bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Longitudinal Study of Emergency Medicine Residents' Malpractice Fear and Defensive Medicine
Authors: Rodriguez Robert M. , Anglin Deirdre , Hankin Abigail , Hayden Steven R. , Phelps Molly , McCollough Lynn , Hendey Gregory W. 
Published: April 2007

Objectives:To determine the baseline level and evolution of defensive medicine and malpractice concern (MC) of emergency medicine (EM) residents. Methods:Using a validated instrument consisting of case scenarios and Likert‐type scale questions, the authors performed a prospective, longitudinal (June 2001 to June 2005) study of EM residents at five 4‐year California residency programs. Results:All 51 EM interns of these residencies were evaluated; four residents left their programs and one took medical leave, resulting in 46 graduating residents evaluated. MC did not affect the residency choice of interns. Although perceived likelihood of serious disease increased in case scenarios over time, defensive medicine decreased in 27% of cases and increased in 20%. On a scale with 1 representing extremely influential and 5 representing not at all influential, the mean (±SD) influence of MC on interns' and graduates' case evaluation and management was 2.5 (±1.1) and 2.7 (±1.0), respectively. Comparing interns and graduates, there was no significant difference in the percentages of respondents who declared MC (mean difference in proportions, 3.3%; 95% CI =−8.4% to 15%) or refused procedures because of MC (11.5%; 95% CI =−1.3% to 24.3%). More interns, however, declared substantial loss of enjoyment of medicine than graduates (48%; 95% CI = 30.3% to 65.5%). Conclusions:Physicians enter four‐year EM residencies in California with moderate MC and defensive medicine, which do not change significantly over time and do not markedly impact their decisions to perform emergency department procedures. Malpractice fear markedly decreases interns' enjoyment of medicine, but this effect decreases by residency completion.
Computational biology of cardiac myocytes: proposed standards for the physiome
Authors: Smith Nicolas P. , Crampin Edmund J. , Niederer Steven A. , Bassingthwaighte James B. , Beard Daniel A. 
Published: April 2007

SUMMARYPredicting information about human physiology and pathophysiology from genomic data is a compelling, but unfulfilled goal of post-genomic biology. This is the aim of the so-called Physiome Project and is, undeniably, an ambitious goal. Yet if we can exploit even a small proportion of the rich and varied experimental data currently available, significant insights into clinically important aspects of human physiology will follow. To achieve this requires the integration of data from disparate sources into a common framework. Extrapolation of available data across species, laboratory techniques and conditions requires a quantitative approach. Mathematical models allow us to integrate molecular information into cellular, tissue and organ-level, and ultimately clinically relevant scales. In this paper we argue that biophysically detailed computational modelling provides the essential tool for this process and, furthermore, that an appropriate framework for annotating, databasing and critiquing these models will be essential for the development of integrative computational biology.
Advanced sequencing technologies and their wider impact in microbiology
Authors: Hall Neil 
Published: April 2007

SUMMARYIn the past 10 years, microbiology has undergone a revolution that has been driven by access to cheap high-throughput DNA sequencing. It was not long ago that the cloning and sequencing of a target gene could take months or years,whereas now this entire process has been replaced by a 10 min Internet search of a public genome database. There has been no single innovation that has initiated this rapid technological change; in fact, the core chemistry of DNA sequencing is the same as it was 30 years ago. Instead, progress has been driven by large sequencing centers that have incrementally industrialized the Sanger sequencing method. A side effect of this industrialization is that large-scale sequencing has moved out of small research labs, and the vast majority of sequence data is now generated by large genome centers. Recently,there have been advances in technology that will enable high-throughput genome sequencing to be established in research labs using bench-top instrumentation. These new technologies are already being used to explore the vast microbial diversity in the natural environment and the untapped genetic variation that can occur in bacterial species. It is expected that these powerful new methods will open up new questions to genomic investigation and will also allow high-throughput sequencing to be more than just a discovery exercise but also a routine assay for hypothesis testing. While this review will concentrate on microorganisms, many of the important arguments about the need to measure and understand variation at the species, population and ecosystem level will hold true for many other biological systems.
Comparative environmental genomics in non-model species: using heterologous hybridization to DNA-based microarrays
Authors: Buckley Bradley A. 
Published: April 2007

SUMMARY
The emerging field of comparative environmental genomics involves the cross-species comparison of broad-scale patterns of gene expression. Often,the goal is to elucidate the evolutionary basis or ecological implications of genomic responses to environmental stimuli. DNA-based microarrays represent powerful means with which to investigate gene expression, and the application of genomic tools to studies on non-model species is becoming increasingly feasible. The use of a microarray generated from one species to probe gene expression in another, a method termed `heterologous hybridization',eliminates the need to fabricate novel microarray platforms for every new species of interest. In this review, recent advances in heterologous hybridization are reviewed, and the technical caveats of this approach are discussed.
Integrative physiology, functional genomics and the phenotype gap: a guide for comparative physiologists
Authors: Dow Julian A. T. 
Published: April 2007

SUMMARYClassical, curiosity-led comparative physiology finds itself at a crossroads. Major funding for classical physiology is becoming harder to find,as grant agencies focus on more molecular approaches or on science with more immediate strategic value to their respective countries. In turn, this shift in funding places Zoology and Animal Science departments under enormous stress: student numbers are buoyant, but how can research funding be maintained at high levels?Our research group has argued for the redefinition of integrative physiology as the investigation of gene function in an organotypic context in the intact animal. Implicit in this definition is the use of transgenics and reverse genetics to manipulate gene function in a cell-specific manner; this in turn implies the use of a genetically tractable `model organism'. The significance of this definition is that it aligns integrative physiology with functional genomics. Again, functional genomics draws heavily on reverse genetics to elucidate the function of novel genes. The phenotype gap (the mismatch between what a genetic model organism's genome encodes and the reasons that it has historically been studied) emphasises the need to attract and empower functional biologists: can all 13 500 genes in Drosophila really be explained in terms of developmental biology? So,by embracing the integrative physiology manifesto, comparative physiologists can not only accelerate their own research, but their functional skills can make them indispensable in the post-genomic endeavour.
Biological impacts and context of network theory
Authors: Almaas Eivind 
Published: April 2007

SUMMARY
Many complex systems can be represented and analyzed as networks, and examples that have benefited from this approach span the natural sciences. For instance, we now know that systems as disparate as the World Wide Web, the Internet, scientific collaborations, food webs, protein interactions and metabolism all have common features in their organization, the most salient of which are their scale-free connectivity distributions and their small-world behavior. The recent availability of large-scale datasets that span the proteome or metabolome of an organism have made it possible to elucidate some of the organizational principles and rules that govern their function,robustness and evolution. We expect that combining the currently separate layers of information from gene regulatory networks, signal transduction networks, protein interaction networks and metabolic networks will dramatically enhance our understanding of cellular function and dynamics.
Interpreting physiological responses to environmental change through gene expression profiling
Authors: Gracey Andrew Y. 
Published: April 2007

SUMMARY
Identification of differentially expressed genes in response to environmental change offers insights into the roles of the transcriptome in the regulation of physiological responses. A variety of methods are now available to implement large-scale gene expression screens, and each method has specific advantages and disadvantages. Construction of custom cDNA microarrays remains the most popular route to implement expression screens in the non-model organisms favored by comparative physiologists, and we highlight some factors that should be considered when embarking along this path. Using a carp cDNA microarray, we have undertaken a broad, system-wide gene expression screen to investigate the physiological mechanisms underlying cold and hypoxia acclimation. This dataset provides a starting point from which to explore a range of specific mechanistic hypotheses at all levels of organization, from individual biochemical pathways to the level of the whole organism. We demonstrate the utility of two data analysis methods, Gene Ontology profiling and rank-based statistical methods, to summarize the probable physiological function of acclimation-induced gene expression changes, and to prioritize specific genes as candidates for further study.
Evolvability of physiological and biochemical traits: evolutionary mechanisms including and beyond single-nucleotide mutation
Authors: Feder Martin E. 
Published: April 2007

SUMMARYA longstanding challenge for biologists has been to explain not just how organisms are adapted to diverse environments, but how these adaptations arise. Although natural selection is clearly sufficient to act on heritable variation, is this heritable variation sufficient to yield complex adaptations and how does this variation itself arise? Much prior focus has been on mutation of single nucleotides in genes. This process is common and can have dramatic phenotypes, but could be limited in its ability to culminate in complex adaptations for two kinds of reasons: (i) because natural selection is powerful, it can purge genetic variation, and (ii) evolutionary transition from the absence to the presence of a complex adaptation seemingly requires multiple mutations at the right place and time and in the right sequence, with each intermediate stage having increased overall fitness; this seems highly improbable. Because the networks that organisms comprise are hierarchical and redundant and have modular structure, however, single-nucleotide mutations can have large and tolerable impacts. Diverse mechanisms, collectively evolutionary capacitors, can shield genetic variation from the purgative of selection. These features can enable evolution to proceed viasingle-nucleotide mutation. Importantly, single-nucleotide mutation usually only modifies existing genes rather than creating new ones, and numerous other mechanisms eclipse single-nucleotide mutation in creating genetic variation. These include gene duplication (both segmental and whole-genome), lateral gene transfer, hybridization, mobile genetic elements and symbiosis. Other processes can scramble and reassemble nucleotide sequence. The mechanisms beyond single-gene mutation offer considerable promise in detailing the evolution of complex physiological and biochemical traits, and have already done so for several morphological traits.
N-Terminal Pro-B-Type Natriuretic Peptide Predicts Total and Cardiovascular Mortality in Individuals with or without Stable Coronary Artery Disease: The Ludwigshafen Risk and Cardiovascular Health Study
Authors: März Winfried , Tiran Beate , Seelhorst Ursula , Wellnitz Britta , Bauersachs Johann , Winkelmann Bernhard R , Boehm Bernhard O 
Published: April 2007

AbstractBackground: Measurement of N-terminal pro-B-type natriuretic peptide (NT-pro-BNP) measurement can be used to predict mortality in patients with acute coronary syndromes. Information on the value of NT-pro-BNP in clinically stable persons scheduled for angiography is limited.Methods: We used Cox proportional hazards regression to examine the effect of NT-pro-BNP on total and cardiovascular mortality in 1135 with and 506 individuals without stable coronary artery disease (CAD).Results: NT-pro-BNP was associated with New York Heart Association functional class, left ventricular (LV) systolic function, and LV end-diastolic pressure. NT-pro-BNP was positively related to age, female sex, hypertension, and former and current smoking and negatively related to body mass index and glomerular filtration rate. During a median follow-up of 5.45 years, NT-pro-BNP concentrations of 100–399, 400-1999, or ≥2000 ng/L resulted in unadjusted hazard ratios (95% CI) for all-cause death of 3.2 (1.8–5.6), 6.63 (3.8–11.6), and 16.5 (9.2–29.8), respectively, compared with concentrations &lt;100 ng/L. Hazard ratios (CI) for death from cardiovascular causes were 3.8 (1.8–8.2), 9. 3 (4.4–19.5), and 22.2 (10.2–48.4). NT-pro-BNP remained predictive of total and cardiovascular mortality after accounting for age, sex, diabetes mellitus, body mass index, smoking, hypertension, dyslipidemia, glomerular filtration rate, presence or absence of CAD on angiography, cardiovascular medication, revascularization at baseline, clinical signs of heart failure, LV systolic function, and C-reactive protein.Conclusions: NT-pro-BNP is predictive of all-cause and cardiovascular mortality in individuals with or without stable angiographic CAD independently of other cardiovascular risk factors, coronary atherosclerosis, and cardiac function.
The −256T&gt;C Polymorphism in the Apolipoprotein A-II Gene Promoter Is Associated with Body Mass Index and Food Intake in the Genetics of Lipid Lowering Drugs and Diet Network Study
Authors: Corella Dolores , Arnett Donna K , Tsai Michael Y , Kabagambe Edmond K , Peacock James M , Hixson James E , Straka Robert J , Province Michael , Lai Chao-Qiang , Parnell Laurence D , Borecki Ingrid , Ordovas Jose M 
Published: April 2007

AbstractBackground: Apolipoprotein A-II (APOA2) plays an ambiguous role in lipid metabolism, obesity, and atherosclerosis.Methods: We studied the association between a functional APOA2 promoter polymorphism (−265T&gt;C) and plasma lipids (fasting and postprandial), anthropometric variables, and food intake in 514 men and 564 women who participated in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study. We obtained fasting and postprandial (after consuming a high-fat meal) measures. We measured lipoprotein particle concentrations by proton nuclear magnetic resonance spectroscopy and estimated dietary intake by use of a validated questionnaire.Results: We observed recessive effects for this polymorphism that were homogeneous by sex. Individuals homozygous for the −265C allele had statistically higher body mass index (BMI) than did carriers of the T allele. Consistently, after multivariate adjustment, the odds ratio for obesity in CC individuals compared with T allele carriers was 1.70 (95% CI 1.02–2.80, P = 0.039). Interestingly, total energy intake in CC individuals was statistically higher [mean (SE) 9371 (497) vs 8456 (413) kJ/d, P = 0.005] than in T allele carriers. Likewise, total fat and protein intakes (expressed in grams per day) were statistically higher in CC individuals (P = 0.002 and P = 0.005, respectively). After adjustment for energy, percentage of carbohydrate intake was statistically lower in CC individuals. These associations remained statistically significant even after adjustment for BMI. We found no associations with fasting lipids and only some associations with HDL subfraction distribution in the postprandial state.Conclusions: The −265T&gt;C polymorphism is consistently associated with food consumption and obesity, suggesting a new role for APOA2 in regulating dietary intake.
Interaction of Epe1 With the Heterochromatin Assembly Pathway inSchizosaccharomyces pombe
Authors: Isaac Sara , Walfridsson Julian , Zohar Tal , Lazar David , Kahan Tamar , Ekwall Karl , Cohen Amikam 
Published: April 2007

AbstractEpe1 is a JmjC domain protein that antagonizes heterochromatization in Schizosaccharomyces pombe. Related JmjC domain proteins catalyze a histone demethylation reaction that depends on Fe(II) and α-ketoglutarate. However, no detectable demethylase activity is associated with Epe1, and its JmjC domain lacks conservation of Fe(II)-binding residues. We report that Swi6 recruits Epe1 to heterochromatin and that overexpression of epe1+, like mutations in silencing genes or overexpression of swi6+, upregulates expression of certain genes. A significant overlap was observed between the lists of genes that are upregulated by overexpression of epe1+ and those that are upregulated by mutations in histone deacetylase genes. However, most of the common genes are not regulated by Clr4 histone methyltransferase. This suggests that Epe1 interacts with the heterochromatin assembly pathway at the stage of histone deacetylation. Mutational inactivation of Epe1 downregulates ∼12% of S. pombe genes, and the list of these genes overlaps significantly with the lists of genes that are upregulated by mutations in silencing genes and genes that are hyperacetylated at their promoter regions in clr6-1 mutants. We propose that an interplay between the repressive HDACs activity and Epe1 helps to regulate gene expression in S. pombe.
A Mechanical Evaluation of Implants Placed With Different Surgical Techniques Into the Trabecular Bone of Goats
Authors: Shalabi Manal M. , Wolke Johannes G. C. , de Ruijter Anja J. E. , Jansen John A. 
Published: April 2007

AbstractThe aim of the study was to assess the effects of surgical technique and implant surface roughness on implant fixation. A total of 48 screw implants with machined or etched surface topographies were placed into the femoral condyles of goats. The implant sites were prepared by a conventional technique, by undersized preparation, or by the osteotome technique. Bone tissue responses were evaluated after 12 weeks of healing by removal torque testing and histologic analysis using scanning electron microscope. The cumulative removal torque value of the etched implants placed with the undersized technique (98 ± 29 Ncm) was higher (50 ± 35 Ncm) to a level of statistical significance than machined surface implants placed by the osteotome technique. Scanning electron microscope evaluation indicated that all implants showed interfacial bone contact. The torque test resulted in fracture at the bone-implant interface for all experimental conditions. Installation of etched implants using an undersized preparation of the implant bed resulted in superior bonding strength with the surrounding bone at 12 weeks after surgery. Evidently, the undersized preparation technique improved the early fixation of oral implants in this study.
Flapless Dental Implant Placement
Authors: Flanagan Dennis 
Published: April 2007

Abstract
Flapless dental implant placement is possible in selected patients but limited to those sites with adequate or augmentable attached gingiva and available bone volume and density. Inadequate attached gingiva, available bone, and bone density may be augmented by pre-, intra-, or postoperative procedures. Bone ridge contour can be approximated by using a described fast set polyvinyl siloxane site evaluation technique. Assuming adequate length and height, a bone width of 5 mm is usually acceptable for standard diameter implants (3.5–4.2 mm). However, implant placement in sites with parabolic shaped ridges may need to be placed deeper to avoid vertical bone loss and implant thread exposure. Inadequate bone volume, less than 5 mm of bone width, may be developed by ridge expansion (split ridge) techniques. With ridge expansion, complications may arise such as malposition and labyrinthine concussion. Malposition may be corrected intraoperatively or grafted for a later implant placement. Labyrinthine concussion is usually of short duration but may be treated with head maneuvers. Sites with 2 mm or less width of available bone may not be treated flaplessly and may be more appropriately treated with extracortical augmentation grafting.
Electronic Percussive Testing of the Stability of an Immediately Provisionalized Implant Placed Into a Fresh Extraction Socket: A Pilot Evaluation
Authors: Orenstein Ira H. , MacDonald Daniel E. , Tao Anita C. , Morris Harold F. 
Published: April 2007

Abstract
It is important to achieve primary stabilization of dental implants that will be immediately loaded. Noninvasive devices that test the stability of immediately provisionalized implants placed into fresh extraction sockets are discussed. A titanium threaded implant was placed into a fresh extraction socket of a patient's nonrestorable mandibular right canine. The implant received an interim restoration immediately following its placement. The stability of the bone-implant complex was evaluated from the day of implant insertion through day 246 using an electronic percussive testing instrument. During the first month the bone-implant complex became progressively less stable reaching a peak measured level of instability at 30 days postimplantation. This was followed by progressive stabilization first measured on day 46 as the implant continued to osseointegrate. These findings suggest that the bone-implant complex became less stable during the first month after implant placement and was followed by a period of progressive stabilization reflecting bone maturation around the implant. A search of the literature found similar results in a study of single-stage implants (not immediately provisionalized) using resonance frequency analysis. The known sequence of wound healing around dental implants is reviewed to explain the findings of this pilot evaluation. Studies that use noninvasive testing devices to assess implant stability at placement and during healing may provide information that can help to optimize implant treatment outcomes.