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At least 325 records · Page 18Linked to original sources

PubMed2004

Filtering of ineffective siRNAs and improved siRNA design tool.

MOTIVATION: Short interfering RNAs (siRNAs) can be used to suppress gene expression and possess many potential applications in therapy, but how to design an effective siRNA is still not clear. Based on the MPI (Max-Planck-Institute) basic principles, a number of siRNA design tools have been developed recently. The set of candidates reported by these tools is usually large and often contains ineffective siRNAs. In view of this, we initiate the study of filtering ineffective siRNAs. RESULTS: The contribution of this paper is 2-fold. First, we propose a fair scheme to compare existing design tools based on real data in the literature. Second, we attempt to improve the MPI principles and existing tools by an algorithm that can filter ineffective siRNAs. The algorithm is based on some new observations on the secondary structure, which we have verified by AI techniques (decision trees and support vector machines). We have tested our algorithm together with the MPI principles and the existing tools. The results show that our filtering algorithm is effective. AVAILABILITY: The siRNA design software tool can be found in the website http://www.cs.hku.hk/~sirna/ CONTACT: smyiu@cs.hku.hk

Algorithms↗

PubMed2004

Simulation tools for biochemical networks: evaluation of performance and usability.

MOTIVATION: Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions. Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools. Knowledge of the properties and capabilities of the simulation tools would help bioscientists in building models based on experimental data. RESULTS: We examine selected simulation tools that are intended for the simulation of biochemical systems. We choose four of them for more detailed study and perform time series simulations using a specific pathway describing the concentration of the active form of protein kinase C. We conclude that the simulation results are convergent between the chosen simulation tools. However, the tools differ in their usability, support for data transfer to other programs and support for automatic parameter estimation. From the experimentalists' point of view, all these are properties that need to be emphasized in the future.

Animals↗

PubMed2005

Ontological analysis of gene expression data: current tools, limitations, and open problems.

Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high throughput experiments and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis. More importantly, in spite of the fact that this type of analysis has been generally adopted, this approach has several important intrinsic drawbacks. These drawbacks are associated with all tools discussed and represent conceptual limitations of the current state-of-the-art in ontological analysis. We propose these as challenges for the next generation of secondary data analysis tools.

Algorithms↗

PubMed2005

Recent additions and improvements to the Onto-Tools.

The Onto-Tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner and Pathway-Express. The Onto-Tools database has been expanded to include various types of data from 12 new databases. Our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. Additionally, our database is also expanded to include complete Gene Ontology (GO) annotations. Using the enhanced database and GO annotations, Onto-Express now allows functional profiling for 24 organisms and supports 17 different types of input IDs. Onto-Translate is also enhanced to fully utilize the capabilities of the new Onto-Tools database with an ultimate goal of providing the users with a non-redundant and complete mapping from any type of identification system to any other type. Currently, Onto-Translate allows arbitrary mappings between 29 types of IDs. Pathway-Express is a new tool that helps the users find the most interesting pathways for their input list of genes. Onto-Tools are freely available at http://vortex.cs.wayne.edu/Projects.html.

Animals↗

PubMed1996

Tool-related injuries among amateur and professional woodworkers.

Although woodworking is a popular hobby and the woodworking industry employs thousands of workers nationwide, few studies have examined injuries associated with this activity, especially in relation to woodshop tool use. We conducted a survey of amateur and professional woodworkers (n = 283) in New Mexico to determine histories and rates of tool-specific injuries. Injuries associated with woodshop tool use were reported by 64% of all respondents. Hammers, chisels/gouges, and table saws were most frequently reported in association with injuries, although the highest tool-specific injury rates were associated with use of jointer-planers (4.9 injuries per 1000 person-hours of use), chisels/ gouges (3.3 injuries), and drill presses (3.1 injuries). One third reported tool use-associated injuries that were severe enough to require professional medical attention; 5% of all respondents suffered partial amputations. Courses in the safe use of shop tools may help to reduce rates of injuries among woodworkers.

Accidents, Occupational↗

PubMed2006

Decision tools for life support: a review and policy analysis.

OBJECTIVE: To identify, describe, and compare published documents intended to guide decisions about the administration, withholding, or withdrawal of life support in critical care. DESIGN: Review article. SETTING AND SOURCES: Publicly available, English-language guidelines or decision tools for life support, identified through systematic literature search. MEASUREMENTS AND MAIN RESULTS: Forty-nine documents were included and coded for authorship, source, development methodology, format, and positions taken on 12 common life-support issues. Sources were independent academics (n=21, 43%), professional organizations (n=19, 44%), and provider organizations. Eighteen documents (37%) described no development method. Twenty-three (47%) were produced collectively (e.g., by committees or consensus conference), 7 (14%) mentioned a literature review, and 2 (4%) were based upon the author's professional experience. Tools differed in format and focus; we characterize three types as decision schemas (involving clinical practice algorithms; n=7, 14%), decision guides (reviewing legal or professional positions; n=29, 59%), and decision counsels (more discursive and focusing typically on ethical issues; n=13, 27%). Tools addressed 12 common life-support issues: advance directives (67%), resource considerations (51%), ICU discharge criteria (27%), ICU admission criteria (16%), whether withholding differs from withdrawing life support (59%), whether nutrition and hydration decisions are different from decisions about other types of life support (61%), euthanasia (49%), double effect (47%), brain death (35%), special considerations for patients in a persistent vegetative state (51%), potential organ donors (12%), and pregnant patients (10%). Positions on these key life-support issues varied. CONCLUSIONS: Published tools for guiding life-support decisions vary widely in their genesis, authorship, format, focus, and practicality. They also differ in their attention to, and positions on, key life-support dilemmas. Future research on decision tools should focus on how users interpret and apply the messages in these tools and their impacts on practice, quality of care, participant experiences, and outcomes.

Decision Support Techniques↗

PubMed1998

Getting the right tool for the job.

In summary, getting the right tool for the job requires several steps prior to using the tool in an anticipated study. Finding obtaining and evaluating the tool are all critical to a successful use of the tool in the study. If any of these factors are not followed, the researcher could be ethically or legally in trouble. Most tool developers want their tools to be used. It is up to the researchers to ensure that credit is given where credit is due, and that due process is followed.

PubMed2004

The crafting of hook tools by wild New Caledonian crows.

The 'crafting' of tools involves (i) selection of appropriate raw material, (ii) preparatory trimming and (iii) fine, three-dimensional sculpting. Its evolution is technologically important because it allows the open-ended development of tools. New Caledonian crows manufacture an impressive range of stick and leaf tools. We previously reported that their toolkit included hooked implements made from leafy twigs, although their manufacture had never been closely observed. We describe the manufacture of 10 hooked-twig tools by an adult crow and its dependent juvenile. To make all 10 tools, the crows carried out a relatively invariant three-step sequence of complex manipulations that involved (i) the selection of raw material, (ii) trimming and (iii) a lengthy sculpting of the hook. Hooked-twig manufacture contrasts with the lack of sculpting in the making of wooden tools by other non-humans such as chimpanzees and woodpecker finches. This fine, three-stage crafting process removes another alleged difference between humans and other animals.

Animals↗

PubMed2006

Design complexity and strength of laterality are correlated in New Caledonian crows' pandanus tool manufacture.

Population-level laterality is generally considered to reflect functional brain specialization. Consequently, the strength of population-level laterality in manipulatory tasks is predicted to positively correlate with task complexity. This relationship has not been investigated in tool manufacture. Here, we report the correlation between strength of laterality and design complexity in the manufacture of New Caledonian crows' three pandanus tool designs: wide, narrow and stepped designs. We documented indirect evidence of over 5,800 tool manufactures on 1,232 pandanus trees at 23 sites. We found that the strength of laterality in tool manufacture was correlated with design complexity in three ways: (i) the strongest effect size among the population-level edge biases for each design was for the more complex, stepped design, (ii) the strength of laterality at individual sites was on average greater for the stepped design than it was for the simpler wide and narrow, non-stepped designs, and (iii) there was a positive, but non-significant, trend for a correlation between the strength of laterality and the number of steps on a stepped tool. These three aspects together indicate that greater design complexity generally elicits stronger lateralization of crows' pandanus tool manufacture.

Animals↗

PubMedDate not supplied

A perception--action perspective on tool use development.

In this essay I argue for a new wave of research on tool use development. Advances in the literature on perception-action development hold important clues for how tool use unfolds in children. These advances suggest that tool use may be a more continuous developmental achievement than has been previously believed. On this view, tool use is rooted in the perception-action routines that infants employ to gain information about their environments. Although tools alter the properties of effector systems, children use tools to explore and change their environments, building on efforts that originate in infancy. Based on this approach, new research directions are suggested, including efforts designed to investigate the processes by which children detect and relate affordances between objects, coordinate spatial frames of reference, and incorporate early-appearing action patterns into instrumental behaviors.

Child↗

PubMed1991

An evaluation of approaches to assessing the quality of nursing care using (predetermined) quality assurance tools.

This paper examines the implementation of four of the most common approaches to nursing quality assurance in England, namely Monitor, Qualpacs, nursing audits and a patient satisfaction questionnaire entitled 'What the Patient Thinks'. The primary aim of the study was to look more closely at the context, processes and outcomes of selecting and implementing specific quality assurance tools. Data were analysed at three distinct levels. The findings are presented around the structure of this three-level framework and indicate that the process of implementing a quality assurance tool is more important than the tool itself. It is suggested that a bottom-up approach to implementation, which locates ownership and control of the quality assurance tool with practitioners, is seen to result in more favourable staff responses and positive programme outcomes. The implementation of Qualpacs is used to illustrate some of the tensions that can occur between the inherent principles of the tool and the method of implementation. In studying the factors that might influence the method of implementing a quality assurance tool, a number of organizational and managerial factors are identified.

Attitude of Health Personnel↗

PubMed2005

Developing an assessment tool for evaluating community involvement.

BACKGROUND: Current UK policy has resulted in greater requirements for public and patient participation in health service planning and decision making. Organizations and services need to be able to monitor and evaluate the effectiveness and quality of their community involvement processes, but there are few appropriate evaluation tools or sets of indicators available. This paper reports on work within Bradford Health Action Zone to develop a self-assessment tool for organizations on community involvement. METHODS: A multi-agency working group developed the tool. A literature search was undertaken and evaluation resources were reviewed. A set of benchmarks for community involvement in regeneration was utilized in developing the assessment areas. A range of individuals with expertise on community involvement practice and performance management was consulted. The tool was then piloted in two primary care trusts prior to final modifications. RESULTS: The process resulted in the production of Well Connected--a self-assessment tool on community involvement designed for organizations to assess their progress and identify areas for improvement. A scoring system assesses evidence of a strategic approach to community involvement, good practice throughout the organization, and a range of opportunities and support. Feedback from the pilots revealed that the tool had facilitated assessment of the strengths and weaknesses of organizational practices. CONCLUSION: The paper discusses some of the methodological challenges pertaining to the measurement of community involvement. Notwithstanding those challenges, it is argued that Well Connected provides a robust and practical framework that health organizations and their partners can use to assess practice.

Community Participation↗

PubMed2005

Assessment tools for screening and monitoring bipolar disorder.

OBJECTIVE: To review the availability and suitability of tools for screening, diagnosing, and monitoring people with bipolar disorder in both psychiatric and general practice. METHODS: Currently available assessment tools suitable for use with patients with bipolar disorder were identified through a MEDLINE search using the following key terms: bipolar, screening, diagnosis, monitoring. Only peer-reviewed papers published in English were considered for further review. RESULTS: A review of the current literature revealed a small number of published and appropriately validated clinical tools suitable for the assessment of bipolar disorder in terms of screening, diagnosis, and long-term monitoring. CONCLUSIONS: While there are a large number of formal rating scales for the assessment of various clinical aspects of bipolar spectrum disorders, there are currently only a limited number of assessment tools well suited for use in routine clinical practice. Widespread use of brief, clinically validated, and easy to use screening tools could facilitate the early identification of patients with bipolar spectrum disorders. A less structured diagnostic approach should facilitate diagnosis of the more subtle forms of the disease, particularly bipolar II disorder. Long-term monitoring tools should strengthen the therapeutic alliance between the patient and clinician and improve long-term quality of care and assessment of outcomes.

Bipolar Disorder↗

PubMed1998

Nickel release from tools on the Swedish market.

Nickel allergy in women has been thoroughly studied: its prevalence, the most important sources of sensitization, and risk factors for elicitation of dermatitis. Preventive measures have also been introduced. Nickel allergy in men has not, however, been equally focused on. Based on clinical experience, some publications indicating that tools may be a risk factor for nickel allergy and hand eczema in men, and the fact that large occupational groups regularly use tools, we decided to carry out a study, of the prevalence on the market of tools that release nickel. 27% of 565 hand-held tools with metal parts that come into contact with the skin were found to be dimethylglyoxime (DMG) test positive. Release of nickel and other metals into artificial sweat and composition of metals on the surface and in the base alloy were also studied. It is suggested that tool producers should consider nickel allergy and avoid nickel-releasing materials, and that analytical methods, relevant for nickel release from tools, should be further developed.

Dermatitis, Allergic Contact↗

PubMedDate not supplied

Tool use, aye-ayes, and sensorimotor intelligence.

Humans, chimpanzees, capuchins and aye-ayes all display an unusually high degree of encephalization and diverse omnivorous extractive foraging. It has been suggested that the high degree of encephalization in aye-ayes may be the result of their diverse, omnivorous extractive foraging behaviors. In combination with certain forms of tool use, omnivorous extractive foraging has been hypothesized to be linked to higher levels of sensorimotor intelligence (stages 5 or 6). Although free-ranging aye-ayes have not been observed to use tools directly in the context of their extractive foraging activities, they have recently been reported to use lianas as tools in a manner that independently suggests that they may possess stage 5 or 6 sensorimotor intelligence. Although other primate species which display diverse, omnivorous extractive foraging have been tested for sensorimotor intelligence, aye-ayes have not. We report a test of captive aye-ayes' comprehension of tool use in a situation designed to simulate natural conditions. The results support the view that aye-ayes do not achieve stage 6 comprehension of tool use, but rather may use trial-and-error learning to develop tool-use behaviors. Other theories for aye-aye encephalization are considered.

Animals↗

PubMed2003

Actions speak louder than functions: the importance of manipulability and action in tool representation.

PET was used to investigate the neural correlates of action knowledge in object representations, particularly the left lateralized network of activations previously implicated in the processing of tools and their associated actions: ventral premotor cortex (VPMCx), posterior middle temporal gyrus (PMTG), and intraparietal sulcus (IPS). Judgments were made about the actions and functions associated with manipulable man-made objects (e.g., hammer); this enabled us to measure activations in response to both explicit and implicit retrieval of knowledge about actions associated with manipulable tools. Function judgments were also made about nonmanipulable artifacts (e.g., traffic light) providing a direct comparison for manipulable objects. Although neither the left VPMCx nor the left PMTG were selective for tool stimuli (nonmanipulable objects also activated these areas relative to a visual control condition), both regions responded more strongly to manipulable objects, suggesting a role for these cortical areas in the processing of knowledge associated with tools. Furthermore, these activations were insensitive to retrieval task, suggesting that visually presented tools automatically recruit both left VPMCx and left PMTG in response to action features that are inherent in tool representations. In contrast, the IPS showed clear selectivity for explicit retrieval of action information about manipulable objects. No regions of cortex were more activated by function relative to action judgments about artifacts. These results are consistent with the brain's preferential responsiveness to how we interact with objects, rather than what they are used for.

Adult↗

PubMed2005

A dissociation between the representation of tool-use skills and hand dominance: insights from left- and right-handed callosotomy patients.

The overwhelming majority of evidence indicates that the left cerebral hemisphere of right-handed humans is dominant both for manual control and the representation of acquired skills, including tool use. It is, however, unclear whether these functions involve common or dissociable mechanisms. Here we demonstrate that the disconnected left hemispheres of both right- and left-handed split-brain patients are specialized for representing acquired tool-use skills. When required to pantomime actions associated with familiar tools (Experiment 2), both patients show a right-hand (left hemisphere) advantage in response to tool names, pictures, and actual objects. Accuracy decreases as stimuli become increasingly symbolic when using the left hand (right hemisphere). Tested in isolation with lateralized pictures (Experiment 3), each patient's left hemisphere demonstrates a significant advantage over the right hemisphere for pantomiming tool-use actions with the contralateral hand. The fact that this asymmetry occurs even in a left-handed patient suggests that the left hemisphere specialization for representing praxis skills can be dissociated from mechanisms involved in hand dominance located in the right hemisphere. This effect is not attributable to differences at the conceptual level, as the left and right hemispheres are equally and highly competent at associating tools with observed pantomimes (Experiment 4).

Adult↗

PubMed2006

Lefties get it "right" when hearing tool sounds.

Our ability to manipulate and understand the use of a wide range of tools is a feature that sets humans apart from other animals. In right-handers, we previously reported that hearing hand-manipulated tool sounds preferentially activates a left hemisphere network of motor-related brain regions hypothesized to be related to handedness. Using functional magnetic resonance imaging, we compared cortical activation in strongly right-handed versus left-handed listeners categorizing tool sounds relative to animal vocalizations. Here we show that tool sounds preferentially evoke activity predominantly in the hemisphere "opposite" the dominant hand, in specific high-level motor-related and multisensory cortical regions, as determined by a separate task involving pantomiming tool-use gestures. This organization presumably reflects the idea that we typically learn the "meaning" of tool sounds in the context of using them with our dominant hand, such that the networks underlying motor imagery or action schemas may be recruited to facilitate recognition.

Acoustic Stimulation↗