bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative promoter region analysis powered by CORG
Authors: Dieterich Christoph , Grossmann Steffen , Tanzer Andrea , Röpcke Stefan , Arndt Peter F , Stadler Peter F , Vingron Martin 
Published: February 2005

Abstract
Background
Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR).

Description
The automated annotation of promoter regions integrates information of two kinds. First, statistically significant cross-species conservation within upstream regions of orthologous genes is detected. Pairwise as well as multiple sequence comparisons are computed. Second, binding site descriptions (position-weight matrices) are employed to predict conserved regulatory elements with a novel approach. Assembled EST sequences and verified transcription start sites are incorporated to distinguish exonic from other sequences.
As of now, we have included 5 species in our analysis pipeline (man, mouse, rat, fugu and zebrafish). We characterized promoter regions of 16,127 groups of orthologous genes. All data are presented in an intuitive way via our web site. Users are free to export data for single genes or access larger data sets via our DAS server http://tomcat.molgen.mpg.de:8080/das. The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set.

Conclusion
The CORG platform is a versatile tool to support analyses of gene regulation in vertebrate promoter regions. Applications for CORG cover a broad range from studying evolution of DNA binding sites and promoter constitution to the discovery of new regulatory sequence elements (e.g. microRNAs and binding sites).
Customized birth weight for gestational age standards: Perinatal mortality patterns are consistent with separate standards for males and females but not for blacks and whites
Authors: Joseph K S , Wilkins Russell , Dodds Linda , Allen Victoria M , Ohlsson Arne , Marcoux Sylvie , Liston Robert 
Published: February 2005

Abstract
Background
Some currently available birth weight for gestational age standards are customized but others are not. We carried out a study to provide empirical justification for customizing such standards by sex and for whites and blacks in the United States.

Methods
We studied all male and female singleton live births and stillbirths (22 or more weeks of gestation; 500 g birth weight or over) in the United States in 1997 and 1998. White and black singleton live births and stillbirths were also examined. Qualitative congruence between gestational age-specific growth restriction and perinatal mortality rates was used as the criterion for identifying the preferred standard.

Results
The fetuses at risk approach showed that males had higher perinatal mortality rates at all gestational ages compared with females. Gestational age-specific growth restriction rates based on a sex-specific standard were qualitatively consistent with gestational age-specific perinatal mortality rates among males and females. However, growth restriction patterns among males and females based on a unisex standard could not be reconciled with perinatal mortality patterns. Use of a single standard for whites and blacks resulted in gestational age-specific growth restriction rates that were qualitatively congruent with patterns of perinatal mortality, while use of separate race-specific standards led to growth restriction patterns that were incompatible with patterns of perinatal mortality.

Conclusion
Qualitative congruence between growth restriction and perinatal mortality patterns provides an outcome-based justification for sex-specific birth weight for gestational age standards but not for the available race-specific standards for blacks and whites in the United States.
Polymorphisms in immunoregulatory genes and the risk of histologic chorioamnionitis in Caucasoid women: a case control study
Authors: Annells Margaret F , Hart Prue H , Mullighan Charles G , Heatley Susan L , Robinson Jeffrey S , McDonald Helen M 
Published: February 2005

Abstract
Background
Chorioamnionitis is a common underlying cause of preterm birth (PTB). It is hypothesised that polymorphisms in immunoregulatory genes influence the host response to infection and subsequent preterm birth. The relationship between histologic chorioamnionitis and 22 single nucleotide polymorphisms in 11 immunoregulatory genes was examined in a case-control study.

Methods
Placentas of 181 Caucasoid women with spontaneous PTB prior to 35 weeks were examined for histologic chorioamnionitis. Polymorphisms in genes IL1A, IL1B, IL1RN, IL1R1, tumour necrosis factor (TNF), IL4, IL6, IL10, transforming growth factor beta-1 (TGFB1), Fas (TNFRSF6), and mannose-binding lectin (MBL2) were genotyped by polymerase chain reaction and sequence specific primers. Multivariable logistic regression including demographic and genetic variables and Kaplan-Meier survival analyses of genotype frequencies and pregnancy outcome were performed.

Results
Sixty-nine (34%) women had histologic evidence of acute chorioamnionitis. Carriage of the IL10-1082A/-819T/592A (ATA) haplotype [Multivariable Odds ratio (MOR) 1.9, P = 0.05] and MBL2 codon 54Asp allele (MOR 2.0, P = 0.04), were positively associated with chorioamnionitis, while the TNFRSF6-1377A/-670G (AG) haplotype (MOR 0.4, P = 0.03) and homozygosity for TGFB1-800G/509T (GT) haplotype (MOR 0.2, P = 0.04) were negatively associated.

Conclusion
These findings demonstrate that polymorphisms in immunoregulatory genes IL10, MBL2, TNFRSF6 and TGFB1 may influence susceptibility to chorioamnionitis.
Quality of life in patients with personality disorders seen at an ordinary psychiatric outpatient clinic
Authors: Narud Kjersti , Mykletun Arnstein , Dahl Alv A 
Published: February 2005

Abstract
Background
Epidemiological studies have found reduced health-related quality of life (QoL) in patients with personality disorders (PDs), but few clinical studies have examined QoL in PDs, and none of them are from an ordinary psychiatric outpatient clinic (POC). We wanted to examine QoL in patients with PDs seen at a POC, to explore the associations of QoL with established psychiatric measures, and to evaluate QoL as an outcome measure in PD patients.

Methods
72 patients with PDs at a POC filled in the MOS Short Form 36 (SF-36), and two established psychiatric self-rating measures. A national norm sample was compared on the SF-36. An independent psychiatrist diagnosed PDs and Axis-I disorders by structured interviews and rated the Global Assessment of Functioning (GAF). All measurements were repeated in the 39 PD patients that attended the 2 years follow-up examination.

Results
PD patients showed high co-morbidity with other PDs and Axis I mental disorders, and they scored significantly lower on all the SF-36 dimensions than age- and gender-adjusted norms. Adjustment for co-morbid Axis I disorders had some influence, however. The SF-36 mental health, vitality, and social functioning were significantly associated with the GAF and the self-rated psychiatric measures. Significant changes at follow-up were found in the psychiatric measures, but only on the mental health and role-physical of the SF-36.

Conclusion
Patients with PDs seen for treatment at a POC have globally poor QoL. Both physical and mental dimensions of the SF-36 are correlated with established psychiatric measures in such patients, but significant changes in these measures are only partly associated with changes in the SF-36 dimensions.
Optimal sampling of MRI slices for the assessment of knee cartilage volume for cross-sectional and longitudinal studies
Authors: Zhai Guangju , Ding Changhai , Cicuttini Flavia , Jones Graeme 
Published: February 2005

Abstract
Background
MRI slices of 1.5 mm thickness have been used in both cross sectional and longitudinal studies of osteoarthritis, but is difficult to apply to large studies as most techniques used in measuring knee cartilage volumes require substantial post-image processing. The aim of this study was to determine the optimal sampling of 1.5 mm thick slices of MRI scans to estimate knee cartilage volume in males and females for cross-sectional and longitudinal studies.

Methods
A total of 150 subjects had a sagittal T1-weighted fat-suppressed MRI scan of the right knee at a partition thickness of 1.5 mm to determine their cartilage volume. Fifty subjects had both baseline and 2-year follow up MRI scans. Lateral, medial tibial and patellar cartilage volumes were calculated with different samples from 1.5 mm thick slices by extracting one in two, one in three, and one in four to compare to cartilage volume and its rate of change. Agreement was assessed by means of intraclass correlation coefficient (ICC) and Bland & Altman plots.

Results
Compared to the whole sample of 1.5 mm thick slices, measuring every second to fourth slice led to very little under or over estimation in cartilage volume and its annual change. At all sites and subgroups, measuring every second slice had less than 1% mean difference in cartilage volume and its annual rate of change with all ICCs ≥ 0.98.

Conclusion
Sampling alternate 1.5 mm thick MRI slices is sufficient for knee cartilage volume measurement in cross-sectional and longitudinal epidemiological studies with little increase in measurement error. This approach will lead to a substantial decrease in post-scan processing time.
Resorbable screws versus pins for optimal transplant fixation (SPOT) in anterior cruciate ligament replacement with autologous hamstring grafts: rationale and design of a randomized, controlled, patient and investigator blinded trial [ISRCTN17384369]
Authors: Stengel Dirk , Matthes Gerrit , Seifert Julia , Tober Volker , Mutze Sven , Rademacher Grit , Ekkernkamp Axel , Bauwens Kai , Wich Michael , Casper Dirk ,   the SPOT Group
Published: February 2005

Abstract

Background
Ruptures of the anterior cruciate ligament (ACL) are common injuries to the knee joint. Arthroscopic ACL replacement by autologous tendon grafts has established itself as a standard of care.
Data from both experimental and observational studies suggest that surgical reconstruction does not fully restore knee stability. Persisting anterior laxity may lead to recurrent episodes of giving-way and cartilage damage. This might at least in part depend on the method of graft fixation in the bony tunnels. Whereas resorbable screws are easy to handle, pins may better preserve graft tension. The objective of this study is to determine whether pinning of ACL grafts reduces residual anterior laxity six months after surgery as compared to screw fixation.

Design/ Methods
SPOT is a randomised, controlled, patient and investigator blinded trial conducted at a single academic institution. Eligible patients are scheduled to arthroscopic ACL repair with triple-stranded hamstring grafts, conducted by a single, experienced surgeon. Intraoperatively, subjects willing to engage in this study will be randomised to transplant tethering with either resorbable screws or resorbable pins. No other changes apply to locally established treatment protocols. Patients and clinical investigators will remain blinded to the assigned fixation method until the six-month follow-up examination.
The primary outcome is the side-to-side (repaired to healthy knee) difference in anterior translation as measured by the KT-1000 arthrometer at a defined load (89 N) six months after surgery. A sample size of 54 patients will yield a power of 80% to detect a difference of 1.0 mm ± standard deviation 1.2 mm at a two-sided alpha of 5% with a t-test for independent samples.
Secondary outcomes (generic and disease-specific measures of quality of life, magnetic resonance imaging morphology of transplants and devices) will be handled in an exploratory fashion.

Conclusion
SPOT aims at showing a reduction in anterior knee laxity after fixing ACL grafts by pins compared to screws.
Sarcocystosis of chital-dhole: conditions for evolutionary stability of a predator parasite mutualism
Authors: Jog Maithili M , Watve Milind G 
Published: February 2005

Abstract
Background
For parasites with a predator-prey life cycle, the completion of the life cycle often depends on consumption of parasitized prey by the predator. In the case of such parasite species the predator and the parasite have common interests and therefore a mutualistic relationship is possible. Some evidence of a predator-parasite mutualism was reported from spotted deer or chital (Axix axis) as a prey species, dhole or Indian wild-dog (Cuon alpinus) as the predator and a protozoan (Sarcocystis axicuonis) as the parasite. We examine here, with the help of a model, the ecological conditions necessary for the evolution and stability of such a mutualistic relationship. A two – level game theory model was designed in which the payoff of a parasite is decided not only by alternative parasite strategies but also by alternative host strategies and vice versa. Conditions for ESS were examined.

Results
A tolerant predator strategy and a low or moderately virulent parasite strategy which together constitute mutualism are stable only at a high frequency of recycling of parasite and a substantial prey – capture benefit to the predator. Unlike the preliminary expectation, parasite will not evolve towards reduced virulence, but reach an optimum moderate level of virulence.

Conclusion
The available data on the behavioral ecology of dhole and chital suggest that they are likely to meet the stability criteria and therefore a predator-parasite mutualism can be stable in this system. The model also points out the gaps in the current data and could help directing further empirical work.
Determining the quality of educational climate across multiple undergraduate teaching sites using the DREEM inventory
Authors: Varma Rajesh , Tiyagi Ekta , Gupta Janesh K 
Published: February 2005

Abstract
Background
Our obstetrics and gynaecology undergraduate teaching module allocates 40–50 final year medical students to eight teaching hospital sites in the West Midlands region. Based on student feedback and concerns relating to the impact of new curriculum changes, we wished to objectively assess whether the educational environment perceived by students varied at different teaching hospital centres, and whether the environment was at an acceptable standard.

Methods
A Dundee Ready Education Environment (DREEM) Questionnaire, a measure of educational environment, was administered to 206 students immediately following completion of the teaching module.

Results
The overall mean DREEM score was 139/200 (70%). There were no differences in the education climate between the teaching centres.

Conclusion
Further research on the use of DREEM inventory, with follow up surveys, may be useful for educators to ensure and maintain high quality educational environments despite students being placed at different teaching centres.
What is important in evaluating health care quality? An international comparison of user views
Authors: Groenewegen Peter P , Kerssens Jan J , Sixma Herman J , van der Eijk Ingrid , Boerma Wienke GW 
Published: February 2005

Abstract
Background
Quality of care from the perspective of users is increasingly used in evaluating health care performance. Going beyond satisfaction studies, quality of care from the users' perspective is conceptualised in two dimensions: the importance users attach to aspects of care and their actual experience with these aspects. It is well established that health care systems differ in performance. The question in this article is whether there are also differences in what people in different health care systems view as important aspects of health care quality. The aim is to describe and explain international differences in the importance that health care users attach to different aspects of health care.

Methods
Data were used from different studies that all used a version of the QUOTE-questionnaire that measures user views of health care quality in two dimensions: the importance that users attach to aspects of care and their actual experience. Data from 12 European countries and 5133 individuals were used. They were analysed using multi-level analysis.

Results
Although most of the variations in importance people attach to aspects of health care is located at the individual level, there are also differences between countries. The ranking of aspects shows similarities. 'My GP should always take me seriously' was in nearly all countries ranked first, while an item about waiting time in the GP's office was always ranked lowest.

Conclusion
Differences between countries in how health care users value different aspects of care are difficult to explain. Further theorising should take into account that importance and performance ratings are positively related, that people compare their experiences with those of others, and that general and instrumental values might be related through the institutions of the health care system.
Muscle oxidative metabolism accelerates with mild acidosis during incremental intermittent isometric plantar flexion exercise
Authors: Homma Toshiyuki , Hamaoka Takafumi , Sako Takayuki , Murakami Motohide , Esaki Kazuki , Kime Ryotaro , Katsumura Toshihito 
Published: February 2005

Abstract
Background
It has been thought that intramuscular ADP and phosphocreatine (PCr) concentrations are important regulators of mitochondorial respiration. There is a threshold work rate or metabolic rate for cellular acidosis, and the decrease in muscle PCr is accelerated with drop in pH during incremental exercise. We tested the hypothesis that increase in muscle oxygen consumption ("Equation missing"o2mus) is accelerated with rapid decrease in PCr (concomitant increase in ADP) in muscles with drop in pH occurs during incremental plantar flexion exercise.

Methods
Five male subjects performed a repetitive intermittent isometric plantar flexion exercise (6-s contraction/4-s relaxation). Exercise intensity was raised every 1 min by 10% maximal voluntary contraction (MVC), starting at 10% MVC until exhaustion. The measurement site was at the medial head of the gastrocnemius muscle. Changes in muscle PCr, inorganic phosphate (Pi), ADP, and pH were measured by 31P-magnetic resonance spectroscopy. "Equation missing"o2mus was determined from the rate of decrease in oxygenated hemoglobin and/or myoglobin using near-infrared continuous wave spectroscopy under transient arterial occlusion. Electromyogram (EMG) was also recorded. Pulmonary oxygen uptake ("Equation missing"o2pul ) was measured by the breath-by-breath gas analysis.

Results
EMG amplitude increased as exercise intensity progressed. In contrast, muscle PCr, ADP, "Equation missing"o2mus, and "Equation missing"o2pul did not change appreciably below 40% MVC, whereas above 40% MVC muscle PCr decreased, and ADP, "Equation missing"o2mus, and "Equation missing"o2pul increased as exercise intensity progressed, and above 70% MVC, changes in muscle PCr, ADP, "Equation missing"o2mus, and "Equation missing"o2pul accelerated with the decrease in muscle pH (~6.78). The kinetics of muscle PCr, ADP, "Equation missing"o2mus, and "Equation missing"o2pul were similar, and there was a close correlation between each pair of parameters (r = 0.969~0.983, p < 0.001).

Conclusion
With decrease in pH muscle oxidative metabolism accelerated and changes in intramuscular PCr and ADP accelerated during incremental intermittent isometric plantar flexion exercise. These results suggest that rapid changes in muscle PCr and/or ADP with mild acidosis stimulate accelerative muscle oxidative metabolism.
Umbilical metastases: current viewpoint
Authors: Gabriele Raimondo , Conte Marco , Egidi Federico , Borghese Mario 
Published: February 2005

Abstract
Background
Umbilical metastases from a malignant neoplasm, also termed Sister Mary Joseph's nodule, are not commonly reported in the English literature, and they have usually been considered as a sign of a poor prognosis for the patient. The present article reports on the current view point on umbilical metastasis besides discussing the epidemiology, clinical presentation, pathophysiology and treatment.

Method
A search of Pubmed was carried out using the term 'umblic*' and 'metastases' or metastasis' revealed no references. Another search was made using the term "Sister Joseph's nodule" or sister Joseph nodule" that revealed 99 references. Of these there were 14 review articles, however when the search was limited to English language it yielded only 20 articles. Articles selected from these form the basis of this report along with cross references.

Results
The primary lesions usually arise from gastrointestinal or genitourinary tract malignancies and may be the presenting symptom or sign of a primary tumour in an unknown site.

Conclusion
A careful evaluation of all umbilical lesions, including an early biopsy if appropriate, is recommended. Recent studies suggest an aggressive surgical approach combined with chemotherapy for such patients may improve survival.
The role of NGOs in global health research for development
Authors: Delisle Hélène , Roberts Janet Hatcher , Munro Michelle , Jones Lori , Gyorkos Theresa W 
Published: February 2005

Abstract
Background
Global health research is essential for development. A major issue is the inequitable distribution of research efforts and funds directed towards populations suffering the world's greatest health problems. This imbalance is fostering major attempts at redirecting research to the health problems of low and middle income countries. Following the creation of the Coalition for Global Health Research – Canada (CGHRC) in 2001, the Canadian Society for International Health (CSIH) decided to review the role of non-governmental organizations (NGOs) in global health research. This paper highlights some of the prevalent thinking and is intended to encourage new thinking on how NGOs can further this role.

Approach
This paper was prepared by members of the Research Committee of the CSIH, with input from other members of the Society. Persons working in various international NGOs participated in individual interviews or group discussions on their involvement in different types of research activities. Case studies illustrate the roles of NGOs in global health research, their perceived strengths and weaknesses, and the constraints and opportunities to build capacity and develop partnerships for research.

Highlights
NGOs are contributing at all stages of the research cycle, fostering the relevance and effectiveness of the research, priority setting, and knowledge translation to action. They have a key role in stewardship (promoting and advocating for relevant global health research), resource mobilization for research, the generation, utilization and management of knowledge, and capacity development. Yet, typically, the involvement of NGOs in research is downstream from knowledge production and it usually takes the form of a partnership with universities or dedicated research agencies.

Conclusion
There is a need to more effectively include NGOs in all aspects of health research in order to maximize the potential benefits of research. NGOs, moreover, can and should play an instrumental role in coalitions for global health research, such as the CGHRC. With a renewed sense of purpose and a common goal, NGOs and their partners intend to make strong and lasting inroads into reducing the disease burden of the world's most affected populations through effective research action.