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PubMed1989

A relational database of protein structures designed for flexible enquiries about conformation.

A relational database of protein structure has been developed to enable rapid and flexible enquiries about the occurrence of many aspects of protein architecture. The coordinates of 294 proteins from the Brookhaven Data Bank have been processed by standard computer programs to generate many additional terms that quantify aspects of protein structure. These terms include solvent accessibility, main-chain and side-chain dihedral angles, and secondary structure. In a relational database, the information is stored in tables with columns holding the different terms and rows holding the different entries for the terms. The different relational base tables store the information about the protein coordinate set, the different chains in the protein, the amino acid residues and ligands, the atomic coordinates, the salt bridges, the hydrogen bonds, the disulphide bridges and the close tertiary contacts. The database was established under ORACLE management system. Enquiries are constructed in ORACLE using SQL (structured query language) which is simple to use and alleviates the need for extensive computer programs. A single table can be searched for entries that meet various criteria, e.g. all protein solved to better than a given resolution. The power of the database occurs when several tables, or the entries in a single table, are cross-correlated. For example the dihedral angles of proline in the fourth position in an alpha-helix in high resolution structures can be rapidly obtained. The structural database provides a powerful tool to obtain empirical rules about protein conformation. This database of protein structures is part of a joint project between Birkbeck College and Leeds University to establish an integrated data resource of protein sequences and structures (ISIS) that encodes the complex patterns of residues and coordinates that define protein conformation. The entire data resource (ISIS) will provide a system to guide all areas of protein modelling including structure prediction, site-directed mutagenesis and de novo protein design. The availability of ISIS is described in the paper.

Computer Simulation↗
PubMed2026

Comparative genomics reveals genotype-phenotype concordance and cryptic resistomes in clinical Pseudomonas aeruginosa.

BACKGROUND: Pseudomonas aeruginosa (P. aeruginosa) is a major pathogen because of its adaptability. It shows rapid evolution of multidrug resistance (MDR). Phenotype-based diagnostics often fail to detect silent resistance determinants and early adaptive changes. This study integrates phenotypic profiling with whole-genome sequencing (WGS) to examine resistance architecture in clinical isolates from eastern India. METHODS: From 1295 culture-positive P. aeruginosa specimens collected at a tertiary care hospital in eastern India. Using predefined criteria, representative MDR and non-MDR isolates were selected, including distinct resistance phenotypes, specimen-source diversity, and hospital and community-acquired settings; multivariate analysis of resistance profiles illustrated phenotypic diversity. Antimicrobial susceptibility assessed using VITEK-2 and Kirby-Bauer disk diffusion, species identity confirmed by 16 S rRNA sequencing, and genomic analysis processed through a reference-guided workflow. Antimicrobial Resistance (AMR) determinants were identified through CARD, and phylogenetic tree constructed from 454 publicly available P. aeruginosa genomes. RESULTS: MDR exhibited greater sequence divergence relative to PA14 (~ 69,000 variants) than the non-MDR isolate (~ 58,700 variants), with > 92% coverage at ≥ 30X depth. Strong genotype-phenotype concordance observed in MDR isolates across five antibiotic classes, associated with β-lactamase variants (PDC-67, OXA-396) and regulatory adaptations (ArmR, cprS). The non-MDR isolate harboured gyrA (T83I) resistance-associated mutations, PDC-1, and OXA-847 without phenotypic expression, indicating silent resistome. Phylogenetically, MDR isolates clustered tightly within the phylogeny, while the non-MDR isolate formed a distinct lineage. CONCLUSION: Observed genomic differences align with adaptation under antimicrobial selection, though confirmation requires larger collections. The non-MDR isolate retained a silent resistome. Findings highlight limitations of phenotype-only diagnostics, support genomic data integration, and emphasize transcriptomics for hidden resistance expression and regulatory dynamics.

Pseudomonas aeruginosa↗
PubMedDate not supplied

Analysis of shotgun proteomics and RNA profiling data from Arabidopsis thaliana chloroplasts.

The integration of data from transcriptional profiling and shotgun proteomics experiments provides additional information about the identified proteins that goes beyond their plain detection. We have analyzed results from MS/MS shotgun detection of 426 Arabidopsis chloroplast proteins and genome-wide RNA profiling to identify correlations between gene expression, protein abundance and protein characteristics that influence their detection in high-throughput proteome analyses. The integrated data analysis revealed a significant molecular mass bias for the detection of proteins that were expressed at low transcript levels. Overall, the sequence coverage of most of the identified proteins increases with transcript levels indicating a positive correlation between transcript and relative protein abundance. This does not apply to a subset of the identified proteins suggesting specific properties that alter their detection in shotgun proteomics. This integrative comparison is a suitable strategy to validate large scale proteomics data and offers an assessment of the depth of the proteome analysis and the confidence in protein identification.

Arabidopsis↗
PubMed2002

Function of the heterocercal tail in sharks: quantitative wake dynamics during steady horizontal swimming and vertical maneuvering.

The function of the heterocercal tail in sharks has long been debated in the literature. Previous kinematic data have supported the classical theory which proposes that the beating of the heterocercal caudal fin during steady horizontal locomotion pushes posteroventrally on the water, generating a reactive force directed anterodorsally and causing rotation around the center of mass. An alternative model suggests that the heterocercal shark tail functions to direct reaction forces through the center of mass. In this paper, we quantify the function of the tail in two species of shark and compare shark tail function with previous hydrodynamic data on the heterocercal tail of sturgeon Acipenser transmontanus. To address the two models of shark heterocercal tail function, we applied the technique of digital particle image velocimetry (DPIV) to quantify the wake of two species of shark swimming in a flow tank. Both steady horizontal locomotion and vertical maneuvering were analyzed. We used DPIV with both horizontal and vertical light sheet orientations to quantify patterns of wake velocity and vorticity behind the heterocercal tail of leopard sharks (Triakis semifasciata) and bamboo sharks (Chiloscyllium punctatum) swimming at 1.0Ls(-1), where L is total body length. Two synchronized high-speed video cameras allowed simultaneous measurement of shark body position and wake structure. We measured the orientation of tail vortices shed into the wake and the orientation of the central jet through the core of these vortices relative to body orientation. Analysis of flow geometry indicates that the tail of both leopard and bamboo shark generates strongly tilted vortex rings with a mean jet angle of approximately 30 degrees below horizontal during steady horizontal swimming. The corresponding angle of the reaction force is much greater than body angle (mean 11 degrees ) and the angle of the path of motion of the center of mass (mean approximately 0 degrees ), thus strongly supporting the classical model of heterocercal tail function for steady horizontal locomotion. Vortex jet angle varies significantly with body angle changes during vertical maneuvering, but sharks show no evidence of active reorientation of jet angle relative to body angle, as was seen in a previous study on the function of sturgeon tail. Vortex jet orientation is significantly more inclined than the relatively horizontal jet generated by sturgeon tail vortex rings, demonstrating substantial differences in function in the heterocercal tails of sharks and sturgeon. We present a summary of forces on a swimming shark integrating data obtained here on the tail with previous data on pectoral fin and body function. Body orientation plays a critical role in the overall force balance and compensates for torques generated by the tail. The pectoral fins do not generate lift during steady horizontal locomotion, but play an important hydrodynamic role during vertical maneuvering.

Animals↗
PubMed1985

Costs of mandates for outpatient mental health care in private health insurance.

Various methods for estimating the cost of mandated mental health benefits have been devised, each resulting in substantially different estimates. These methods neglect to distinguish between the two components of cost to the insurer: social cost (due to increased utilization) and shifted cost (from other sources of payment). We apply a method we developed for estimating the two types of costs of mandates for outpatient mental health services that integrates data from insurers with information from the literature on financing of mental health services. We applied our method to legislation recently proposed in Massachusetts that would double the mandated minimum benefit level from +500 to +1,000. We expect payments by the largest carrier in the state to increase by a factor of 1.65. More than half of this increase represents shifted costs rather than new costs to society.

Ambulatory Care↗
PubMed1999

Dynamics of parenchymal cell division, differentiation, and apoptosis in the young adult female mouse submandibular gland.

The submandibular salivary gland of the young adult female mouse has two secretory cell types, acinar and granular duct, which are separated by intercalated ducts. Based on the occurrence of autologous cell division in these cells, they have been traditionally classified as expanding populations. However, differentiation from stem or progenitor cells in the intercalated ducts, usually associated with renewing populations, has also been detected. The question of renewing or expanding populations is resolved by quantitating and integrating the rates of autologous cell division, differentiation, and apoptosis for each cell type. The integrated data shows that both acinar and granular duct cell populations exhibit a substantial positive growth index, whereas the growth index for the intercalated duct cells is moderately negative. On balance, it suggests that the submandibular gland of the young adult female mouse is still growing. Comparison of young female mice with older females suggests that, although overall parenchymal growth slows with age, there is no longer a net loss of intercalated duct cells. Comparison with young adult male submandibular glands indicates that gender differences exist in the rates and mechanisms used for maintaining the different cell populations. The acinar and granular duct cell populations in young adult female mouse submandibular glands are expanding at the expense of the intercalated duct cell population, which appears to be contracting.

Age Factors↗
PubMedDate not supplied

Emerging and recurrent issues in drug development.

This paper reviews several emerging and recurrent issues relating to the drug development process. These emerging issues include changes to the FDA regulatory environment, internationalization of drug development, advances in computer technology and visualization tools, and efforts to incorporate meta-analysis methodology. Recurrent issues include: renewed interest in statistical methods for handling subgroups in the design and analysis of clinical trials; renewed interest in alternatives to the 'intention-to-treat' analysis in the presence of non-compliance in randomized clinical trials; renewed interest in methodology to address the multiplicities resulting from a variety of sources inherent in the drug development process, and renewed interest in methods to assure data integrity. These emerging and recurrent issues provide a continuing challenge to the international community of statisticians involved in drug development. Moreover, the involvement of statisticians with different perspectives continues to enrich the field and contributes to improvement in the public health.

Computer-Aided Design↗
PubMed2000

Genetics, genomics, and drug discovery.

Genetics and genomics are altering the drug discovery process and changing the practice of medicine. Genetic mapping and positional cloning will lead to the identification of disease susceptibility alleles of different genes and this will be further enabled by the publication of the DNA sequence of the human genome. Single nucleotide polymorphisms discovered by comparative sequencing and other methods will also speed up positional cloning and allow pharmacogenetics to proceed in a more comprehensive way than heretofore. Gene expression arrays coupled with studies in model organisms will help to define the function of all genes and determine how the products interact-the next big step. High throughput protein structure determination will also provide large-scale descriptions of protein function but with more biochemical clarity. In all of these studies data integration remains the biggest challenge.

Drug Design↗
PubMed2003

Individual psychotherapy in the outpatient treatment of adults with anorexia nervosa.

BACKGROUND: Anorexia nervosa is a disorder of high morbidity and significant mortality. It is commonest in young adult women, in whom the incidence may be increasing. The focus of treatment has moved to an outpatient setting and a number of differing psychotherapies are presently used in treatment. OBJECTIVES: The aim of the present review was to evaluate the evidence from randomised controlled trials for the efficacy of outpatient psychotherapies used in the treatment of older adolescents and adults with anorexia nervosa SEARCH STRATEGY: The strategy comprised database searches of MEDLINE, EXTRAMED, EMBASE,PSYCLIT, CURRENT CONTENTS, Cochrane Collaboration Controlled Trials Register and the Depression and Anxiety Neuroses Cochrane Group (CCDAN), a hand-search of The International Journal of Eating Disorders, and he reference lists of all papers selected. Personal letters were sent to identified notable researchers published in the area, requesting information on trials that are unpublished or in progress. SELECTION CRITERIA: All randomised controlled trials of adult individual outpatient therapy for anorexia nervosa as defined by the DSM-IV or similar international criterion. Quality ratings were made according to the CCDAN criteria and in addition, whether the trial had examined treatment integrity. DATA COLLECTION AND ANALYSIS: A range of outcome variables were selected, including physical state, severity of eating disorder attitudes and beliefs, interpersonal function, and general psychiatric symptom severity. Continuous outcome data comparisons were made with the standardized mean difference statistic, and binary outcome comparisons made with the relative risk statistic. Reliability of data extraction and quality ratings were made with the kappa statistic. Sensitivity analyses to evaluate the effects of trial quality and subgroup analyses to explore specific questions of treatment effects from different settings, frequency and duration of therapies were planned. MAIN RESULTS: Six small trials only, two of which included children or adolescents, were identified from the search and aggregation of data was not possible. Bias was possible due particularly to lack of blinding of outcome assessments. The results in two trials suggested that 'treatment as usual' or similar may be less efficacious than a specific psychotherapy. No specific treatment was consistently superior to any other specific approach. Dietary advice as a control arm had a 100% non-completion rate in one trial. REVIEWER'S CONCLUSIONS: No specific approach can be recommended from this review. It is unclear why 'treatment as usual' performed so poorly or why dietary advice alone appeared so unacceptable as the reasons for non-completion were not reported. There is an urgent need for large well-designed trials in his area.

Adolescent↗
PubMed2006

Habitat-specific ranging patterns of Dian's tarsiers (Tarsius dianae) as revealed by radiotracking.

Dian's tarsier Tarsius dianae, one of the smallest primates on earth, is endemic to the central regions of Sulawesi, Indonesia. To evaluate the effects of increasing land use by humans on the ranging patterns of this nocturnal insect hunter, four study plots along a gradient of anthropogenic disturbance were selected for this study. In these plots, 71 tarsiers were captured with mist nets, and 30 of these were fitted with 3.9 g radiotransmitters and subsequently tracked over the course of 2 weeks per animal. The average home ranges were 1.1-1.8 ha in size, with the smallest ranges in slightly disturbed habitat and the largest ranges in a heavily disturbed plantation. These findings coincide with different estimates of insect abundance in the study plots. Nightly travel distances were smallest in undisturbed old-growth forest and slightly increased along a gradient of human disturbance. The tarsiers were most active shortly after dusk and just before dawn. The results of this comprehensive radiotracking study on tarsiers show that T. dianae adapts its ranging behavior to the degree and type of human land use. Integrated data on home range size and travel distance indicate that slightly disturbed forest is as favorable to these animals as undisturbed habitat. However, with increasing anthropogenic effects, the living conditions of the tarsiers appear to deteriorate, resulting in the necessity for larger home and night ranges. The results of this study provide an important tool for directing conservation efforts targeted at the survival of this primate in central Sulawesi.

Animal Identification Systems↗
PubMed2001

Limb myosin heavy chain isoproteins and muscle fiber types in the adult goat (Capra hircus).

The primary focus of this study was the accurate classification of limb skeletal muscle fiber types in adult goats (Capra hircus) according to the myosin heavy chain (MHC) isoform they express. Combined methodologies of gel electrophoresis, immunoblotting, immunohistochemistry, myofibrillar ATPase (mATPase), and quantitative metabolic enzyme histochemistry of M. semitendinosus samples were developed. Three MHCs were identified and tentatively designated as types I, IIA, and IIX. Five fiber types were defined immunohistochemically according to their MHC content: I, I+IIA, IIA, IIAX, and IIX. The hybrid fast-twitch fibers (IIAX) totaled 21% of the fiber population analyzed. The three major pure fibers (I, IIA, and IIX) could be objectively separated upon the basis of their mATPase activities after acid and alkaline preincubations. The prominent number of hybrid fibers, however, could not be delineated with these mATPase methods. Metabolic and size properties of muscle fibers varied according to their MHC content, but overlapped the full range of muscle fiber phenotypes. These integrated data demonstrate that type II skeletal muscle fibers of small ruminants have been misclassified in previous studies. The immunohistochemical approach developed in the present study offers new prospects for muscle fiber typing in caprine experimental studies and meat production technologies.

Animals↗
PubMed2006

Ontologies for data and knowledge sharing in biology: plant ROS signaling as a case study.

Modern technologies have rapidly transformed biology into a data-intensive discipline. In addition to the enormous amounts of existing experimental data in the literature, every new study can produce a large amount of new data, resulting in novel ideas and more publications. In order to understand a biological process as completely as possible, scientists should be able to combine and analyze all such information. Not only molecular biology and bioinformatics, but all the other domains of biology including plant biology, require tools and technologies that enable experts to capture knowledge within distributed and heterogeneous sources of information. Ontologies have proven to be one of the most-useful means of constructing and formalizing expert knowledge. The key feature of an ontology is that it represents a computer-interpretable model of a particular subject area. This article outlines the importance of ontologies for systems biology, data integration and information analyses, as illustrated through the example of reactive oxygen species (ROS) signaling networks in plants.

Computational Biology↗
PubMed2003

Substrate aggregation due to aerial hyphae during discontinuously mixed solid-state fermentation with Aspergillus oryzae: experiments and modeling.

Solid-state fermentation (SSF) is prone to process failure due to channeling caused by evaporative cooling and the formation of an interparticle mycelium network. Mixing is needed to break the mycelium network and to avoid such failure. This study presents the first attempt to quantify and predict the effect of mycelium bonds on particle mixing and vice versa. We developed a novel experimental set-up to measure the tensile strength of hyphal bonds in SSF: Aspergillus oryzae was cultivated between two wheat-dough disks and the tensile strength of the aerial mycelium was measured with a texture analyzer. Tensile strength at different incubation times was related to oxygen consumption, to allow a translation to a rotating drum with A. oryzae cultivated on wheat grain. We performed several discontinuously mixed solid-state fermentations in the drum fermentor and measured the number and size of grain-aggregates remaining after the first mixing action. We integrated data on mycelium tensile strength into a previously developed two-dimensional discrete-particle model that calculates forces acting on individual substrate particles and the resulting radial-particle movements. The discrete-particle model predicted the quantity and size of the aggregates remaining after mixing successfully. The results show that the first mixing event in SSF with A. oryzae is needed to break mycelium to avoid aggregate formation in the grain bed, and not to distribute water added to compensate for evaporation losses, or smooth out temperature gradients.

Aspergillus↗
PubMed2001

Family history information in biomedical research.

Family history information has been widely used in biomedical research for many years. Ethical concerns have recently been raised about the collection of such information. This article reviews the major roles played by family history information in biomedical research, explores what "private" means in the context of the collection of such information, examines the possible sources of harm from the collection of family history information, and discusses the implications of the possible special restrictions on "sensitive" family history information about psychiatric and drug use disorders. Family history information is vital to many aspects of biomedical research, especially human molecular and epidemiologic genetics. Substantial uncertainty remains about who "owns" family history information, and in several cases, such as childhood sexual abuse, it is hard to justify the position that "third-party" consent is needed. In many instances, the risk to third-party subjects can be minimized by safeguards to confidentiality and data integrity. Adding special restrictions for the collection of family history information on psychiatric and drug abuse disorders may reinforce stigma and substantially burden researchers examining these vital public health problems.

Confidentiality↗
PubMed2004

Concise review of atrial fibrillation: treatment update considerations in light of AFFIRM and RACE.

Atrial fibrillation (AF) is the most common clinically significant arrhythmia seen by clinicians. Prevalence is as high as 9.0% in patients aged > or = 80 years, and incidence is projected to be more than 5.6 million patients in the U.S. by 2050. Recently, new trials have challenged the traditional belief that rhythm control is inherently superior to rate control in these patients. This article reviews the basic tenets of treatment for AF and discusses how new trial data integrate into these protocols. A concise treatment algorithm is provided and new and upcoming more aggressive interventional treatment options are discussed. This review is designed to help the general practitioner decide how to treat patients in the outpatient setting, evaluate which patients should be hospitalized for management, and which patients should be referred to a cardiologist.

Anti-Arrhythmia Agents↗
PubMed1989

Comprehensive quality assessment approach for flow cytometric immunophenotyping of human lymphocytes.

Flow cytometric immunophenotypic (IPT) evaluation has become an important adjunct to clinical patient management and epidemiological studies. This has precipitated a need for stringent quality assessment (QA) procedures to ascertain data integrity. We evaluated a QA approach to monitor all elements of the immunophenotyping process, inclusive of blood collection and processing procedures as well as of staining reagent and instrument performance. Central to our approach was preparation each day, in parallel with clinical analytes, of lymphocytes from healthy donors, selected from a 15 donor panel. IPT parameters evaluated over a 19 month period included frequencies of CD3+, CD4+, CD8+, and CD20+ lymphocytes and the ratio of CD4+ to CD8+ lymphocytes. The sensitivity for analytical error detection was reflected by median coefficients of variation of these parameters within individual panel donors, which were 4.1%, 4.5%, 3.9%, 8.2%, and 10.1%, respectively. IPT parameter values were determined each day for two of the panel donors, then averaged and standardized to obtain a quality or Q variate, which was the basis of QA. Error detection sensitivity decreased 0.6-1.7% and the number of false rejections increased 1.2-3.3% when one panel donor rather than two was used daily for QA. This study also illuminated important aspects of what constitutes the norm for longitudinal IPT parameter variation in healthy individuals including: 1) a generally low degree of temporal parameter variation within individual donors, but 2) significant differences between donors with respect to variance estimates for CD3+ and CD8+ lymphocyte frequencies and CD4+/CD8+ lymphocyte ratios, and 3) an apparent seasonal pattern of variation in CD4+ T-cell frequencies.

Antibodies, Monoclonal↗
PubMed2002

Constructing the hindbrain: insights from the zebrafish.

The hindbrain is responsible for controlling essential functions such as respiration and heart beat that we literally do not think about most of the time. In addition, cranial nerves projecting from the hindbrain control muscles in the jaw, eye, and face, and receive sensory input from these same areas. In all vertebrates that have been studied, the hindbrain passes through a segmented phase shortly after the neural tube has formed, with a series of seven bulges--the rhombomeres--forming along the anterior-posterior extent of the neural tube. Our current understanding of vertebrate hindbrain development comes from integrating data from several model systems. Work on the chick has helped us to understand the cell biology of the rhombomeres, whereas the power of mouse molecular genetics has allowed investigation of the molecular mechanisms underlying their development. This review focuses on the special insights that the zebrafish system has provided to our understanding of hindbrain development. As we will discuss, work in the zebrafish has elucidated inductive events that specify the presumptive hindbrain domain and has identified genes required for hindbrain segmentation and the specification of segment identities.

Animals↗
PubMed1994

Use of glycated hemoglobin to assess Glycemic control in Wistar diabetic fatty rats and Zucker fatty rats.

The Wistar Diabetic Fatty rat (WDF fafa) is a congenic strain of the Wistar Kyoto rat. Studies using blood glucose reveal that only fatty male (not female) WDF rats spontaneously develop hyperglycemia when fed a stock diet. Blood glucose values have not provided consistent results for evaluation of glycemic status in fatty male WDF rats. Zucker fatty (fafa) rats, while sharing the fa gene and the development of hyperinsulinemia and hyperlipemia, do not spontaneously become hyperglycemic. In order to examine strain differences and the effects of age on long-term average glycemic status in WDF and Zucker rats, glycated hemoglobin (GHb) was analyzed. Glycated hemoglobin was measured in male lean and obese WDF and Zucker rats at 2, 3, 6, and 12 months of age. Nonfasted plasma glucose was measured in male lean and obese WDF rats at 2, 3, 6, and 12 months of age and in lean and obese Zucker rats at 3, 6, and 12 months of age. Plasma insulin was measured in lean and obese WDF and Zucker rats at 3, 6, and 12 months of age. Obese WDF rats had significantly elevated GHb compared to lean controls at 3, 6, and 12 months of age. Glycated hemoglobin was substantially above the normal range (3.8-6.5%) at 3 months of age (14.1%). Glycated hemoglobin significantly declined in the obese WDF rats between 6 and 12 months of age. Nonfasted plasma glucose was significantly elevated in the obese WDF rats at 3 months (14.1 +/- 2.1 mM/L) and 6 months of age (16.2 +/- 2.3 mM/L) compared to lean controls. At 12 months of age there was no difference in plasma glucose between obese and lean WDF rats. Obese and lean Zucker rats had similar levels of GHb and plasma glucose at all ages. In conclusion, GHb provides more integrated data for classifying disease status of WDF rats and evaluation of potential long-term complications associated with hyperglycemia.

Age Factors↗