bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjusting for publication bias: modelling the selection process
Authors: Preston Carrol , Ashby Deborah , Smyth Rosalind 
Published: June 2004

Abstract
Rationale, aims and background  Systematic review with meta‐analysis, a statistical technique for combining results of several studies, is progressively being used to guide decisions in medicine. Publication bias is acknowledged as a threat to the validity of systematic reviews and its existence may lead to inappropriate decisions about patient management or health policy. It is said to occur when the results of research available in the literature are not representative of the totality of all research. The selection mechanism that causes publication bias is complex, yet despite an extensive literature of empirical research identifying risk factors for publication, little work has been done to improve models of selection.
Methods  Methods that adjust combined meta‐analytic estimates for publication bias are compared and applied to a systematic review of oral rehydration solution in the treatment of dehydration. Within a weighted distributions framework models of the selection process are considered and developed further.
Conclusions  Weighted distributions offer a flexible approach that allows the potential to modify the selection function to incorporate other factors. Methods that adjust combined estimates should not be used to provide an alternative answer but to consider the robustness of the combined estimate to publication bias.
Attitudes and knowledge of primary care professionals towards evidence‐based practice: a postal survey
Authors: O'Donnell Catherine A. 
Published: June 2004

Abstract
Objectives  To describe the attitudes, awareness and use of evidence across key professional groups working in primary care.
Methods  A postal questionnaire was sent to all lead/chairs, general managers, clinical governance leads, lead nurses, lead pharmacists and public health practitioners working in local health care cooperatives in Scotland.
Results  289 (66.1%) health care professionals responded, ranging from 51% of general managers to 80% of lead nurses. All professional groups supported evidence‐based practice. General practitioners (GPs) were less likely to agree that they had the skills to carry out literature reviews or appraise evidence compared to nurses and public health facilitators (36% vs. 75% vs. 80%; 51% vs. 64% vs. 70%). Access to the internet and bibliographic databases was good for all groups but GPs used a narrower spectrum of evidence‐based journals, relying mainly on medical literature. Only nurses and public health practitioners appeared to have any understanding of qualitative research terms. Public health practitioners were also least likely to view guidelines or protocols developed by others as the best source of evidence for primary care. The major perceived barrier to practising evidence‐based practice was time. Consequently the most important facilitator was protected time, but increased resources (financial and staff) and training were also cited. Professional groups other than GPs perceived inter‐professional boundaries as a barrier and suggested multi‐professional teamworking and learning as potential supports for evidence‐based practice.
Conclusions  While all professional groups welcome and support evidence‐based practice, there are clear differences in the starting point and perspectives across the groups. These need to recognized and addressed to ensure that learning the skills of evidence‐based practice and implementing evidence are effective. This will also enhance the ability of primary care organizations to develop robust mechanisms for supporting key aspects of clinical governance.
A multidisciplinary guideline for the acute phase of stroke: barriers perceived by Dutch neurologists
Authors: Van Der Weijden Trudy , Hooi Jurenne D. , Grol Richard , Limburg Martien 
Published: June 2004

Abstract
Rationale, aims and objectives  Guidelines for stroke management should improve quality of care. Dissemination of guidelines, however, does not guarantee guideline adherence. The aim of this paper is to investigate barriers for guideline adherence to bring about suggestions for possible implementation strategies.
Method  Questionnaire survey among all Dutch neurologists working on neurology wards in general hospitals during the year 2000 in The Netherlands.
Results  The neurologists expressed a high degree of agreement with the diagnostic and preventive recommendations, but expressed doubts with regard to the therapeutic recommendations, especially for the recombinant tissue plasminogen activator therapy. In general, barriers at the organizational and the multidisciplinary team level were most prominent.
Conclusions  Active implementation of the guidelines seems necessary. Implementation strategies should be focused on the different sources of barriers: the caregiver, the patient and the organization of care.
Clinical trials: deliberations on their essence and value
Authors: Schelling Franz A. 
Published: June 2004

AbstractRationale, aim & objectives  In the context of the evidence‐based medicine (EBM) movement, the clinical trial has come to be hailed as the ultimate source of medical knowledge, and especially of clinical pharmacology. By subjecting the premises of this procedure to a thorough analysis, the author hopes to achieve a sound rating of its epistemological significance in the context of medical research.Method  Current claims on the basic importance of the evidence provided by standardized clinical trials are confronted with conflicting observations concerning their current application in medical practice. The stereotyped trials of present research in multiple sclerosis serve as an example to illustrate this point.Results  Traditional assumptions concerning the validity of standardized clinical trials are based on an illusion of absolute objectivity and reliability. Apart from being subject to tough publish (conveniently)‐or‐perish and commercial influences, the results of clinical trials, especially drug trials, are of limited informative value in diverse respects, such as (i) clinical trials do not identify every possible drug reaction for every instance of a disease; (ii) their results never allow the prediction of the efficacy of a specific drug in any given individual; (iii) clinical trials have no inherent potential to provide concrete insights into the nature and cause(s) of a definite morbid condition; and (iv) extensions of clinical drug trials to ever‐larger study groups indicate serious problems in basic theoretical respects.Conclusion  A clinical trial cannot indicate a certain prevention or cure for any particular instance of a disease, and the correctness of its individual predictions is always only contingent. This can be explained by the fact that the correspondence between the nature of each of all pathological conditions presented by the different members of a clinical trial population and by the individual patients being treated according to the results of the trial is never complete.
Is there life after evidence‐based medicine?
Authors: Porta Massimo 
Published: June 2004

AbstractRecent years have witnessed the rising star of evidence‐based medicine (EBM) as an approach towards rationalizing clinical practice in the face of an exponentially growing body of knowledge. Along with it, however, a sense of unease is rising among practising doctors, as they feel that well‐intentioned principles may be increasingly applied to disease management, with its economic and cost‐cutting implications, rather than disease cure or treatment. There is a fear that any procedure, however time‐honoured, that was not or cannot be subjected to randomized controlled clinical trial, may some day be discouraged, more or less strongly, based on statistical rather than clinical considerations. Resistance to EBM ranges from a ‘we‐know‐best’ uncompromising non‐acceptance to a ‘you‐may‐be‐right‐sometimes‐but‐don’t‐ever‐tell‐me‐what‐to‐do’ sort of openness. The problem is one of measure, in more than one sense: measure of how effective individual practitioners are in treating their patients, measure of how useful EBM is, measure in promoting what may become a dogmatic application of probability laws to the very improbable practice of medicine, measure in siding with the supporters of health care on a budget. There is much that EBM can give to clinical medicine by its ability to organize complex data sets for the ultimate benefit of patients, but there is also much that can stifle practice by forcing a dogmatic implementation, rather than a flexible common sense approach, of its principles.
Hospital doctors’ self‐rated skills in and use of evidence‐based medicine – a questionnaire survey
Authors: Oliveri Roberto S. , Gluud Christian , Wille‐Jørgensen Peer A. 
Published: June 2004

Abstract
Rationale, aims and objectives  Problems in understanding basic aspects of evidence‐based medicine (EBM) may form barriers to its implementation into clinical practice. We examined hospital doctors’ skills in EBM terms and related these skills to their use of information sources, critical appraisal, and implementation of EBM into clinical practice.
Methods  A self‐administered questionnaire was sent to all hospital doctors (n = 376) at a university hospital in Denmark, including 12 questions on methodological terms frequently used in evidence‐based literature plus one non‐existing dummy term. Furthermore, participants were asked about their use of various information sources, self‐rated skills of critical appraisal of standard scientific literature, and level of implementation of evidence‐based principles in daily clinical settings. Based on the answers to the 12 evidence‐based methodological terms, we calculated a familiarity score.
Results  Proportion of responding was 60% (n = 225), but representative for all hospital doctors regarding background data. Ten doctors (4.4%) could define and explain all 12 methodological terms. The majority of all doctors showed interest in knowing more about the terms. Fifty‐six per cent knew the dummy term. Doctors mainly consulted traditional and possibly insufficient sources (textbooks, colleagues, scientific journals) when searching for clinical evidence. The Cochrane Library was the least consulted information source and had never been consulted by 49%. Only 18% always practised EBM. More reliance on PubMed and The Cochrane Library as information sources, more competence of critical appraisal, and more frequent practise of EBM were significantly (P < 0.001) associated with a higher familiarity score. Compared to seldom or never users of The Cochrane Library, frequent users had significantly higher academic degree (P = 0.01), familiarity score (P < 0.001),  and  use of PubMed (P = 0.0004).
Discussion and conclusions  Most hospital doctors seem to lack knowledge of key methodological evidence‐based medicine terms. This may form a barrier when consulting EBM sources and to the implementation of EBM into clinical practice.
The doctor, his patient, and the computerized evidence‐based guideline
Authors: Lipman Toby 
Published: June 2004

AbstractThis paper explores some of the issues raised by the finding in a randomized controlled trial (RCT) that general practitioners (GPs) taking part failed to use a computerized evidence‐based guideline, nor did it have any impact on patient outcomes. GPs are expected to ‘make an initial decision on every problem [patients] may present’ and to address psychological and social problems in addition to biomedical ones. The computerized guideline imposed an external, largely biomedical, agenda that superseded the patient’s. This disrupted the normal pattern of GP consultations and it was therefore ignored. Guidelines for any particular disease are effective if backed up by a detailed programme of education and audit. However, the large number of different conditions seen in general practice means that it is impractical to have such programmes for more than a small fraction of the clinical workload. The reductionist assumptions underlying the construction of evidence‐based guidelines from systematic reviews lead to inflexible recommendations on the management of disease. Anthropologists and sociologists make an important distinction between scientifically defined diseases and the culturally constructed experience of illness. Because GPs deal with patients suffering illness that may or may not result from disease, disease‐centred guidelines often conflict with their needs and wishes. The development of evidence‐based medicine (EBM) was intended as a tool to help doctors make sense of evidence in the context of individual patients’ problems. Few GPs are skilled in it, and it has been appropriated by powerful expert groups such as guidelines developers and the pharmaceutical industry. It is suggested that more understanding of EBM by GPs leads to better informed decision making by them and their patients.
Lipoprotein processing is required for virulence of Mycobacterium tuberculosis†
Authors: Sander P. , Rezwan M. , Walker B. , Rampini S. K. , Kroppenstedt R. M. , Ehlers S. , Keller C. , Keeble J. R. , Hagemeier M. , Colston M. J. , Springer B. , Böttger E. C. 
Published: June 2004

SummaryLipoproteins are a subgroup of secreted bacterial proteins characterized by a lipidated N‐terminus, processing of which is mediated by the consecutive activity of prolipoprotein diacylglyceryl transferase (Lgt) and lipoprotein signal peptidase (LspA). The study of LspA function has been limited mainly to non‐pathogenic microorganisms. To study a potential role for LspA in the pathogenesis of bacterial infections, we have disrupted lspA by allelic replacement in Mycobacterium tuberculosis, one of the world's most devastating pathogens. Despite the presence of an impermeable lipid outer layer, it was found that LspA was dispensable for growth under in vitro culture conditions. In contrast, the mutant was markedly attenuated in virulence models of tuberculosis. Our findings establish lipoprotein metabolism as a major virulence determinant of tuberculosis and define a role for lipoprotein processing in bacterial pathogenesis. In addition, these results hint at a promising new target for therapeutic intervention, as a highly specific inhibitor of bacterial lipoprotein signal peptidases is available.
New Listeria monocytogenes prfA* mutants, transcriptional properties of PrfA* proteins and structure–function of the virulence regulator PrfA
Authors: Vega Yolanda , Rauch Markus , Banfield Mark J. , Ermolaeva Svetlana , Scortti Mariela , Goebel Werner , Vázquez‐Boland José A. 
Published: June 2004

SummaryPrfA, a transcription factor structurally related to Crp/Fnr, activates Listeria monocytogenes virulence genes during intracellular infection. We report two new PrfA* mutations causing the constitutive overexpression of the PrfA regulon. Leu‐140Phe lies in αD adjacent to the DNA‐binding motif in the C‐terminal domain, like a previously characterized PrfA* mutation (Gly‐145Ser). Ile‐45Ser, in contrast, maps to the N‐terminal β‐roll, a structure similar to that of the Crp cAMP binding site. The in vitro transcriptional properties of recombinant PrfA*I45S and PrfA*G145S were compared to those of PrfAWT at two differentially regulated PrfA‐dependent promoters, PplcA and PactA. The two PrfA* mutations increased the affinity for the target DNA to a different extent, and the differences in DNA binding (PrfA*G145S > PrfA*I45S >>> PrfAWT) correlated with proportional differences in transcriptional activity. The use of the PrfA* proteins revealed that PplcA had a greater affinity for, and was more sensitive to, PrfA than PactA. RNA polymerase (RNAP) initiated transcription independently of PrfA at PplcA, but not at PactA, consistent with bandshift experiments suggesting that PplcA has a greater affinity for RNAP than PactA. Thus, differences in affinity for both PrfA and RNAP appear to determine the different expression pattern of PrfA‐regulated promoters. Modelling of the PrfA* mutations in the crystal structure of PrfA and comparison with structure–function analyses of Crp, in which similar mutations lead to constitutively active (cAMP‐independent) Crp* proteins, suggested that PrfA shares with Crp an analogous mechanism of cofactor‐mediated allosteric shift. Our data support a regulatory model in which changes in PrfA‐dependent gene expression are primarily accounted for by changes in PrfA activity.
Are rhoptries in Apicomplexan parasites secretory granules or secretory lysosomal granules?
Authors: Ngô Huân M. , Yang Mei , Joiner Keith A. 
Published: June 2004

SummaryThe club‐shaped rhoptries in Apicomplexan parasites are one of the most unusual secretory organelles among the eukaryotes, containing unusual lipid and protein cargo that is specialized for intracellular parasitism. Rhoptries have traditionally been viewed strictly as regulated secretory granules. We discuss in this article recent data on the cargo, function and biogenesis of rhoptries in two parasitic model systems, Toxoplasma and Plasmodium. Current findings suggest that rhoptries receive products from both biosynthetic and endocytic pathways and, therefore, they are most analogous to secretory lysosomal granules found in mammalian cells.
Involvement of multiple DNA elements in iron‐inducible transcription of the ap65‐1 gene in the protozoan parasite Trichomonas vaginalis
Authors: Ong Shiou‐Jeng , Huang Shen‐Chi , Liu Hsing‐Wei , Tai Jung‐Hsiang 
Published: June 2004

SummaryA reputed iron‐responsive region, which contains multiple nuclear protein‐binding DNA sequences, was shown previously to regulate iron‐inducible transcription of the ap65‐1 gene in the protozoan pathogen, Trichomonas vaginalis. These DNA sequences include two overlapping MYB recognition elements (MRE‐1/MRE‐2r) and three abutted T‐tract elements. Additional nuclear protein‐binding DNA sequences flanking the 5′ (AGTGAAGTGA) and 3′ (MRE‐2f) of the iron‐responsive region were identified in the present study. A stable promoter assay and primer extension revealed that transcriptional activity of the ap65‐1 promoter is iron inducible as well as growth related, being lowest in the early logarithmic phase and highest in the mid‐logarithmic phase. Subsequent mutational analysis of individual DNA elements of the ap65‐1 promoter suggests that closely spaced T‐tract elements together with an intervening GAAGGAAG sequence within the iron‐responsive region are most critical for regulation of overall transcriptional activity, whereas an additional AGTGAAGTGA and MRE‐2f together with an upstream T‐rich region are required for optimal iron‐inducible activity, and the MRE‐1/MRE‐2r overlap is only involved in growth‐related activity. These observations suggest that expression of the ap65‐1 gene is dynamically regulated under various growth conditions via interactions among multiple DNA regulatory elements.
Role of the amino‐terminal GAF domain of the NifA activator in controlling the response to the antiactivator protein NifL
Authors: Martinez‐Argudo Isabel , Little Richard , Dixon Ray 
Published: June 2004

SummaryThe NifA protein from Azotobacter vinelandii belongs to a family of enhancer binding proteins (EBPs) that activate transcription by RNA polymerase containing the sigma factor σ54. These proteins have conserved AAA+ domains that catalyse ATP hydrolysis to drive conformational changes necessary for open complex formation by σ54‐RNA polymerase. The activity of the NifA protein is highly regulated in response to redox and fixed nitrogen through interaction with the antiactivator protein NifL. Binding of NifL to NifA inhibits the ATPase activity of NifA, and this interaction is controlled by the amino‐terminal GAF domain of NifA that binds 2‐oxoglutarate. Mutations conferring resistance to NifL are located in both the GAF and the AAA+ domains of NifA. To investigate the mechanism by which the GAF domain regulates the activity of the AAA+ domain, we screened for second‐site mutations that suppress the NifL‐resistant phenotype of mutations in the AAA+ domain. One suppressor mutation, F119S, in the GAF domain restores inhibition by NifL to an AAA+ domain mutation, E356K, in response to fixed nitrogen but not in response to oxygen. The biochemical properties of this mutant protein are consistent with the in vivo phenotype and demonstrate that interdomain suppression results in sensitivity to inhibition by NifL in the presence of the signal transduction protein GlnK, but not to the oxidized form of NifL. In the absence of an AAA+ domain mutation, the F119S mutation confers hypersensitivity to repression by NifL. Isothermal titration calorimetry demonstrates that this mutation prevents binding of 2‐oxoglutarate to the GAF domain. Our data support a model in which the GAF domain plays an essential role in preventing inhibition by NifL under conditions appropriate for nitrogen fixation. These observations are of general significance in considering how the activities of EBPs are controlled in response to environmental signals.
Biosynthesis of the angiogenesis inhibitor borrelidin by Streptomyces parvulus Tü4055: insights into nitrile formation†
Authors: Olano Carlos , Moss Steven J. , Braña Alfredo F. , Sheridan Rose M. , Math Vidya , Weston Alison J. , Méndez Carmen , Leadlay Peter F. , Wilkinson Barrie , Salas José A. 
Published: June 2004

SummaryThe 18‐membered polyketide macrolide borrelidin exhibits a number of important biological activities, including potent angiogenesis inhibition. This has prompted two recent total syntheses as well as the cloning of the biosynthetic gene cluster from Streptomyces parvulus Tü4055. Borrelidin possesses some unusual structural characteristics, including a cyclopentane carboxylic acid moiety at C17 and a nitrile moiety at C12 of the macrocyclic ring. Nitrile groups are relatively rare in nature, and little is known of their biosynthesis during secondary metabolism. The nitrile group of borrelidin is shown here to arise from the methyl group of a methylmalonyl‐CoA extender unit incorporated during polyketide chain extension. Insertional inactivation of two genes in the borrelidin gene cluster, borI (coding for a cytochrome P450 monooxygenase) and borJ (coding for an aminotransferase), generated borrelidin non‐producing mutants. These mutants accumulated different compounds lacking the C12 nitrile moiety, with the product of the borI‐minus mutant (12‐desnitrile‐12‐methyl‐borrelidin) possessing a methyl group and that of the borJ‐minus mutant (12‐desnitrile‐12‐carboxyl‐borrelidin) a carboxyl group at C12. The former but not the latter was converted into borrelidin when biotransformed by an S. parvulus mutant that is deficient in the biosynthesis of the borrelidin starter unit. This suggests that 12‐desnitrile‐12‐methyl‐borrelidin is a competent biosynthetic intermediate, whereas the carboxylated derivative is a shunt metabolite. Bioconversion of 12‐desnitrile‐12‐methyl‐borrelidin into borrelidin was also achieved in a heterologous system co‐expressing borI and borJ in Streptomyces albus J1074. This bioconversion was more efficient when borK, which is believed to encode a dehydrogenase, was simultaneously expressed with borI and borJ. On the basis of these findings, a pathway is proposed for the formation of the nitrile moiety during borrelidin biosynthesis.