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At least 1,693 records · Page 94Linked to original sources
PubMed2003

Compensation by the muscle limits the metabolic consequences of lipodystrophy in PPAR gamma hypomorphic mice.

Peroxisome proliferator-activated receptor gamma (PPAR gamma) is a nuclear receptor, which controls adipocyte differentiation. We targeted with homologous recombination the PPAR gamma 2-specific exon B, resulting in a white adipose tissue knockdown of PPAR gamma. Although homozygous (PPAR gamma hyp/hyp) mice are born with similar weight as the WT mice, the PPAR gamma hyp/hyp animals become growth retarded and develop severe lipodystrophy and hyperlipidemia. Almost half of these PPAR gamma hyp/hyp mice die before adulthood, whereas the surviving PPAR gamma hyp/hyp animals overcome the growth retardation, yet remain lipodystrophic. In contrast to most lipodystrophic models, the adult PPAR gamma hyp/hyp mice only have mild glucose intolerance and do not have a fatty liver. These metabolic consequences of the lipodystrophy are relatively benign because of the induction of a compensatory gene expression program in the muscle that enables efficient oxidation of excess lipids. The PPAR gamma hyp/hyp mice unequivocally demonstrate that PPAR gamma is the master regulator of adipogenesis in vivo and establish that lipid and glucose homeostasis can be relatively well maintained in the absence of white adipose tissue.

Adipose Tissue↗
PubMedDate not supplied

Strategy and actions for achieving productive aging in Japan.

The objective of this study was to develop basic strategies for determining the ideal form of corporate management that meets the needs of an aging work force, specifically with the intent to develop a method of calculating functional age, one of the determining factors of such strategies. A literature search was made of annual reports of research conducted jointly by the Association of Employment for Senior Citizens and Japanese corporations. We tested the physical, physiological, and psychomotor functions of 271 male workers ranging in age from 20 to 59, and we used the results to examine the means of creating a formula to calculate functional age. Many of the measures adopted by Japanese corporations to deal with aging involve job redesign. This category accounts for 58.5% of such measures in all research fields. Night vision, standing trunk flexion, timed vital capacity, systolic blood pressure, and jumping reaction time each have an important influence on functional age calculation.

Aging↗
PubMed2004

A pRb-independent mechanism preserves the postmitotic state in terminally differentiated skeletal muscle cells.

In skeletal muscle differentiation, the retinoblastoma protein (pRb) is absolutely necessary to establish definitive mitotic arrest. It is widely assumed that pRb is equally essential to sustain the postmitotic state, but this contention has never been tested. Here, we show that terminal proliferation arrest is maintained in skeletal muscle cells by a pRb-independent mechanism. Acute Rb excision from conditional knockout myotubes caused reexpression of E2F transcriptional activity, cyclin-E and -A kinase activities, PCNA, DNA ligase I, RPA, and MCM2, but did not induce DNA synthesis, showing that pRb is not indispensable to preserve the postmitotic state of these cells. Muscle-specific gene expression was significantly down-regulated, showing that pRb is constantly required for optimal implementation of the muscle differentiation program. Rb-deleted myotubes were efficiently reactivated by forced expression of cyclin D1 and Cdk4, indicating a functionally significant target other than pRb for these molecules. Finally, Rb removal induced no DNA synthesis even in pocket-protein null cells. Thus, the postmitotic state of myotubes is maintained by at least two mechanisms, one of which is pocket-protein independent.

Animals↗
PubMed2002

Determination of melting temperature for variant detection using dHPLC: a comparison between an empirical approach and DNA melting prediction software.

Detection of DNA sequence variants by the use of denaturing high-performance liquid chromatography (dHPLC) is a relatively new method (Underhill et al., 1997) and has distinct advantages over other methods such as single-strand conformation polymorphism (SSCP), direct sequencing, and DNA chip hybridization. The dHPLC-based single-nucleotide polymorphism (SNP) screening relies on different DNA thermodynamic properties between perfectly matched base pairs in homoduplex molecules and single base-pair mismatches in heteroduplex DNAs. Separation of the two forms of duplex DNAs by dHPLC is based on ionic forces between the negatively charged DNA and the hydrophobic stationary phase, which consists of C(18) chains on PSDVB (polystyrene-divinylbenzene) beads coated with a positively charged ion-pairing agent (TEAA, triethylammonium acetate). Removal of the DNA from the TEAA-coated beads is dependent upon a mobile organic phase, in the form of a linear acetonitrile gradient. The major factor that influences the success of dHPLC to detect sequence variation is the thermal stability of the duplex DNA, which is determined by the melting temperature (TM(50)), where 50% of the DNA strand is single stranded and 50% is double stranded. The TM(50) predicts the best probability of detecting a single base-pair change based on the altered thermodynamics it imparts to the DNA duplex. Generally, there are two ways to determine this melting temperature, either empirically or with the aid of predictive DNA melting analysis software. Such programs include the DNAMelt program located on the Stanford University DNA Sequencing and Technology Center website, MeltCalc (Schutz and von Ahsen 1999), and WAVEMAKER, the proprietary melting analysis software provided with the Transgenomic WAVE dHPLC system. The goal of the current study was to determine whether currently available predictive DNA melting programs could be used to increase efficiency and throughput of SNP detection. A wide range of amplicons, differing in both size and GC composition, were selected for analysis to simulate the broad spectrum of PCR products that may be encountered during a large-scale dHPLC screening project.

Chromatography, High Pressure Liquid↗
PubMed2006

Protein image alignment via piecewise affine transformations.

We present a new approach for aligning families of 2D gels. Instead of choosing one of the gels as reference and performing a pairwise alignment, we construct an ideal gel that is representative of the entire family and obtain a set of piecewise affine transformations that optimally align each gel of the family to the ideal gel. The coefficients defining the transformations as well as the ideal landmarks are obtained as the solution of a large-scale quadratic programming problem that can be solved efficiently by interior-point methods.

Animals↗
PubMed1988

Automation of routine coagulation testing using a random access centrifugal analyzer.

The results are reported of a clinical and laboratory evaluation of the use of a random-access centrifugal analyzer linked to a personal computer in the management of the routine workload of a hemostasis laboratory. Over a three-month period, prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin clotting time (TCT), and derived fibrinogen (Fib) were performed on a total of 929 samples. Included in the study were 448 samples from patients receiving anticoagulants (oral anticoagulants, 228; heparin, 166; heparin and warfarin, 130) and 351 samples from patients requiring coagulation screens (PT, APTT, TCT, Fib). Tests were done in parallel with tilt-tube manual techniques and the results correlated. The correlation coefficients were PT, 0.99; TCT, 0.72; APTT, 0.96; Fib, 0.97. Discrepancies were analyzed and were due to hypofibrinogenemia and hyperlipidemia. The poorer correlation coefficient of TCT was attributable both to lower reproducibility of the manual test and the effect of dysfibrinogenemia or FDPs in liver disease. In no case was an abnormality or diagnosis missed using the centrifugal analyzer. In several cases the increased sensitivity of the analyzer improved the detection of the lupus anticoagulant. The use of automation was accompanied by a major reduction in workload and reagent costs. The machine has been used to assay a wide range of coagulation tests by clot based and chromogenic substrate methods. In conclusion, a programmed centrifugal analyzer is a safe, efficient, and flexible way of automating routine coagulation tests. It widens the reportoire of tests performed in the Hemostasis laboratory by using a machine capable of being used in other areas of pathology.

Blood Coagulation Tests↗
PubMed1991

Designing a neural network simulator--the MENS modelling environment for network systems: I.

During recent years, the field of neural network research has increasingly attracted the interest of workers from a large number of different disciplines. Current research topics include aspects as different as detailed simulations in brain physiology, predictions of protein structure in biochemistry, database organization in computer science, or various technical applications. The common scheme behind these different approaches is the use of distributed networks of simple computational elements that communicate with each other by means of weighted links. Computer simulations of neural networks require an appropriate software environment. Due to the computational similarities of many classes of such networks, simulation software can be structured into modular components that, to a large degree, are independent of specific applications. The aim of this and the following paper is to discuss some of the design considerations concerning software for neural network simulations. The aspects presented are interesting for both the development of new simulation software and the efficient use and modification of existing programs. Therefore, the general user as well as the software designer may hopefully benefit from this material. This paper briefly introduces some of the basic principles of neural networks. After a short discussion of different approaches to software design, two simple example applications are presented in order to demonstrate a conceptual framework common to many network simulations. The transfer of these considerations to the design of simulation software is then shown by example of the MENS network simulator developed in the Max-Planck-Institute for Brain Research. The paper gives a general introduction to the layout of data structures and different software components. Using the two introductory examples some aspects of network analysis are demonstrated. The following paper then considers further details of the design of a neural network simulator with respect to performance, implementation, and testing.

Animals↗
PubMed2025

vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.

MOTIVATION: Accurate quantification of genotype uncertainty is pivotal in ensuring the reliability of genetic inferences drawn from NGS data. Genotype uncertainty is typically modeled using Genotype Likelihoods (GLs), which can help propagate measures of statistical uncertainty in base calls to downstream analyses. However, the effects of errors and biases in the estimation of GLs, introduced by biases in the original base call quality scores or the discretization of quality scores, as well as the choice of the GL model, remain under-explored. RESULTS: We present vcfgl, a versatile tool for simulating genotype likelihoods associated with simulated read data. It offers a framework for researchers to simulate and investigate the uncertainties and biases associated with the quantification of uncertainty, thereby facilitating a deeper understanding of their impacts on downstream analytical methods. Through simulations, we demonstrate the utility of vcfgl in benchmarking GL-based methods. The program can calculate GLs using various widely used genotype likelihood models and can simulate the errors in quality scores using a Beta distribution. It is compatible with modern simulators such as msprime and SLiM, and can output data in pileup, Variant Call Format (VCF)/BCF, and genomic VCF file formats, supporting a wide range of applications. The vcfgl program is freely available as an efficient and user-friendly software written in C/C++. AVAILABILITY AND IMPLEMENTATION: vcfgl is freely available at https://github.com/isinaltinkaya/vcfgl.

Software↗
PubMed2004

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins.

MOTIVATION: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence-structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence-structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence and compactness. RESULTS: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the three-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology, but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.

Algorithms↗
PubMed1998

Competition through physician-managed care: the case for capitated multispecialty group practices.

The dominant managed care model in the USA is the individual practice association (IPA), in which physicians in separate practices contract with a health plan. One alternative model, the capitated multispecialty group practice (CMGP), has some distinct advantages: (i) the best randomized trial comparing a health management organization (HMO) with indemnity insurance showed equivalent health outcomes for a prepaid group-practice model HMO, with about a 40% saving in cost, mostly from lower hospital utilization. There is no comparable evidence for IPA-style HMO's; (ii) most managed care plans control costs through 'gatekeeper' primary care physicians or capitated payment. Strong financial disincentives to care, applied to small practices, lead to a significant risk of withholding needed care. Large capitated groups diffuse the risk among hundreds or thousands of physicians; (iii) small practices also lack the financial resources and expertise to develop information systems, continuous quality improvement programs, and other means of improving efficiency. Larger groups can integrate specialty and primary care, laboratory, pharmacy, information technology and other services, to improve quality and cost-effectiveness, while maintaining physician control of the process; (iv) in urban California, HMO enrollment in six large capitated groups increased by 91% from 1990 to 1994. Hospital utilization for these groups was less than half the USA average; (v) because it is self-insured, the CMGP could contract directly with purchasers, eliminating the need for the insurance intermediary. The CGMP offers an ethical, effective alternative that maintains the primacy of the physician in health care: physician-managed care.

California↗
PubMed2025

Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.

Pathogen genomic data are increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this is highly challenging when the outbreak under study is only partially sampled, so that both genomic and epidemiological data are missing for intermediate links in the transmission chains. Here, we present a new dynamic programming algorithm to perform this task efficiently. We implement this methodology into the well-established TransPhylo framework to reconstruct partially sampled outbreaks using a combination of genomic and epidemiological data. We use simulated datasets to show that including epidemiological data can improve the accuracy of the inferred transmission links compared with inference based on genomic data only. This also allows us to estimate parameters specific to the epidemiological data (such as transmission rates between particular groups), which would otherwise not be possible. We then apply these methods to two real-world examples. First, we use genomic data from an outbreak of tuberculosis in Argentina, for which data was also available on the HIV status of sampled individuals, in order to investigate the role of HIV coinfection in the spread of this tuberculosis outbreak. Second, we use genomic and geographical data from the 2003 epidemic of avian influenza H7N7 in the Netherlands to reconstruct its spatial epidemiology. In both cases, we show that incorporating epidemiological data into the genomic analysis allows us to investigate the role of epidemiological properties in the spread of infectious diseases.

Humans↗
PubMed2002

The TB structural genomics consortium crystallization facility: towards automation from protein to electron density.

The crystallization facility of the TB (Tuberculosis) structural genomics consortium, one of nine NIH sponsored p50 structural genomic centres, provides TB consortium members with automated crystallization, data collection and basic molecular replacement (MR) structure solution up to bias minimized electron density maps. Crystallization setup of up to ten proteins per day follows the CRYSTOOL combinatorial screen protocol using a modular and affordable robotic design with an open architecture. Components include screen preparation, plate setup, automated image acquisition and analysis, and optimisation design. A new 96 well crystallization plate has been designed for optimal robotic handling while maintaining ease of manual crystal harvesting. Robotic crystal mounting, screening, and data collection are conducted in-house and at the Advanced Light Source (ALS) in Berkeley. A simple automated protocol based on MR and homology based structure prediction automatically solves modestly difficult problems. Multiple search models are evaluated in parallel MR and the best multi-segment rigid body refined MR solution is subjected to simulated annealing torsion angle molecular dynamics using CNS, bringing even marginal MR solutions within the convergence radius of the subsequent highly effective bias removal and map reconstruction protocol, Shake&wARP, used to generate electron density for initial rebuilding. Real space correlation plots allow rapid assessment of local structure quality. Modular design of robotics and automated scripts using publicly available programs for structure solution allow for efficient high throughput crystallography - at a reasonable cost.

Automation↗
PubMed2000

The gap between knowledge and practice in the treatment and prevention of cardiovascular disease.

There is a gap between the current knowledge of the treatment of cardiac conditions derived from evidence-based medicine and the widespread application of this knowledge. The use of ACE inhibitors for patients with congestive heart failure, beta blockers in postmyocardial infarction patients, anticoagulation in patients with chronic atrial fibrillation, cholesterol medications for either primary or secondary prevention of coronary artery disease, and antihypertensive treatment, are of proven benefit, yet all are underutilized by cardiologists, as well as other medical practitioners. There is evidence that there are methods to improve the prescribing of medication, but further studies are required to identify the best ways of doing this. A challenge for the future will be to identify and apply the best educational programs to improve the quality and efficiency of medical care. (c) 2000 by CHF, Inc.

Journal Article↗
PubMed1997

Quality assurance for the laboratory aspects of prosthodontic treatment.

Inconsistency in the product returned from the commercial dental laboratory led to the development of a formal quality assurance (QA) program at the University of Detroit Mercy School of Dentistry in 1994. The goal of the program was to improve the quality of prosthodontic laboratory submissions and the returned product, facilitate laboratory communications, and, ultimately, enhance the quality and timeliness of patient care. Each student submission is evaluated with a criterion-referenced evaluation form. Deficiencies are communicated to the student, and the corrected submission is then sent to the laboratory. Three-year remake data from the main clinic (QA site) and an extramural clinic (non-QA site) demonstrate the effectiveness of the program. The major benefits are more efficient, cost-effective patient care, as well as the provision of a model for the student to practice the skills needed for effective communication with the dental technician, upon graduation.

Humans↗
PubMedDate not supplied

Adaptation of the nursing audit to community health nursing.

A selected literature review has revealed some of the ways in which the audit can be adapted to effectively evaluate the quality of care provided by community health professionals. Although a complex issue, the strengths of the audit can outweigh its limitations when a shared philosophy is adhered to and a review of the quality monitoring process occurs on a regular basis. But its success depends both on the approach and on the action taken. One requirement for an effective audit is a strong commitment of staff to reflect accurately nursing practice in nursing documentation. As the audit is neither inclusive nor exclusive, it should be used in conjunction with other quality assurance mechanisms, and in collaboration with other disciplines. Commitment at all levels--consumer, provider, administrator--is essential for success. There is no doubt that the variety of nursing audit instruments and techniques in existence have served to enhance the effectiveness and efficiency of community health nursing audit programs as well as contributing to community health nursing quality assurance. However, the audit clearly remains a challenging issue, requiring further research to establish the reliability and validity of current audit measures and to develop innovative approaches to future community-based audits.

Canada↗
PubMed2005

Trends in recall, biopsy, and positive biopsy rates for screening mammography in an academic practice.

PURPOSE: To retrospectively evaluate whether recall, biopsy, and positive biopsy rates for a group of radiologists who met requirements of Mammography Quality Standards Act of 1992 (MQSA) demonstrated any change over time during a 27-month period (nine consecutive calendar quarters). MATERIALS AND METHODS: Institutional review board approved study protocol, and informed consent was waived. All screening mammograms that had been interpreted by MQSA-qualified radiologists between January 1, 2001, and March 31, 2003, were reviewed. Group recall rates, biopsy rates, and detected cancer rates for nine calendar quarters were computed and attributed to performance date of original screening mammogram. Type of biopsy performed was classified as follows: stereotactic vacuum-assisted biopsy, ultrasonography (US)-guided core biopsy, US-guided fine-needle aspiration biopsy, surgical excision, and multiple biopsies. chi(2) Test for trend (two sided) and linear regression were used to assess trends over time for recall and biopsy rates, biopsy rates according to type of biopsy performed, and percentage of biopsy results positive for cancer. RESULTS: Group recall rate did not show a statistically significant trend during period studied (P = .59). Biopsy rates increased significantly from 13.02 to 20.12 per 1000 screening examinations (P < .001). A corresponding substantial decrease was seen in percentage of biopsies in which malignancy was found, although this trend was not statistically significant (P = .24). A significant increase (from 4.72 to 9.88 per 1000 screening examinations) was found in rate of stereotactic vacuum-assisted 11-gauge core biopsies performed (P < .001). CONCLUSION: Observed increase in biopsy rates reinforces the need to carefully select patients for biopsy to achieve efficient, efficacious, and cost-effective programs for early detection of breast cancers.

Biopsy↗