bluuebunny/crossref_metadata_2025_split huggingface dataset:
Speeding disease gene discovery by sequence based candidate prioritization
Authors: Adie Euan A , Adams Richard R , Evans Kathryn L , Porteous David J , Pickard Ben S 
Published: March 2005

Abstract
Background
Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation to knowledge of the disease or phenotype in question. However, here we show that disease genes share patterns of sequence-based features that can provide a good basis for automatic prioritization of candidates by machine learning.

Results
We examined a variety of sequence-based features and found that for many of them there are significant differences between the sets of genes known to be involved in human hereditary disease and those not known to be involved in disease. We have created an automatic classifier called PROSPECTR based on those features using the alternating decision tree algorithm which ranks genes in the order of likelihood of involvement in disease. On average, PROSPECTR enriches lists for disease genes two-fold 77% of the time, five-fold 37% of the time and twenty-fold 11% of the time.

Conclusion
PROSPECTR is a simple and effective way to identify genes involved in Mendelian and oligogenic disorders. It performs markedly better than the single existing sequence-based classifier on novel data. PROSPECTR could save investigators looking at large regions of interest time and effort by prioritizing positional candidate genes for mutation detection and case-control association studies.
Proposal to create subspecies of Rickettsia conorii based on multi-locus sequence typing and an emended description of Rickettsia conorii
Authors: Zhu Yong , Fournier Pierre-Edouard , Eremeeva Marina , Raoult Didier 
Published: March 2005

Abstract
Background
Rickettsiae closely related to the Malish strain, the reference Rickettsia conorii strain, include Indian tick typhus rickettsia (ITTR), Israeli spotted fever rickettsia (ISFR), and Astrakhan fever rickettsia (AFR). Although closely related genotypically, they are distinct serotypically. Using multilocus sequence typing (MLST), we have recently found that distinct serotypes may not always represent distinct species within the Rickettsia genus. We investigated the possibility of classifying rickettsiae closely related to R. conorii as R. conorii subspecies as proposed by the ad hoc committee on reconciliation of approaches to bacterial systematics. For this, we first estimated their genotypic variability by using MLST including the sequencing of 5 genes, of 31 rickettsial isolates closely related to R. conorii strain Malish, 1 ITTR isolate, 2 isolates and 3 tick amplicons of AFR, and 2 ISFR isolates. Then, we selected a representative of each MLST genotype and used multi-spacer typing (MST) and mouse serotyping to estimate their degree of taxonomic relatedness.

Results
Among the 39 isolates or tick amplicons studied, four MLST genotypes were identified: i) the Malish type; ii) the ITTR type; iii) the AFR type; and iv) the ISFR type. Among these four MLST genotypes, the pairwise similarity in nucleotide sequence varied from 99.8 to 100%, 99.4 to 100%, 98.2 to 99.8%, 98.4 to 99.8%, and 99.2 to 99.9% for 16S rDNA, glt A, omp A, omp B, and sca 4 genes, respectively. Representatives of the 4 MLST types were also classified within four types using MST genotyping as well as mouse serotyping.

Conclusion
Although homogeneous genotypically, strains within the R. conorii species show MST genotypic, serotypic, and epidemio-clinical dissimilarities. We, therefore, propose to modify the nomenclature of the R. conorii species through the creation of subspecies. We propose the names R. conorii subsp. conorii subsp. nov. (type strain = Malish, ATCC VR-613), R. conorii subspecies indica subsp. nov. (type strain = ATCC VR-597), R. conorii subspecies caspia subsp. nov. (type strain = A-167), and R. conorii subspecies israelensis subsp. nov. (type strain = ISTT CDC1). The description of R. conorii is emended to accomodate the four subspecies.
Functional characterization of two newly identified Human Endogenous Retrovirus coding envelope genes
Authors: Blaise Sandra , de Parseval Nathalie , Heidmann Thierry 
Published: March 2005

Abstract
A recent in silico search for coding sequences of retroviral origin present in the human genome has unraveled two new envelope genes that add to the 16 genes previously identified. A systematic search among the latter for a fusogenic activity had led to the identification of two bona fide genes, named syncytin-1 and syncytin-2, most probably co-opted by primate genomes for a placental function related to the formation of the syncytiotrophoblast by cell-cell fusion. Here, we show that one of the newly identified envelope gene, named envP(b), is fusogenic in an ex vivo assay, but that its expression – as quantified by real-time RT-PCR on a large panel of human tissues – is ubiquitous, albeit with a rather low value in most tissues. Conversely, the second envelope gene, named envV, discloses a placenta-specific expression, but is not fusogenic in any of the cells tested. Altogether, these results suggest that at least one of these env genes may play a role in placentation, but most probably through a process different from that of the two previously identified syncytins.
Tezosentan-induced attenuation of lung injury in endotoxemic sheep is associated with reduced activation of protein kinase C
Authors: Kuklin Vladimir , Kirov Mikhail , Sovershaev Mikhail , Andreasen Thomas , Ingebretsen Ole C , Ytrehus Kirsti , Bjertnaes Lars 
Published: March 2005

Abstract
Introduction
Studies in vitro reveal that endothelin-1 (ET-1) activates the α isoform of protein kinase C (PKC-α) in cultures of endothelial cells, thereby deranging cellular integrity. Sepsis and endotoxemia are associated with increased plasma concentrations of ET-1 that induce acute lung injury (ALI). We recently reported that non-selective ET-1 receptor blockade attenuates ALI in sheep by reducing the endotoxin-induced increase in extravascular lung water index (EVLWI). The aim of this study was to find out whether this attenuation is associated with reduced translocation of PKC-α from the cytosolic to the membrane fraction of lung tissue homogenate.

Methods
Seventeen awake, instrumented sheep were randomly assigned to a sham-operated group (n = 3), a lipopolysaccharide (LPS) group (n = 7) receiving an intravenous infusion of Escherichia coli 15 ng/kg per min for 24 hours, and a tezosentan group (n = 7) subjected to LPS and, from 4 hours, an intravenous injection of tezosentan 3 mg/kg followed by infusion at 1 mg/kg per hour for the reminder of the experiment. Pulmonary micro-occlusion pressure (Pmo), EVLWI, plasma concentrations of ET-1, tumor necrosis factor-a (TNF-a), and interleukin-8 (IL-8) were determined every 4 hours. Western blotting was used to assess PKC-α.

Results
In non-treated sheep a positive correlation was found between the plasma concentration of ET-1 and Pmo in the late phase of endotoxemia (12 to 24 hours). A positive correlation was also noticed between Pmo and EVLWI in the LPS and the LPS plus tezosentan groups, although the latter was significantly reduced in comparison with LPS alone. In both endotoxemic groups, plasma concentrations of ET-1, TNF-α, and IL-8 increased. In the LPS group, the cytosolic fraction of PKC-α decreased by 75% whereas the membrane fraction increased by 40% in comparison with the sham-operated animals. Tezosentan completely prevented the changes in PKC-α in both the cytosolic and the membrane fractions, concomitantly causing a further increase in the plasma concentrations of ET-1, TNF-α, and IL-8.

Conclusion
In endotoxemic sheep, ET-1 receptor blockade alleviates lung injury as assessed by a decrease in EVLWI paralleled by a reduction in Pmo and the prevention of activation of PKC-α.
Disruption of granulocyte macrophage-colony stimulating factor production in the lungs severely affects the ability of mice to controlMycobacterium tuberculosisinfection
Authors: Gonzalez-Juarrero Mercedes , Hattle Jessica M , Izzo Angelo , Junqueira-Kipnis Ana Paula , Shim Tae S , Trapnell Bruce C , Cooper Andrea M , Orme Ian M 
Published: March 2005

AbstractMice lacking expression of granulocyte macrophage-colony stimulating factor (GM-CSF KO) are unable to contain Mycobacterium tuberculosis (M. tuberculosis) growth and succumb to infection by 35 days following pulmonary challenge. GM-CSF KO mice do not express normal levels of the inflammatory cytokine tumor necrosis factor α (TNF-α) nor the chemokines, regulated on activation, normal T expressed and secreted (RANTES), macrophage-inflammatory protein-1β (MIP-1β), MIP-1α, and lymphotactin, which are required for recruitment of lymphocytes and expression of a T helper cell type 1 (TH1) response within the lungs. In contrast, transgenic mice overexpressing GM-CSF in the lungs but with a lack of GM-CSF in other organs (GM+) are able to recruit lymphocytes and to express a TH1 response with production of TNF-α and interferon-γ in the lungs. However, GM+ mice succumb to infection between 60 and 90 days post-challenge, as they are unable to develop a normal granulomatous response. Although GM+ mice are able to express the chemokine RANTES, they lack the ability to express other inflammatory chemokines such as lymphotactin and MIP-1β. We conclude that GM-CSF is essential to the recruitment of lymphocytes and expression of a TH1 response in the lung, to the generation of a normal mononuclear granuloma, and most importantly, to the containment of M. tuberculosis bacterial growth.
A validated procedure for determining the buoyancy-induced flow in ducts
Authors: Brinkworth BJ , Sandberg M 
Published: March 2005

A procedure is set out for calculating the buoyant flow induced in a duct with heat input at the wall, as in the cooling ducts used behind photovoltaic arrays. In these, buoyancy is opposed by various pressure losses, due to obstructions at the inlet and outlet, fluid friction at the walls and structural support members passing transversely through the duct. New methods are developed for calculating these losses, and each is validated separately by tests in a purpose-built isothermal rig. Measurements are also reported for some further losses, not yet amenable to calculation, due to nets and hoods at the duct ends, as might be used to exclude rain and wildlife. Finally, the whole procedure is validated by measurement of a duct with one heated wall. Practical application: Verified by measurements at every stage of its development, the method reported gives greater confidence in the routine calculation of the flow induced in ductwork where there is heat gain, as in systems for PV cooling and natural ventilation. The new treatments given for the hydrodynamic losses at basic components apply wherever these are used in the field of HEVAC.
Sustainability analysis of window frames
Authors: Asif M , Muneer T , Kubie J 
Published: March 2005

The characteristics of the frame materials have significant impacts on the properties of a window. A window itself plays a crucial role in determining the overall energy performance of the building. This article analyses four different frame types; aluminium, aluminium-clad timber, Polyvinyl chloride (PVC) and timber make, from the sustainability perspective. These frame types have been studied on various parameters such as; environmental impacts during production/extraction of frame materials and disposal of frames; embodied energy, durability and service life; and maintenance and repair of frames. A price comparison and market scenario has also been discussed. It has been found that timber- and aluminium-clad timber windows are sustainable products due to their environment-friendly characteristics i.e., low embodied energy, low environmental impacts, better durability and longer service life. While aluminium and PVC frames have high values of embodied energy and associated environmental impacts. Practical application: In the present sustainability-conscious age, the window industry is emphasising how to enhance the energy and environmental performance of their products. This article will be of interest not only to modern window manufacturers but also to customers as it addresses the key sustainability features of windows, i.e., energy and environmental performance, durability and service life, and maintenance and life cycle costing.
Translation, adaptation and validation of the Shoulder Rating Questionnaire (SRQ) into the Dutch language
Authors: Vermeulen Henricus M , Boonman Dies CG , Schüller Hans M , Obermann Wim R , van Houwelingen Hans C , Rozing Piet M , Vlieland Thea PM Vliet 
Published: March 2005

Objective: To translate and adapt the original English version of the Shoulder Rating Questionnaire (SRQ) into the Dutch language (SRQ-DLV) and evaluate its internal consistency, reliability, validity and responsiveness to clinical changes. Design: Prospective study. Setting: Outpatient departments of orthopaedics, radiology and physical therapy of an academic and a non-academic hospital. Subjects: One hundred and seven patients treated for unilateral shoulder disorder (adhesive capsulitis 68, calcifying tendinitis 22, impingement syndrome or rotator cuff tear 17). Methods: The original SRQ was translated and adapted following international guidelines. The SRQ-DLV was used among other measures of body function and structure, activities and societal participation in order to determine reliability, internal consistency, validity and responsiveness. Assessments were done at baseline and three months after treatment, with the SRQ-DLV being re-administered within one week before the baseline measurement and the start of the treatment for testing reliability. Results: Cronbach's alpha for internal consistency was 0.89 for the total questionnaire and 0.81, 0.80, 0.72 and 0.84 for the domains pain, daily activities, sports/recreational activities and work, respectively. Test-retest reliability of the SRQ-DLV and its subscales ranged from 0.63 to 0.86. The summary score of the SRQ-DLV correlated with measures of shoulder function, daily activities and quality of life. Except for the work subscale of the SRQ-DLV, large effect sizes, reflecting its responsiveness to clinical changes after treatment, were found for both the summary and the subscales scores. Conclusions: Empirical data support that the SRQ-DLV is a reliable, valid and responsive measure to be used in clinical trials including Dutch patients with various shoulder disorders.
Gait outcomes after additional backward walking training in patients with stroke: a randomized controlled trial
Authors: Yang Yea-Ru , Yen Jyh-Geng , Wang Ray-Yau , Yen Lu-Lu , Lieu Fu-Kong 
Published: March 2005

Objective: To examine the effectiveness of additional backward walking training on gait outcome of patients post stroke. Design: Randomized controlled trial. Setting: Medical centre. Subjects: Twenty-five subjects with stroke, who were lower extremity Brunnstrom motor recovery stage at 3 or 4 and were able to walk 11 m with or without a walking aid or orthosis, randomly allocated to two groups, control (n = 12) and experimental (n = 13). Interventions: Subjects in both groups participated in 40 min of conventional training programme three times a week for three weeks. Subjects in experimental group received additional 30 min of backward walking training for three weeks at a frequency of three times per week. Main measures: Gait was measured using the Stride Analyzer. Gait parameters of interest were walking speed, cadence, stride length, gait cycle and symmetry index. Measures were made at baseline before commencement of training (pre-training) and at the end of the three-week training period (post-training). Results: After a three-week training period, subjects in experimental group showed more improvement than those in control group for walking speed (change score: 8.609 ± 6.95 versus 3.659 ± 2.92, p-value = 0.032), stride length (change score: 0.0909 ± 0.076 versus 0.00649 ± 0.078, p-value = 0.006), and symmetry index (change score: 44.079 ± 53.29 versus 5.309 ± 13.91, p-value = 0.018). Conclusions: This study demonstrated that asymmetric gait pattern in patients post stroke could be improved from receiving additional backward walking therapy.
Effect of pulsed short-wave diathermy on pain and function of subjects with osteoarthritis of the knee: a placebo-controlled double-blind clinical trial
Authors: Laufer Y , Zilberman R , Porat R , Nahir A M 
Published: March 2005

Objective: To examine the effects of pulsed short-wave diathermy (PSWD), delivered at an intensity sufficient to induce a thermal sensation and at an athermal intensity, in comparison with a placebo short-wave diathermy treatment, on reported pain, stiffness and functional ability and on mobility performance of patients with osteoarthritis of the knee. Design: A placebo-controlled double-blind trial with sequential allocation of patients to different treatment groups. Setting: Outpatient physiotherapy department. Subjects: One hundred and three consecutive patients, mean age 73.7 (9 = 6.6) years with osteoarthritis of one or both knees for at least three months. Interventions: All participants received three 20-min-long treatments per week for three weeks. One group received PSWD with mean power of 18 W (thermal effect), one group received PSWD with mean power of 1.8 W (athermal effect), and one group received sham short-wave diathermy treatment. Patients were assessed before the initial treatment, immediately following the last treatment, and at a three-month follow-up. Main measures: Outcome measures included the WOMAC Osteoarthritis Index, which assessed reported pain, stiffness, and functional ability, and four measures of mobility performance: Timed Get Up and Go test (TGUG), stair-climbing, stairdescending and a 3-min walk. Results: A difference across time was observed for the pain and stiffness categories of the WOMAC Osteoarthritis Index (p < 0.033 and p < 0.008, respectively), with no differences between groups. No other significant differences across time or between groups were observed in any of the other measures. Conclusion: The findings do not demonstrate pulsed short-wave diathermy, as it is utilized in clinical settings, to be effective in the treatment of osteoarthritis of the knee.
The association of marital status and hospice use in the USA
Authors: Lackan Nuha A , Ostir Glenn V , Kuo Yong-Fang , Freeman Jean L 
Published: March 2005

Background: Married individuals are more likely to use hospice than unmarried individuals. We examine this association and how it is influenced by gender. Methods: Medicare beneficiaries dying of cancer were studied. Results: Currently married (OR 1.36 95% C.I. 1.28 1.45) or ever married (OR 1.23 95% C.I. 1.16 1.31) subjects were more likely to use hospice than never married subjects. A significant interaction between marital status and gender (PB .001) was observed. Conclusions: Subjects likely to enroll in hospice are subjects likely to have greater supportive relationships.
Language aptitude and its relationship to instructional effectiveness in second language acquisition
Authors: Erlam Rosemary 
Published: March 2005

Experimental second language acquisition research typically investigates the effectiveness of instruction in terms of overall group gains. A particular instructional method may not, however, benefit all learners uniformly. This study, conducted in a New Zealand secondary school, establishes whether there is any relationship between the effectiveness of three instructional methods, and learner aptitude. Students (n = 60) were assigned to one of three groups (deductive instruction group, inductive instruction group, structured input instruction group) and received instruction that targeted direct object pronouns in L2 French. All students were assessed on the following three measures of language aptitude: (a) language analytic ability, (b) phonemic coding ability and (c) working memory. Results indicate that deductive instruction that gives students opportunities to produce language output may neutralize individual differences in language aptitude.
Biomarker Changes During Neoadjuvant Anastrozole, Tamoxifen, or the Combination: Influence of Hormonal Status and HER-2 in Breast Cancer—A Study from the IMPACT Trialists
Authors: Dowsett Mitch , Ebbs Steve R. , Dixon J. Michael , Skene Anthony , Griffith Clive , Boeddinghaus Irene , Salter Janine , Detre Simone , Hills Margaret , Ashley Susan , Francis Stephen , Walsh Geraldine , Smith Ian E. 
Published: March 2005

PurposeTo investigate the relationships between biomarker changes in breast cancer during neoadjuvant (preoperative) endocrine therapy.Patients and MethodsThe IMPACT trial compared the preoperative use of tamoxifen with anastrozole alone or in combination in postmenopausal women (n = 330) with primary breast cancer. Biomarkers were measured in tumor biopsy specimens taken at baseline, and after 2 and 12 weeks of treatment.ResultsA decrease in the proliferation marker Ki67 occurred in the majority of patients: 52 (93%) of 56, 46 (85%) of 54, and 37 (84%) of 44 patients in the anastrozole, tamoxifen, and combination groups, respectively. There was a significantly greater suppression of Ki67 in the anastrozole-treated group than in the tamoxifen- or combination-treated groups, which is parallel to the greater efficacy seen for anastrozole over these two treatments in the Arimidex, Tamoxifen, Alone or in Combination adjuvant trial. A positive relationship was noted between estrogen-receptor level and Ki67 suppression in all patients. Ki67 was reduced to a greater extent in progesterone receptor-positive tumors compared with progesterone receptor-negative tumors. HER-2-negative tumors tended to show a greater reduction in Ki67 compared with HER-2-positive tumors, but the difference was only significant in the tamoxifen group after 2 weeks, and in the anastrozole group after 12 weeks.ConclusionThese results confirm the value of Ki67 as a molecular marker, and provide information regarding the relationships between treatment-induced changes in Ki67 and other important biomarkers. Studies such as this should help integrate agents targeted at growth factor signaling with endocrine agents in breast cancer.