EGFR is reported to occur in 40%–80% of NSCLC cases, and EGFR mutations are associated with a significantly higher response rate and longer duration of response following treatment with EGFR TKIs. Another option is antiangiogenesis: the growth and persistence of solid tumors and their metastases are angiogenesis dependent, and so antiangiogenic therapies have been developed, such as the use of TKIs that block the vascular endothelial growth factor receptor. In fact, many commonly used chemotherapeutic drugs have antiangiogenic activity. Ongoing studies are focusing on patient selection and targeted therapies, and there are many new agents undergoing clinical trials.
Local Control of Regional and Metastatic Lesions and Indication for Systemic Chemotherapy in Patients with Non-Small Cell Lung Cancer
Authors: Sekine Ikuo , Sumi Minako , Saijo Nagahiro 
Published: February 2008

Abstract
Systemic chemotherapy is the mainstay of treatment in patients with advanced non-small cell lung cancer. Local control of regional and metastatic lesions may be needed before systemic therapy can be started in patients with pleural effusions or bone or brain metastases. The indication for systemic chemotherapy depends on the symptoms and performance status of the patient. In addition, a risk assessment considering complications such as hemodynamic and respiratory compromise by effusions, pathological bone fractures, and neurologic deterioration caused by brain metastases is critical in selecting which patients should receive first-line systemic chemotherapy before local therapy, although predictive factors for these complications have not yet been established. Chemotherapy has been considered to have only a limited role in the treatment of patients with pleural effusions and brain and bone metastases, but recently developed anticancer agents have shown substantial antitumor effects in these types of patients with a good general condition.
Running Training After Stroke: A Single-Subject Report
Authors: Miller Ellen W , Combs Stephanie A , Fish Caryn , Bense Brooke , Owens Amanda , Burch Andrea 
Published: February 2008

Background and PurposeAlthough many people who have had a stroke are primarily interested in learning to walk, some are able to focus on a return to recreational and sporting activities. This study was carried out to investigate the feasibility and effectiveness of the use of intensive task-oriented training in the body-weight–support/treadmill environment to improve running for a subject after stroke.SubjectThe subject was a 38-year-old man who had a stroke 2.5 years previously.MethodsA single-subject design with baseline, intervention, immediate postintervention, and 6-month postintervention phases was conducted. Dependent variables included 25-m sprint time, single-leg balance, running step width, running step length ratio, Stroke Impact Scale, 6-minute walk test, and lower-extremity strength (force-generating capacity).ResultsAt the 6-month postintervention phase, sprint speed, left single-leg balance, and step width changed significantly from the baseline phase. Step length ratio trended toward less symmetry but more consistency, and muscle strength improved more than 20% in 6 of 8 muscle groups in the involved lower extremity and 4 of 8 muscle groups in the uninvolved lower extremity.Discussion and ConclusionIntensive task-specific training was feasible and effective for retraining running ability in the study subject. He returned to recreational running, which provided him with a greatly improved outlook and a better quality of life.
The effect of the expansion of the clonal grass Calamagrostis epigejos on the species turnover of a semi‐arid grassland
Authors: Somodi Imelda , Virágh Klára , Podani János 
Published: February 2008

Question: How does the dominance of Calamagrostis epigejos influence species turnover of a grassland?Location: Loess grassland at the foothills of Bükk Mountains, Hungary (47°54’ N., 20°35’ E).Methods: Presence/absence of vascular plants and different performance attributes of C. epigejos were recorded in a plot‐subplot system between 2002 and 2005. Appearance and disappearance rates of grassland species were calculated for pairs of consecutive years. 1. Mean appearance and disappearance rates were compared in grassland plots dominated by C. epigejos and in plots free from this species, based on Monte Carlo randomization. 2. Mean appearance rates were assessed for categories of C. epigejos performance and their confidence intervals were calculated via Monte Carlo randomization. For two performance variables (percentage cover and shoot number) analyses were performed at two spatial scales.Results: 1. C. epigejos.‐dominated plots differed from unaffected ones by significantly lower appearance rates. 2. Change in appearance rates was best explained by differences in percentage cover of C. epigejos. Coarse‐scale C. epigejos performance had a closer correspondence with appearance rate change than fine‐scale performance. Low level C. epigejos performance enhanced appearance rate compared to intact stands, while high level performance decreased it, regardless of the choice of performance measure.Conclusions: C. epigejos lowers species number by hindering reappearance of species of the original grassland. This is best explained by the increased shading effect at the coarse scale. The marked non‐linear initial enhancement in appearance rate, however, can also be taken as an early sign of future species loss.
The suppression ofDendroctonus frontalisand subsequent wildfire have an impact on forest stand dynamics
Authors: Coleman T.W. , Meeker James R. , Clarke Stephen R. , Rieske L.K. 
Published: February 2008

Question:Interacting disturbance effects fromDendroctonus frontalisoutbreaks and wildfire are thought to maintainPinusspp. composition in the southeastern U. S. Our objective was to assess forest composition, structure, and succession following the interaction of two frequently occurring disturbance events in southernPinusspp. forests: cut‐and‐leave suppression, a commonly used means for managingD. frontalisoutbreaks, and wildfire.Location:Western Gulf Coastal Plain, Louisiana, USA.Method:Pinus taedastands with cut‐and‐leave suppression and subsequent wildfire were compared to stands undisturbed byD. frontalisbut with the same wildfire events twenty years afterPinusspp. mortality. The woody plant community was assessed in three different size classes and used to predict future forest types with the Forest Vegetation Simulator (50 years).Results:P. taedais the most abundant (> 50%) species of saw‐ and poletimber‐sizes following cut‐and‐leave suppression with wildfire and in stands only with fire. Using canonical correspondence analysis, vegetation assemblages were primarily explained by slope position and elevation (7.6% variation explained). Fire intensity and stand age also accounted for variance in the ordination (4.4% and 3.1%, respectively). Dominant and co‐dominantP. taedaforest types were predicted by the model to be the most abundant forest types in each disturbance regime. In addition, new regeneration represents high hazard for future mortality fromD. frontalis.Conclusion:Our study demonstrates that cut‐and‐leave suppression with additional wildfire disturbance maintainsP. taedacomposition, and does not alter forest composition differently from stands receiving only wildfire. As a result, predictedPinusspp. basal area under both disturbances is great enough to facilitate future bark beetle disturbance.
Cloning of Small RNA Molecules
Authors: Pfeffer Sébastien , Lagos‐Quintana Mariana , Tuschl Thomas 
Published: February 2008

AbstractSmall RNAs that are derived from dsRNA precursors act as guide RNAs during sequence‐specific epigenetic regulation of eukaryotic gene expression. These small regulatory RNAs are between 20 and 30 nucleotides in length, and fall into one or more of the following categories: small interfering RNAs (siRNAs), microRNAs (miRNAs), and heterochromatic siRNAs (hsiRNAs). Procedures to record the profile of small RNAs expressed in cultured cells or tissues are described. The small RNAs are directionally cloned after isolation from total RNA. The methods rely on T4 RNA ligase‐based joining of adapter oligonucleotides to the 3′ and 5′ termini of the pool of small RNAs. The ligation products are reverse transcribed and PCR‐amplified. It is recommended to directionally concatamerize the relatively short PCR products before cloning in order to increase the number of RNA sequences obtained per clone.
RNAi in Transgenic Plants
Authors: Yin Yanhai , Chory Joanne , Baulcombe David 
Published: February 2008

AbstractRNA silencing in plants is a rapid and facile approach for assignment of gene function and virus resistance. It allows selective RNA degradation through a mechanism that is given specificity by short interfering RNAs. The RNA silencer sequences are normally delivered as transgenes or a part of virus‐vectors. This unit provides Basic Protocols for transgene and virus induced silencing. It also includes a Basic Protocol for protein overexpression using viral proteins that suppress silencing.