bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patika
web: a Web interface for analyzing biological pathways through advanced querying and visualization
Authors: Dogrusoz U. , Erson E. Z. , Giral E. , Demir E. , Babur O. , Cetintas A. , Colak R. 
Published: November 2005

Abstract
Summary: Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.
Availability: The Web site is freely accessible to non-commercial users from
Contact: patikaweb@cs.bilkent.edu.tr
Supplementary information: Detailed information is available on the tool Web site (), including key features, screenshots and User’s Guide.
Highly consistent patterns for inherited human diseases at the molecular level
Authors: López-Bigas Núria , Blencowe Benjamin J. , Ouzounis Christos A. 
Published: November 2005

Abstract
Over 1600 mammalian genes are known to cause an inherited disorder, when subjected to one or more mutations. These disease genes represent a unique resource for the identification and quantification of relationships between phenotypic attributes of a disease and the molecular features of the associated disease genes, including their ascribed annotated functional classes and expression patterns. Such analyses can provide a more global perspective and a deeper understanding of the probable causes underlying human hereditary diseases. In this perspective and critical view of disease genomics, we present a comparative analysis of genes reported to cause inherited diseases in humans in terms of their causative effects on physiology, their genetics and inheritance modes, the functional processes they are involved in and their expression profiles across a wide spectrum of tissues. Our analysis reveals that there are more extensive correlations between these attributes of genetic disease genes than previously appreciated. For instance, the functional pattern of genes causing dominant and recessive diseases is markedly different. Also, the function of the genes and their expression correlate with the type of disease they cause when mutated. The results further indicate that a comparative genomics approach for the analysis of genes linked to human genetic diseases will facilitate the elucidation of the underlying molecular and cellular mechanisms.
Contact: nuria.lopez@crg.es; ouzounis@ebi.ac.uk
Supplementary information:
Automatic assignment of biomedical categories: toward a generic approach
Authors: Ruch Patrick 
Published: November 2005

Abstract
Motivation: We report on the development of a generic text categorization system designed to automatically assign biomedical categories to any input text. Unlike usual automatic text categorization systems, which rely on data-intensive models extracted from large sets of training data, our categorizer is largely data-independent.
Methods: In order to evaluate the robustness of our approach we test the system on two different biomedical terminologies: the Medical Subject Headings (MeSH) and the Gene Ontology (GO). Our lightweight categorizer, based on two ranking modules, combines a pattern matcher and a vector space retrieval engine, and uses both stems and linguistically-motivated indexing units.
Results and Conclusion: Results show the effectiveness of phrase indexing for both GO and MeSH categorization, but we observe the categorization power of the tool depends on the controlled vocabulary: precision at high ranks ranges from above 90% for MeSH to &lt;20% for GO, establishing a new baseline for categorizers based on retrieval methods.
Contact: Patrick.Ruch@sim.hcuge.ch
An efficient randomized algorithm for contact-based NMR backbone resonance assignment
Authors: Kamisetty Hetunandan , Bailey-Kellogg Chris , Pandurangan Gopal 
Published: November 2005

Abstract
Motivation: Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call ‘contact-based’, seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were ‘close enough’. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for α-helices and β-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise.
Results: This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental β-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to uncover large consistent sets of interactions.
Availability: Our algorithm has been implemented in the platform-independent Python code. The software can be freely obtained for academic use by request from the authors.
Contact: cbk@cs.dartmouth.edu
Risk factors for glucose intolerance in Danish women with polycystic ovary syndrome
Authors: Trolle Birgitta , Lauszus Finn Friis 
Published: November 2005

Background.  Women with polycystic ovary syndrome (PCOS) are reported to be at risk for glucose intolerance. The aim of the study was to describe these risk factors in a population of Danish PCOS women attending a gynecologic clinic and to identify the parameters with the strongest correlation to the fasting blood glucose levels. In addition, we studied whether the oral glucose tolerance test (OGTT) diagnosed more cases of glucose intolerance in this PCOS population than the fasting plasma glucose value (FPG) alone.Methods.  Cross‐sectional study of 91 women with oligomenorrhea or amenorrhea and elevated serum testosterone, followed by an OGTT in 27 of the women.Results.  Women with a FPG above normal were older and had a higher body mass index (BMI), cholesterol, and triglycerides and a lower sexual hormone binding globulin (SHBG). Of the 21 women older than 34, eight (38%) had a FPG above normal. The OGTT study showed that one of five with abnormal glucose tolerance would not have been diagnosed, if the FPG alone had been performed.Conclusions.  In this study, 38% of women with symptoms of PCOS over the age of 34 had abnormal blood glucose values. These women should receive blood glucose testing regardless of BMI, testosterone levels and family history of type 2 diabetes mellitus. An OGTT may be necessary to find all cases of impaired glucose intolerance.
The impact of oxygen tension on developmental competence of post‐thaw human embryos
Authors: Petersen Astrid , Mikkelsen Anne Lis , Lindenberg Svend 
Published: November 2005

The present study compares the culture of human embryos using two different culture systems: a conventional culture incubator with humidified atmospheric air supplemented with 5% CO2 and a closed culture incubator with a humidified 5% O2 and 5% (5.2–5.5) CO2 and 90% N2 partial pressure.A total of 225 cryopreserved embryos were donated after informed consent and thawed in two batches of 100 and 125 embryos separated by 1 week. A total of 126 (56%) embryos survived the thawing procedure having at least one living blastomere. After thawing, the embryos were randomly allocated to culture in a 5% oxygen partial pressure (n = 65) or to culture in a 20% oxygen partial pressure (n = 61). The embryos were hereafter cultured for 4 days and the number of embryos developed to morula stage or blastocyst stage was examined.The results of the embryo culture in the two trials performed showed an increase from 43% to 68% (19 to 68%) morula formation in trial 1 (trial 2), i.e. on the whole the morula yield more than doubled in favor of culture in a 5% oxygen partial pressure compared with a 20% oxygen partial pressure.
Routine ultrasound screening in the third trimester: a population‐based study
Authors: Sylvan Kerstin , Ryding Elsa Lena , Rydhstroem Håkan 
Published: November 2005

Background.  No population‐based study has evaluated the effects of third trimester ultrasound screening on prognosis.Objective.  To study the effects of routine ultrasound screening in the third trimester on perinatal/infant mortality, prevalence of small for gestational age infants (SGA) and low Apgar score.Study design.  Two university clinics using routine ultrasound screening in the third trimester were compared with seven county or district hospitals with no routine screening. Deliveries between 1985 and 1996 were included. In all, 16 municipalities including 56 371 pregnancies with routine screening were compared with 59 municipalities and 153 355 pregnancies without third trimester screening. An observational design was applied, using data stored during pregnancy, delivery, and during the first year (infant mortality) at the Swedish Medical Birth Registry, The National Board of Health and Welfare. Odds ratio with 95% confidence interval was used in the evaluation. End‐points included incidence of SGA, perinatal/infant mortality, Apgar score at 5 min, cesarean section and instrumental delivery in areas with versus without routine third trimester screeningResults.  No significant difference was seen in the prevalence of the most extreme SGA (< −3 SD from the mean), perinatal complications including cesarean section or instrumental delivery, or perinatal/infant mortality between units with versus without routine ultrasound screening in the third trimester.Conclusion.  Added to the findings of previous small randomized studies, it seems as if routine third trimester ultrasound screening in an unselected population does not reduce perinatal mortality or early neonatal morbidity, expressed as Apgar scores or SGA.
Gestational diabetes: a reappraisal of HBA1c as a screening test
Authors: Agarwal Mukesh M. , Dhatt Gurdeep S. , Punnose John , Koster Gertrude 
Published: November 2005

Background.  Recent technological advances have made HBA1c a more standardized and user‐friendly test with wide availability. This study evaluated HBA1c as a screening test for gestational diabetes mellitus (GDM) in a high‐risk population.Methods.  A total of 442 pregnant women were assessed by HBA1c. Two thresholds were used to ‘rule in or rule out’ GDM, which was confirmed by the ‘gold‐standard’ 75‐g OGTT (World Health Organization criteria).Results.  Eighty‐four (19%) women had GDM while 358 (81%) women were normal; there was a complete overlap of the HBA1c histograms of the two populations. The area under receiver operating characteristic curve of HBA1c to detect GDM was 0·54 (95% CI 0·48–0·61). Using a value of <5·5% to rule out GDM; a sensitivity of 82·1% was achieved, with 15 (16·7%) of 90 women below the threshold being false‐negatives (NPV = 83·3%). Using a threshold of HBA1c ≥ 7·5% to rule‐in GDM; the specificity was 95·8% with 15 (71·4%) of 21 patients over the threshold being false‐positives (PPV = 28·6%). HBA1c would eliminate the need for an OGTT in 25·1% (111/442) of whom 27% (30/111) women would be misclassified. At any HBA1c threshold with an acceptable sensitivity, the false‐positive rate remained high making it necessary for too many healthy women to undergo the confirmatory OGTT.Conclusion.  Despite all the progress in methodology, HBA1c remains a poor test to screen for GDM.
Sympathetic responsibility in ethically difficult situations*
Authors: Danerek Margaretha , Udén Giggi , Dykes Anna‐Karin 
Published: November 2005

Background. Ethical issues arise in many obstetric situations and demand constant consideration by obstetricians. The aim of this study was to highlight the meaning of being in an ethically difficult situation as narrated by obstetricians.Methods. A descriptive design with a qualitative approach using a hermeneutic phenomenological method for analysis. Interviews were performed with 14 obstetricians working in a Swedish hospital setting.Results. The overriding theme wasSympathetic responsibility in the decisions of critical importance for the mother and her infant. Five related themes were to: (i) proceed with a moral reasoning that leads to the choice of a possible solution; (ii) balance one's own medical knowledge and moral insight with the needs and requests of the parents; (iii) be aware of one's medical and moral responsibility in relation to the decision made; (iv) experience the ability to take action and to make and carry out difficult and important decisions relating to the health of the mother and infant; and (v) reflect on a given situation in a manner leading to a rational acceptance of one's own conduct.Conclusions. Sympathetic responsibility is the structure of the meaning of the obstetricians' lived experience, which means that the obstetricians with the help of their medical knowledge and their desire to support the mother's autonomy do what is best for the mother and her infant. Implications include that an exchange of ethical thoughts and moral reasoning should lead to a higher degree of mutual understanding between colleagues and between the different professionals. Co‐operation is important to achieve the best outcome for the mother and her infant.
Response of pregnancy leg edema to a single immersion exercise session
Authors: Hartmann Sabine , Huch Renate 
Published: November 2005

Background.  To quantify the effect of a single immersion exercise session on uncomplicated dependent edema in pregnancy.Methods.  Lower leg volume was measured by water displacement volumetry and limb circumference in nine women with marked dependent edema, but otherwise normal second or third trimester pregnancy, before and after upright water immersion exercise session (Aqua‐Fit®) for 45 min. Maternal heart rate was monitored continuously throughout the session. Blood pressure was measured before and after the session.Results.  Mean left leg volume decreased by 112 ml from 1665 to 1553 ml, and right leg volume by 84 ml from 1665 to 1581 ml (P = 0.007). Cardiovascular parameters fluctuated within the normal range, well below the upper limits recommended in pregnancy.Conclusions.  A single immersion exercise session is a safe, effective, and enjoyable complement, or alternative, to compression stockings for reduction of gestational dependent edema. Further study is required to determine its duration of effect and the optimum interval between sessions.
Beat‐to‐beat estimate of fetal cardiac time intervals using magnetocardiography: longitudinal charts of normality ranges and individual trends
Authors: Comani Silvia , Liberati Marco , Mantini Dante , Merlino Biagio , Alleva Giovanna , Gabriele Elisabetta , Di Luzio Silvano , Romani Gian Luca 
Published: November 2005

Background.  Fetal magnetocardiography (fMCG) records fetal cardiac electro‐physiological activity during the second half of gestation. We aimed at assessing normality values, related variability, and trends of fetal cardiac time intervals (fCTI) evaluated longitudinally from beat‐to‐beat fMCG analysis in uncomplicated pregnancies.Materials and methods.  The fMCG were recorded with multi‐channel system in shielded room. FCTI were estimated on more than 2600 fetal cardiac cycles from 51 fMCG data sets of uncomplicated pregnancies. Independent component analysis (ICA) allowed reconstructing reliable fetal signals for beat‐to‐beat identification of fCTI (RR, P wave, PQ, PR, QT, QTc, QRS, ST, and T wave); intra‐individual variability analysis and trends were calculated; reference longitudinal charts accounted for intra‐ and inter‐individual variations and were compared with figures estimated on averaged signals.Results.  For each data set, fCTI were calculated beat‐to‐beat on rhythm strips of more than 50 beats (95% overall detection rate). FCTI values, variability, and trends were in good agreement with available reference figures; intervals related to P and T waves were, respectively, underestimated and overestimated with respect to those estimated on averaged signals or obtained by other research groups. Errors were reduced and individual trends could be drawn.Conclusions.  ICA permitted the reconstruction of reliable time course of fetal cardiac signals and the beat‐to‐beat calculation of time intervals, and normality ranges, with smaller errors with respect to previous studies. The retrieval of fetal traces with clear morphology and the longitudinal character of the study allowed estimating individual trends and beat‐to‐beat characterization, impossible with cross‐sectional studies on averaged beats.
In vitro fertilization in Sweden: maternal characteristics
Authors: Källén Bengt , Finnström Orvar , Nygren Karl‐Gösta , Otterblad Olausson Petra 
Published: November 2005

Background.  Deliveries among women who had an in vitro fertilization (IVF) are characterized by increased risks for both the mother and the infant/child. Part of these effects may be due to maternal characteristics.Methods.  Using reports from all clinics performing IVF in Sweden, 12 186 women who gave birth after such procedures were identified (13 261 deliveries, 16 280 infants born). Various social and medical characteristics of the women were studied and compared with all women giving birth. Information was retrieved by interviews in early pregnancy or by linkage with various registers.Results.  Women who had IVF were older than other women who gave birth and were older after standard IVF than after intracytoplasmatic sperm injection (ICSI). They were more often of first parity and smoked less than other delivered women. There were more women with high body mass index: they worked outside home less often and were more often of Swedish nationality. Women who had standard IVF had more previous miscarriages than expected, but this was not true for women who had ICSI. Their pattern of drug usage differed from that of other women who had given birth.Conclusions.  Women who underwent IVF and gave birth showed marked deviations from other women who gave birth. Some of these characteristics may help to explain the increased risks associated with these procedures. Women who had ICSI were less deviating than women who had standard IVF.
Combined bromodeoxyuridine immunocapture and terminal‐restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species
Authors: Artursson Veronica , Finlay Roger D. , Jansson Janet K. 
Published: November 2005

SummaryHigh numbers of bacteria are associated with arbuscular mycorrhizal (AM) fungi, but their functions and in situ activities are largely unknown and most have never been characterized. The aim of the present study was to study the impact of Glomus mosseae inoculation and plant type on the active bacterial communities in soil by using a molecular approach, bromodeoxyuridine (BrdU) immunocapture in combination with terminal‐restriction fragment length polymorphism (T‐RFLP). This approach combined with sequence information from clone libraries, enabled the identification of actively growing populations, within the total bacterial community. Distinct differences in active bacterial community compositions were found according to G. mosseae inoculation, treatment with an antifungal compound (Benomyl) and plant type. The putative identities of the dominant bacterial species that were activated as a result of G. mosseae inoculation were found to be mostly uncultured bacteria and Paenibacillus species. These populations may represent novel bacterial groups that are able to influence the AM relationship and its subsequent effect on plant growth.
Aerobic anoxygenic photosynthesis genes and operons in uncultured bacteria in the Delaware River
Authors: Waidner Lisa A. , Kirchman David L. 
Published: November 2005

SummaryPhotosynthesis genes and operons of aerobic anoxygenic photosynthetic (AAP) bacteria have been examined in a variety of marine habitats, but genomic information about freshwater AAP bacteria is lacking. The goal of this study was to examine photosynthesis genes of AAP bacteria in the Delaware River. In a fosmid library, we found two clones bearing photosynthesis gene clusters with unique gene content and organization. Both clones contained 37 open reading frames, with most of those genes encoding known AAP bacterial proteins. The genes in one fosmid were most closely related to those of AAP bacteria in the Rhodobacter genus. The genes of the other clone were related to those of freshwater beta‐proteobacteria. Both clones contained the acsF gene, which is required for aerobic bacteriochlorophyll synthesis, suggesting that these bacteria are not anaerobes. The beta‐proteobacterial fosmid has the puf operon B‐A‐L‐M‐C and is the first example of an uncultured bacterium with this operon structure. The alpha‐3‐proteobacterial fosmid has a rare gene order (Q‐B‐A‐L‐M‐X), previously observed only in the Rhodobacter genus. Phylogenetic analyses of photosynthesis genes revealed a possible freshwater cluster of AAP beta‐proteobacteria. The data from both Delaware River clones suggest there are groups of freshwater or estuarine AAP bacteria distinct from those found in marine environments.
Scientific Vocations in Crisis in France: explanatory social developments and mechanisms
Authors: CONVERT BERNARD , GUGENHEIM FRANCIS 
Published: November 2005

Bernard Convert, Centre national de la recherche scientifique (CLERSE, Lille, France), Francis Gugenheim, OFIP‐Université de Lille 1, FranceThis article examines why numbers have declined in French science universities. It shows that the main causes of this decline are the growth in student numbers between 1985 and 1995 and the changes that this brought about in the educational and social composition of the student population.Since the mid‐1990s, increasingly fewer French students have been enrolling for science subjects at university. Speaking of a ‘loss of interest in science among young people’ is nevertheless premature. The phenomenon is primarily due to socio‐demographic changes. As a result of their position in French higher education, universities, which do not operate a selective admission policy, are a last resort for students rejected by the selective options. Between 1985 and 1995, when student demographics grew apace, universities absorbed most of this growth. After 1995, the supply of selective training increased, while student demographics stagnated. As a result, university enrolments have declined, especially in the sciences. At the same time, holders of science baccalaureates have not been as top‐notch, educationally and socially, as they were fifteen years previously. These students from more modest backgrounds and performing less well in education are shying away from the sciences which are reputed to be more difficult and less ‘profitable’ than other subjects.