bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced Classifications of Engineered Paved Surfaces for Urban Systems Modeling
Authors: Golden Jay , Chuang W. C. , Stefanov W. L. 
Published: June 2009

AbstractThere is a greater need than ever for the ability to accurately model urban system impacts resulting around the planet. Rapid urbanization is transforming landscapes from vegetation to an engineered infrastructure and thus altering land cover and land use. These alterations impact urban and global climate change, energy demand, human health, and ecological service functions. This article presents an overview of a refined land-cover classification protocol that seeks to refine current land-cover classifications of engineered paved surfaces. This new approach provides those who model urban systems and engineer the environment as well as other scientists and policy makers an expanded understanding of how intervention to the system can most effectively be accomplished through enhanced modeling. An object-oriented analysis regime is presented for an industrial park utilizing commercial software in conjunction with multispectral and panchromatic Quickbird satellite imagery. A detailed examination of hot-mix asphalt paved surfaces was undertaken in relation to the materials’ engineered function such as various types of streets, parking, etc. The results were validated using a commercial raster graphics editor and data analysis software as well as on-site inspections. An overall accuracy of 95% was achieved.
The Long-term Effect of 2 Postoperative Rehabilitation Programs After Anterior Cruciate Ligament Reconstruction
Authors: Risberg May Arna , Holm Inger 
Published: June 2009

Background There is no consensus regarding the optimal postoperative rehabilitation program after anterior cruciate ligament (ACL) reconstruction. Purpose The purpose of this study was to examine the long-term outcome of a 6-month neuromuscular exercise (NE) training program versus a traditional strength exercise (SE) training program after ACL reconstruction. Study Design Randomized controlled trial; Level of evidence, 1. Methods Seventy-four patients were randomly assigned to either a NE program or a SE program and tested preoperatively and at 6 months, 1 year, and 2 years after ACL reconstruction. Outcome measurements were as follows: Cincinnati knee score, visual analog scale for pain and global function, Short Form 36, functional knee tests, and isokinetic muscle strength tests. Results There were no significant differences between the NE and SE programs 1 and 2 years after ACL reconstruction for the primary outcome measurement (Cincinnati knee score). There were significantly improved knee function (global function) and reduced pain during activity for the NE group, compared with the SE group, and significantly improved hamstring muscle strength for the SE group, compared with the NE group, 2 years after ACL reconstruction. Conclusion On the basis of these results, a postoperative program combining both NE and SE should be included after ACL reconstruction to improve knee function.
Glypican 5 is an interferon-beta response gene: a replication study
Authors: Cénit MDC , Blanco-Kelly F , de las Heras V , Bartolomé M , de la Concha EG , Urcelay E , Arroyo R , Martínez A 
Published: June 2009

Background Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system. Interferon-beta is the most usual therapy in relapsing-remiting MS. However, approximately 50% of the treated patients do not respond adequately. Very recently, a genome-wide association study on interferon-beta pharmacogenetics has described polymorphisms at several genes that are associated with response to this treatment. Our aim is to replicate the results obtained at the two loci most strongly implicated in the response to interferon-beta treatment, HAPLN1 and GPC5. Patients and methods We performed a case–control study, analyzing 199 patients with MS treated with interferon-beta for at least 2 years and at least two documented relapses over the 2 years, previous to treatment onset. Responders had neither relapses nor increase in expanded disability status scale (EDSS) over the 2-year follow-up period, whereas nonresponders had at least two relapses or an increase in EDSS of at least 1 point. We studied three single-nucleotide polymorphisms (SNPs) in the GPC5 locus and three SNPs in the HAPLN1 locus by TaqMan technology. Allelic frequencies between responders and nonresponders were compared by a chi-square test. Results An association was found between GPC5 polymorphisms and the response to interferon-beta therapy in patients with MS, in agreement with earlier data (responder vs nonresponder patients: rs10492503, P = 0.0005). The other locus studied ( HAPLN1) did not show association with treatment response to interferon-beta (all SNPs P > 0.05). Conclusions We confirm the association of polymorphisms within GPC5 with response to interferon-beta therapy in patients with MS.
The development of patient-reported outcome indices for multiple sclerosis (PRIMUS)
Authors: Doward LC , McKenna SP , Meads DM , Twiss J , Eckert BJ 
Published: June 2009

Background Complex diseases such as multiple sclerosis (MS) present dilemmas over the choice of patient-reported outcome measures as no single scale can inform on all types of MS impact from the patient’s perspective. Objective To develop an outcome tool, the Patient-Reported Indices for Multiple Sclerosis (PRIMUS), to assess MS symptoms, activities, and quality of life. Methods PRIMUS content was derived from qualitative interviews with UK MS patients and checked by clinical experts. Semi-structured cognitive debriefing interviews assessed scale face and content validity. PRIMUS scaling properties, reliability, and construct validity were assessed by a test–retest postal survey. Results Cognitive debriefing interviews ( n = 15) demonstrated scale clarity, relevance, and comprehensiveness. The postal survey was completed by 135 patients with MS. After removal of misfitting items and those exhibiting differential item functioning, all scales fitted the Rasch model, confirming unidimensionality. For all scales, test–retest reliability exceeded 0.80. Scale scores were related to perceived MS severity, general health, and symptoms of depression. Moderate correlations were observed between PRIMUS and Nottingham Health Profile scores. Conclusions Clinicians and researchers can have confidence in scores obtained by respondents on the PRIMUS. The PRIMUS will aid the assessment of the impact of MS from the patient’s perspective.
Home administration of intravenous methylprednisolone for multiple sclerosis relapses: the experience of French multiple sclerosis networks
Authors: Créange A , Debouverie M , Jaillon-Rivière V , Taithe F , Liban D , Moutereau A , Clavelou P , Defer G 
Published: June 2009

Background One single center study has provided support for a home-based approach to the therapeutic management of multiple sclerosis (MS) relapse. Objective To report a multicenter series of patients with MS who were treated at home for a relapse with a 3-day course of intravenous methylprednisolone. Methods The home administration of intravenous methylprednisolone was coordinated by four MS networks in France; patients with MS with a relapse were referred by their neurologists, and treatment was administered by a local nurse. We analyzed the safety and efficiency of this approach and estimated the related cost savings. Patients completed a patient satisfaction questionnaire. Results Eight hundred and seven patients received intravenous methylprednisolone at home. The mean disease duration was 10.3 ± 7.9 years. Treatment was often prescribed by community-based neurologists. The delay between prescription and treatment was 2.8 ± 0.5 days if treatment was initiated at home and 1.9 ± 3.0 days if treatment was initiated in hospital (the subsequent two injections were always administered at home). Home treatment was well tolerated; three serious side effects requiring hospital transfer were observed (anxiety, thoracic oppression, and arrhythmia), which were fully reversible. Overall, 93.8% of patients were satisfied with the treatment approach, and 98% wished to receive future treatment courses at home. The overall cost savings of home-based treatment versus hospital-based treatment were evaluated at EUR1,091,482. Conclusion Safety data, patient satisfaction, and economic considerations support home-based treatment of MS relapses with intravenous methylprednisolone, provided strict patient selection criteria are observed and the process is coordinated and closely monitored by an MS network.
The development and validation of the Unidimensional Fatigue Impact Scale (U-FIS)
Authors: Meads DM , Doward LC , McKenna SP , Fisk J. , Twiss J. , Eckert B. 
Published: June 2009

Background: The multidimensional assessment of fatigue is complicated by the interrelation of its multiple causes and effects. Objective: The purpose of the research was to develop a unidimensional assessment of fatigue (U-FIS). Methods: Data collected with the Fatigue Impact Scale (FIS) were subjected to Rasch analysis to identify potential problems with the scale. Additional items for the U-FIS were generated from interviews with UK MS patients. The U-FIS was tested for face and content validity in patient interviews and included in a validation survey to determine dimensionality (Rasch model), reliability and validity. Results: The original FIS was not unidimensional when subscale items were combined. The modification of the FIS and addition of a number of items allowed the development of a 22-item unidimensional scale (U-FIS) that was reliable (Cronbach Alpha = 0.96; test-retest = 0.86,) and valid given correlations with the Nottingham Health Profile and ability to distinguish between MS severity groups. There was no significant difference in U-FIS scores according to MS type. Conclusion: It is valid to conceptualize the functional impact of fatigue as unidimensional. The U-FIS is a reliable and valid questionnaire that will allow the measurement of this construct in clinical studies.
How I treat mantle cell lymphoma
Authors: Ghielmini Michele , Zucca Emanuele 
Published: June 2009

AbstractMantle cell lymphoma is included in the World Health Organization classification as distinct lymphoma subtype characterized by the t(11;14)(q13;q32) translocation, which results in overexpression of Cyclin D1. The clinical presentation often includes extranodal involvement, particularly of the bone marrow and gut. The prognosis of patients with mantle cell lymphoma (median overall survival, 3-5 years) is poorest among B-cell lymphoma patients, even though a prospectively difficult to identify subgroup can survive for years with little or no treatment. Conventional chemotherapy is not curative but obtains frequent remissions (60%-90%) which are usually shorter (1-2 years) compared with other lymphoma entities. Very intensive regimens, including autologous and allogeneic stem cell transplantation, seem required to improve the outcome, but with the median age of diagnosis being 60 years or more, such approaches are feasible only in a limited proportion of patients. The possibility of treating patients based on prognostic factors needs to be investigated prospectively.
Repression of BMI1 in normal and leukemic human CD34+ cells impairs self-renewal and induces apoptosis
Authors: Rizo Aleksandra , Olthof Sandra , Han Lina , Vellenga Edo , de Haan Gerald , Schuringa Jan Jacob 
Published: June 2009

AbstractHigh expression of BMI1 in acute myeloid leukemia (AML) cells is associated with an unfavorable prognosis. Therefore, the effects of down-modulation of BMI1 in normal and leukemic CD34+ AML cells were studied using a lentiviral RNA interference approach. We demonstrate that down-modulation of BMI1 in cord blood CD34+ cells impaired long-term expansion and progenitor-forming capacity, both in cytokine-driven liquid cultures as well as in bone marrow stromal cocultures. In addition, long-term culture-initiating cell frequencies were dramatically decreased upon knockdown of BMI1, indicating an impaired maintenance of stem and progenitor cells. The reduced progenitor and stem cell frequencies were associated with increased expression of p14ARF and p16INK4A and enhanced apoptosis, which coincided with increased levels of intracellular reactive oxygen species and reduced FOXO3A expression. In AML CD34+ cells, down-modulation of BMI1 impaired long-term expansion, whereby self-renewal capacity was lost, as determined by the loss of replating capacity of the cultures. These phenotypes were also associated with increased expression levels of p14ARF and p16INK4A. Together our data indicate that BMI1 expression is required for maintenance and self-renewal of normal and leukemic stem and progenitor cells, and that expression of BMI1 protects cells against oxidative stress.
Soy consumption and risk of COPD and respiratory symptoms: a case-control study in Japan
Authors: Hirayama Fumi , Lee Andy H , Binns Colin W , Zhao Yun , Hiramatsu Tetsuo , Tanikawa Yoshimasa , Nishimura Koichi , Taniguchi Hiroyuki 
Published: June 2009

Abstract

Background
To investigate the relationship between soy consumption, COPD risk and the prevalence of respiratory symptoms, a case-control study was conducted in Japan.

Methods
A total of 278 eligible patients (244 men and 34 women), aged 50–75 years with COPD diagnosed within the past four years, were referred by respiratory physicians, while 340 controls (272 men and 68 women) were recruited from the community. All participants underwent spirometric measurements of respiratory function. Information on demographics, lifestyle characteristics and habitual food consumption was obtained using a structured questionnaire.

Results
Total soy consumption was positively correlated with observed lung function measures. The mean soy intake was significantly higher among controls (59.98, SD 50.23 g/day) than cases (44.84, SD 28.5 g/day). A significant reduction in COPD risk was evident for highest versus lowest quartile of daily intake of total soybean products, with adjusted odds ratio (OR) 0.392, 95% CI 0.194–0.793, p for trend 0.001. Similar decreases in COPD risk were associated with frequent and higher intake of soy foods such as tofu and bean sprouts, whereas respiratory symptoms were inversely associated with high consumption of soy foods, especially for breathlessness (OR 0.989, 95% CI 0.982–0.996).

Conclusion
Increasing soy consumption was associated with a decreased risk of COPD and breathlessness.
Lymphocyte apoptosis in murine Pneumocystis pneumonia
Authors: Shi Xin , LeCapitaine Nicole J , Rudner Xiaowen L , Ruan Sanbao , Shellito Judd E 
Published: June 2009

AbstractBackgroundApoptosis of lymphocytes is important in the termination of an immune response to infection but has also been shown to have detrimental effects in animal models of systemic infection and sepsis. We sought to characterize lymphocyte apoptosis in an animal model of pneumonia due toPneumocystis murina, an infection localized to the lungs.MethodsControl mice and mice depleted of CD4+ lymphocytes were inoculated withPneumocystis. Apoptosis of lung and spleen lymphocytes was assayed by flow cytometry and PCR assay of apoptotic proteins.ResultsIn control mice, apoptosis of lung lymphocytes was maximal just after the infection was cleared from lung tissue and then declined. However, in CD4-depleted mice, apoptosis was also upregulated in recruited lymphocytes in spite of progressive infection. In splenic lymphocytes, apoptosis was observed early at 1 week after inoculation and then declined. Apoptosis of lung lymphocytes in control mice was associated with a decrease in mRNA for Bcl-2 and an increase in mRNA for Bim. In CD4-depleted mice, lavaged CD8+ cells did change intracellular Bcl-2 but showed increased mRNA for Bim.ConclusionApoptosis of both pulmonary and extrapulmonary lymphocytes is part of the normal host response toPneumocystisbut is also triggered in CD4-deficient animals with progressive infection. In normal mice apoptosis of pulmonary lymphocytes may serve to terminate the immune response in lung tissue. Apoptosis of lung lymphocytes takes place via both the intrinsic and extrinsic apoptotic pathways and is associated with changes in both pro- and anti-apoptotic proteins.
Protection from pulmonary ischemia-reperfusion injury by adenosine A2A receptor activation
Authors: Sharma Ashish K , Linden Joel , Kron Irving L , Laubach Victor E 
Published: June 2009

AbstractBackgroundLung ischemia-reperfusion (IR) injury leads to significant morbidity and mortality which remains a major obstacle after lung transplantation. However, the role of various subset(s) of lung cell populations in the pathogenesis of lung IR injury and the mechanisms of cellular protection remain to be elucidated. In the present study, we investigated the effects of adenosine A2Areceptor (A2AAR) activation on resident lung cells after IR injury using an isolated, buffer-perfused murine lung model.MethodsTo assess the protective effects of A2AAR activation, three groups of C57BL/6J mice were studied: a sham group (perfused for 2 hr with no ischemia), an IR group (1 hr ischemia + 1 hr reperfusion) and an IR+ATL313 group where ATL313, a specific A2AAR agonist, was included in the reperfusion buffer after ischemia. Lung injury parameters and pulmonary function studies were also performed after IR injury in A2AAR knockout mice, with or without ATL313 pretreatment. Lung function was assessed using a buffer-perfused isolated lung system. Lung injury was measured by assessing lung edema, vascular permeability, cytokine/chemokine activation and myeloperoxidase levels in the bronchoalveolar fluid.ResultsAfter IR, lungs from C57BL/6J wild-type mice displayed significant dysfunction (increased airway resistance, pulmonary artery pressure and decreased pulmonary compliance) and significant injury (increased vascular permeability and edema). Lung injury and dysfunction after IR were significantly attenuated by ATL313 treatment. Significant induction of TNF-α, KC (CXCL1), MIP-2 (CXCL2) and RANTES (CCL5) occurred after IR which was also attenuated by ATL313 treatment. Lungs from A2AAR knockout mice also displayed significant dysfunction, injury and cytokine/chemokine production after IR, but ATL313 had no effect in these mice.ConclusionSpecific activation of A2AARs provides potent protection against lung IR injury via attenuation of inflammation. This protection occurs in the absence of circulating blood thereby indicating a protective role of A2AAR activation on resident lung cells such as alveolar macrophages. Specific A2AAR activation may be a promising therapeutic target for the prevention or treatment of pulmonary graft dysfunction in transplant patients.
Ab initio and homology based prediction of protein domains by recursive neural networks
Authors: Walsh Ian , Martin Alberto JM , Mooney Catherine , Rubagotti Enrico , Vullo Alessandro , Pollastri Gianluca 
Published: June 2009

Abstract

Background
Proteins, especially larger ones, are often composed of individual evolutionary units, domains, which have their own function and structural fold. Predicting domains is an important intermediate step in protein analyses, including the prediction of protein structures.

Results
We describe novel systems for the prediction of protein domain boundaries powered by Recursive Neural Networks. The systems rely on a combination of primary sequence and evolutionary information, predictions of structural features such as secondary structure, solvent accessibility and residue contact maps, and structural templates, both annotated for domains (from the SCOP dataset) and unannotated (from the PDB). We gauge the contribution of contact maps, and PDB and SCOP templates independently and for different ranges of template quality. We find that accurately predicted contact maps are informative for the prediction of domain boundaries, while the same is not true for contact maps predicted ab initio. We also find that gap information from PDB templates is informative, but, not surprisingly, less than SCOP annotations. We test both systems trained on templates of all qualities, and systems trained only on templates of marginal similarity to the query (less than 25% sequence identity). While the first batch of systems produces near perfect predictions in the presence of fair to good templates, the second batch outperforms or match ab initio predictors down to essentially any level of template quality.
We test all systems in 5-fold cross-validation on a large non-redundant set of multi-domain and single domain proteins. The final predictors are state-of-the-art, with a template-less prediction boundary recall of 50.8% (precision 38.7%) within ± 20 residues and a single domain recall of 80.3% (precision 78.1%). The SCOP-based predictors achieve a boundary recall of 74% (precision 77.1%) again within ± 20 residues, and classify single domain proteins as such in over 85% of cases, when we allow a mix of bad and good quality templates. If we only allow marginal templates (max 25% sequence identity to the query) the scores remain high, with boundary recall and precision of 59% and 66.3%, and 80% of all single domain proteins predicted correctly.

Conclusion
The systems presented here may prove useful in large-scale annotation of protein domains in proteins of unknown structure. The methods are available as public web servers at the address: http://distill.ucd.ie/shandy/ and we plan on running them on a multi-genomic scale and make the results public in the near future.
Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species
Authors: Wu Chengcang , Proestou Dina , Carter Dorothy , Nicholson Erica , Santos Filippe , Zhao Shaying , Zhang Hong-Bin , Goldsmith Marian R 
Published: June 2009

Abstract

Background

Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date.

Results
We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences.

Conclusion
The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes.