Screening protein and nucleic acid sequences against libraries of patterns.

We describe programs that can screen nucleic acid and protein sequences against libraries of motifs and patterns. Such comparisons are likely to play an important role in interpreting the function of sequences determined during large scale sequencing projects. In addition we report programs for converting the Prosite protein motif library into a form that is compatible with our searching programs. The programs work on VAX and SUN computers.     

Quality assurance activities of the College of American Pathologists

Since its inception, the College of American Pathologists (CAP) has played a fundamental and pivotal role in the development and execution of quality assurance programs for laboratories. Within the realm of anatomic pathology, operational programs include those in surgical pathology, immunohistochemistry and cytopathology. The emphasis of prior cytopathology programs on cervical cytology has now been expanded to include body fluids and fine needle aspiration material. CAP's role in the expansion of quality assurance programs in cytology may be enhanced in the future by intersociety cooperation with established cytology organizations and will also be influenced by and closely linked to the expansion of its quality assurance programs in surgical pathology. As for the Papanicolaou smear, it can no longer be regarded as the "Cinderella of cytology"; it is in fact the present-day cynosure in the laboratory. In recognition of this, CAP has undertaken efforts to help heighten public awareness about the value of Papanicolaou smear testing and is encouraging women to become more informed about the process involved in the examination of their smears.     

Possible involvement of central pacemakers in clinical disorders of movement.

This review considers the evidence for possible involvement of central nervous system pacemaker neurons in several clinical disorders of movement. Two basic types of tremor are discussed from this point of view, i.e., 4--7/sec parkinsonian tremor, of possible thalamocortical origin, and 7--11/sec essential tremor of possible olivo-cerebellar origin. The importance of motor programs and abnormalities in their utilization are considered with reference to the loss of motor function in parkinsonism (? loss of motor programs), and the inappropriate release of such programs as a possible basis for the involuntary movements seen in other movement disorders, such as chorea, athetosis, dystonia, and hemiballismus. The possible role of pacemaker neurons controlling such programs is considered. Finally, the subject of locomotion and the pacemaker model of the spinal locomotor pattern generator for stepping are considered in relation to clinical disorders of gait. While critical evidence is lacking for pacemaker inovlvement in any of these disorders, their possible role is emphasized.     

基因组学研究中一些常用软件的概述

基因组学是以一个物种的全部遗传信息为研究对象,在整体上研究遗传信息的分子组成、组织结构、表达调控和进化等内在机制的基础性学科。基因组学研究中海量数据的存储、管理和检索,以及对这些数据进行挖掘等过程, 必须借助于生物信息学的方法。 目前,大量成熟的软件广泛地应用在基因组学研究中,它们大都可通过互联网免费访问或索取。本文拟对人类基因组计划中常用的一些软件如序列比对、序列组装、重复序列鉴定和基因预测等软件的原理作一介绍,并结合典型软件加以说明。 Abstract:Genomics is a novel subject that has been developed accompanying with the progress of human genome project.Genomics deals with the chemistry component,structure organization and evolution of genome at global level.As genomics associated with huge data,bioinformatics plays an important role in these processes of data production,data management and data mining.At present,many reliable programs have been used in genomic research successfully,which are usually accessible and downloaded freely.We address here the principles of some programs used wildly in genomics such as sequence alignment,sequence assembly,repeat identification and gene prediction,which are exemplified with typical programs respectively.     

Coastal Resource Management and Social Differences in Philippine Fishing Communities

Class, ethnic, and gender differences among fisherfolk powerfully influence how the benefits and costs of coastal resource management programs are perceived and experienced in Philippine fishing communities. These and other social differences also limit the efficacy of community participation in these programs and hence the role that local communities can be expected to play in fisheries co-management regimes. Greater attention to institutional changes is needed if the management potential of such regimes is to be realized.     

Tom Pollard,father of life science policy advocacy

Tom Pollard has played an instrumental role in the creation of the life science policy and advocacy programs familiar to life scientists today. This article reviews the creation of that program and the role Tom played. In addition, it briefly discusses advocacy activities now available to life scientists and why they should participate in these activities.     

IMPORTANCE OF REFERENCE STANDARDS IN TRAINING PANELISTS

When training a sensory evaluation panel, reference standards play an important role in developing appropriate terminology, establishing intensity ranges and showing the action of an ingredient. In addition, use of reference standards reduces the amount of training time while providing documentation for terminology. Product characteristics can be demonstrated through reference standards for application in plant quality assurance programs as well as for project planning in new product development, product maintenance (i.e., shelf-life), product improvement and cost reduction programs.     

Programs of the IAEA utilizing nuclear analytical techniques in the life sciences

Biological Trace Element Research - Nuclear analytical techniques have an important role in the IAEA in life sciences programs relating to human health. A major effort has recently been devoted to...     

Disparate views of community in primary health care: understanding how perceptions influence success

The importance of community in primary health care (PHC) is evident in the role of community participation and in the types of programs that are routinely implemented (community health-worker [CHW] programs, community clinics, community-based disease-control programs). Few health care providers and program administrators, however, have considered the meaning of community. Instead, they frequently impose their own definition of community and assume that it corresponds to local realities. This is problematic because target populations may have different ideas about what a community is and how it functions. When disparate ideas of community exist, they can affect the implementation of PHC programs, leading to low rates of acceptance, participation, and utilization. Using two examples, a community clinic in El Alto, Bolivia, and a CHW program in Rio Branco, Brazil, this article discusses some of the problems that arise when local definitions of community do not correspond to programmatic definitions.     

For what purpose the arts? An analysis of the mission statements of urban arts high schools in Canada and the United States

While general arts programs have declined in many schools across the United States and Canada, the number of specialized art programs in public secondary schools has swelled since the 1980s. While this increase is often celebrated by arts educators, questions about the justification of specialized arts programs are rarely raised, and their value is often taken for granted. In this article, we examine the mission statements of eighty-four specialized arts programs across two countries to examine the ideas, values, and commitments that are expressed in these public statements. In addition to a close thematic analysis, we describe how these mission statements reflect different conceptions of the role of the arts in education and consider the ways in which arguments that seek to broaden access to the arts are combined with the goal of serving a narrow subset of the student population. We argue that analyzing mission statements provides a clearer picture of the ideas that shape these programs, and that in order to foster an informed public conversation about the purpose and value of an education in the arts, educators committed to the arts must engage in this serious discussion.     

Evaluation of Gene Structure Prediction Programs

We evaluate a number of computer programs designed to predict the structure of protein coding genes in genomic DNA sequences. Computational gene identification is set to play an increasingly important role in the development of the genome projects, as emphasis turns from mapping to large-scale sequencing. The evaluation presented here serves both to assess the current status of the problem and to identify the most promising approaches to ensure further progress. The programs analyzed were uniformly tested on a large set of vertebrate sequences with simple gene structure, and several measures of predictive accuracy were computed at the nucleotide, exon, and protein product levels. The results indicated that the predictive accuracy of the programs analyzed was lower than originally found. The accuracy was even lower when considering only those sequences that had recently been entered and that did not show any similarity to previously entered sequences. This indicates that the programs are overly dependent on the particularities of the examples they learn from. For most of the programs, accuracy in this test set ranged from 0.60 to 0.70 as measured by the Correlation Coefficient (where 1.0 corresponds to a perfect prediction and 0.0 is the value expected for a random prediction), and the average percentage of exons exactly identified was less than 50%. Only those programs including protein sequence database searches showed substantially greater accuracy. The accuracy of the programs was severely affected by relatively high rates of sequence errors. Since the set on which the programs were tested included only relatively short sequences with simple gene structure, the accuracy of the programs is likely to be even lower when used for large uncharacterized genomic sequences with complex structure. While in such cases, programs currently available may still be of great use in pinpointing the regions likely to contain exons, they are far from being powerful enough to elucidate its genomic structure completely.     

Opportunities and Challenges for Ecological Restoration within REDD+

The Reducing Emissions from Deforestation and Forest Degradation (REDD+) mechanism has the potential to provide the developing nations with significant funding for forest restoration activities that contribute to climate change mitigation, sustainable management, and carbon‐stock enhancement. In order to stimulate and inform discussion on the role of ecological restoration within REDD+, we outline opportunities for and challenges to using science‐based restoration projects and programs to meet REDD+ goals of reducing greenhouse gas emissions and storing carbon in forest ecosystems. Now that the REDD+ mechanism, which is not yet operational, has expanded beyond a sole focus on activities that affect carbon budgets to also include those that enhance ecosystem services and deliver other co‐benefits to biodiversity and communities, forest restoration could play an increasingly important role. However, in many nations, there is a lack of practical tools and guidance for implementing effective restoration projects and programs that will sequester carbon and at the same time improve the integrity and resilience of forest ecosystems. Restoration scientists and practitioners should continue to engage with potential REDD+ donors and recipients to ensure that funding is targeted at projects and programs with ecologically sound designs.     

A training primer for Institutional Officials

The laws and policies governing the care and use of animals in research in the US require institutions to establish training programs to assure that personnel are qualified for their roles in animal care and use programs. Few programs define specific training requirements for the Institutional Official (IO), one of the most important roles in an animal care program. In some cases, IOs may have little or no experience in biomedical science. In this article, the author provides an overview of the IO's role in an animal care and use program as defined by US government laws and policies for use in training IOs and chief executive officers. The author outlines the key responsibilities of the IO in an animal care program, the implications of noncompliance with federal requirements and some of the pitfalls in program design.     

An analysis of gene-finding programs for Neurospora crassa.

MOTIVATION: Computational gene identification plays an important role in genome projects. The approaches used in gene identification programs are often tuned to one particular organism, and accuracy for one organism or class of organism does not necessarily translate to accurate predictions for other organisms. In this paper we evaluate five computer programs on their ability to locate coding regions and to predict gene structure in Neurospora crassa. One of these programs (FFG) was designed specifically for gene-finding in N.crassa, but the model parameters have not yet been fully 'tuned', and the program should thus be viewed as an initial prototype. The other four programs were neither designed nor tuned for N.crassa. RESULTS: We describe the data sets on which the experiments were performed, the approaches employed by the five algorithms: GenScan, HMMGene, GeneMark, Pombe and FFG, the methodology of our evaluation, and the results of the experiments. Our results show that, while none of the programs consistently performs well, overall the GenScan program has the best performance on sensitivity and Missing Exons (ME) while the HMMGene and FFG programs have good performance in locating the exons roughly. Additional work motivated by this study includes the creation of a tool for the automated evaluation of gene-finding programs, the collection of larger and more reliable data sets for N.crassa, parameterization of the model used in FFG to produce a more accurate gene-finding program for this species, and a more in-depth evaluation of the reasons that existing programs generally fail for N.crassa. AVAILABILITY: Data sets, the FFG program source code, and links to the other programs analyzed are available at http://jerry.cs.uga.edu/~wang/genefind.html. CONTACT: eileen@cs.uga.edu.     

Natural Products in High Throughput Screening: Automated High-Quality Sample Preparation

At present, compound libraries from combinatorial chemistry are the major source for high throughput screening (HTS) programs in drug discovery. On the other hand, nature has been proven to be an outstanding source for new and innovative drugs. Secondary metabolites from plants, animals, and microorganisms show a striking structural diversity that supplements chemically synthesized compounds or libraries in drug discovery programs. Unfortunately, extracts from natural sources are usually complex mixtures of compounds, often generated in time-consuming and, for the most part, manual processes. Because quality and quantity of the provided samples play a pivotal role in the success of HTS programs, this poses serious problems. In order to make samples of natural origin competitive with synthetic compound libraries, we devised a novel, automated sample preparation procedure based on solid-phase extraction (SPE). By making use of modified Zymark (Hopkinton, MA) RapidTrace? SPE workstations, we developed an easy-to-handle and effective fractionation method that generates high-quality samples from natural origin, fulfilling the requirements for an integration in high throughput drug discovery programs.     

Dynamics of additional food provided predator–prey system with mutually interfering predators

Use of additional/alternative food source to predators is one of the widely recognised practices in the field of biological control. Both theoretical and experimental works point out that quality and quantity of additional food play a vital role in the controllability of the pest. Theoretical studies carried out previously in this direction indicate that incorporating mutual interference between predators can stabilise the system. Experimental evidence also point out that mutual interference between predators can affect the outcome of the biological control programs. In this article dynamics of additional food provided predator–prey system in the presence of mutual interference between predators has been studied. The mutual interference between predators is modelled using Beddington–DeAngelis type functional response. The system analysis highlights the role of mutual interference on the success of biological control programs when predators are provided with additional food. The model results indicate the possibility of stable coexistence of predators with low prey population levels. This is in contrast to classical predator–prey models wherein this stable co-existence at low prey population levels is not possible. This study classifies the characteristics of biological control agents and additional food (of suitable quality and quantity), permitting the eco-managers to enhance the success rate of biological control programs.     

Spontaneous succession in Central‐European man‐made habitats: What information can be used in restoration practice?

Abstract. The results of previous studies concerning spontaneous vegetation succession in various man‐made or disturbed habitats in Central Europe are discussed in relation to restoration ecology. An attempt is made to answer the main questions which are important to restoration programs. These concern the rate and direction of succession; participation of target species and communities, woody species, ruderals and aliens; arresting or diverting succession; changes in species diversity; variability of successional pathways and the role of abiotic environmental conditions. The great potential for using successional theory in restoration programs is emphasized.     

Molecular aspects of leaf senescence

Senescence is the last stage of leaf development and one type of programmed cell death that occurs in plants. The relationships among senescence programs that are induced by a variety of factors have been addressed at a molecular level in recent studies. Furthermore, an overlap between the pathogen-response and senescence programs is beginning to be characterized. The complexity of the senescence program is also evident in studies of senescence-specific gene regulation and the role of photosynthesis and plant hormones in senescence regulation. New molecular-genetic approaches are expected to be useful in unraveling the molecular mechanisms of the leaf senescence program.     

A microcomputer system for the measurement of finger forces

In the analysis of hand functions, the production and control of forces exerted during voluntary contraction of the finger muscles plays an important role; unfortunately such an analysis is rarely seen in routine clinical examinations of neurological patients. A microcomputer controlled system for the measurement and analysis of finger forces is described. The system consists of a modified Z80 based microcomputer, a commercially available high precision force transducer, a specially designed force signal amplifier and a suite of menu-driven user interactive programs. A variety of tasks is implemented by means of the computer programs. In addition to the measurement of maximum hand grip force, the system is able to record forces continuously as a function of time. Task characteristics and the type of feedback presented to the subject are under user control; they can be varied to meet clinical or experimental requirements. Examples of programs and clinical applications are presented and discussed.