Australian burden of disease estimates appeared inconsistent with the reported repetitive and ubiquitous nature of dental problems. The aims of the study were to measure the nature, severity and duration of symptoms for specific oral conditions, and calculate disability weights from these measures.Data were collected in 2001–02 from a random sample of South Australian dentists using mailed self-complete questionnaires. Dentists recorded the diagnosis of dental problems and provided patients with self-complete questionnaires to record the nature, severity and duration of symptoms using the EuroQol instrument. Data were available from 378 dentists (response rate = 60%).Disability weights were highest for pulpal infection (0.069), caries (0.044) and dentinal sensitivity (0.040), followed by denture problems (0.026), periodontal disease (0.023), failed restorations (0.019), tooth fractures (0.014) and tooth wear (0.011). Aesthetic problems had a low disability weight (0.002), and both recall/maintenance care and oral hygiene had adjusted weights of zero.Disability weights for caries (0.044), periodontal disease (0.023) and denture problems (0.026) in this study were higher than comparable oral health conditions in the Australian Burden of Disease and Injury Study . A range of common problems such as pulpal infection, failed restorations and tooth fracture that were not included in the Australian Burden of Disease and Injury Study had relatively high disability weights. The inclusion of a fuller range of oral health problems along with revised disability weights would result in oral health accounting for a larger amount of disability than originally estimated. Although dental problems are widespread in number and impose a large burden on society in terms of lost production, pain and suffering, and health expenditure there is a tendency to underestimate their importance due to the generally non-fatal nature of most oral diseases and complacency arising from acknowledged improvements in oral health, such as trends toward lower caries levels among children and decreased edentulism in adults. Australians spend $2.6 billion on dental services, some 5.4% of recurrent health expenditure for 1998–99 , and perThe disability-adjusted life year or DALY ,6 providEstimates of DALYs are limited by inadequate information on the distribution of severity of disease and the course of a disease. Due to limitations in the data many of the disease models are necessarily simple and approximate, with their precision reflecting the source and nature of the data underlying the model. Also, the lack of Australian disease weights may mean that they are not completely representative of Australian societal preferences . Hence tThe DALY estimates for oral health in the Australian Burden of Disease and Injury Study seemed inconsistently low with other reports of the high prevalence and incidence of oral health conditions such as dental caries and periodontal disease . There aThe broad aims of the project were to evaluate methods used to measure the burden of disease associated with oral conditions in Australia. The specific aims were to obtain measures of burden of disease related to specific oral conditions, measure these in terms of the nature, severity and duration of symptoms, and calculate disability weights from these measures.The study was conducted using a 2-stage sampling design whereby dentists were randomly sampled from the South Australian Dental Register, randomised into one of seven equal-sized study groups and sent a mailed self-complete dentist questionnaire along with up to five self-complete patient questionnaires depending on the study group. Dentists were provided with a practitioner logbook in which to record for the first 1 to 5 adult patients (depending on study group assignment of dentist) of a random clinical day the treatment they performed and diagnosis of the oral disease or condition treated. At the conclusion of treatment the practitioner passed on a survey kit to their sampled patient(s) containing a patient questionnaire, cover letter and explanation sheet. Sampled patients completing the patient questionnaire recording basic socio-demographic characteristics and data concerning the nature, severity and duration of their symptoms. The patient questionnaires were identified using the practitioner identification number allowing linkage between the practitioner logbook data and patient questionnaire data, but maintaining the anonymity of each patient to the investigators.The emphasis of the project was to obtain precise estimates of the component measures of the burden of oral disease. These are typically expressed as percentages, such as the percentage of persons or percentage of time experiencing symptoms of a given degree of severity. Taking a parameter size of 10% as a reference estimate for any given measure, in order to achieve a level of precision of 20% or less relative standard error, a minimum target sample of 225 patients was required. This would provide an acceptable minimum level of precision for estimates as low as 10% in size, and better precision for any estimates larger than 10% in size.Data were collected during 2001–2 with a primary approach letter sent initially to each dentist, followed a week later by the survey materials, with a reminder card two weeks later, and up to four follow-up mailings of survey materials to dentists who had not yet responded in order to ensure higher response rates .Dentists recorded the details of the dental conditions that patients had, and patients recorded their experience of those dental conditions. Diagnosis of dental conditions was collected from dentists using an open-ended question in the dentist questionnaire and coded using the coding scheme adopted in the Longitudinal Study of Dentists' Practice Activity . Data onFollowing descriptive analysis of response rates and characteristics of respondents, the distribution of dental conditions was examined for the 11 most common dental conditions. These dental conditions were then examined in terms of the nature, severity and duration of each condition. Disability weights were then calculated for each dental condition by using a health state valuation algorithm based on UK population data . A patieA total of 378 dentists responded to the survey (response rate = 60%). Response rates between study groups ranged from 49% to 70% and tended to be higher in study groups that required dentists to sample less patients, but the effect was not monotonic Table . Data weThe characteristics of patients are presented in Table The distribution of dental conditions is presented in Fig Dental conditions are presented in Table a) were highest for pulpal infection, dentinal sensitivity and caries, followed by denture problems, periodontal disease, tooth wear and tooth fractures (Table b) were reduced. Pulpal infection remained the highest adjusted disability weight, followed by caries and dentinal sensitivity, followed by denture problems, periodontal disease and failed restorations. Subtracting the intercept from the unadjusted disability weight reduced all weights (DWc) by a constant amount.Unadjusted disability weights derived from the additive model (DWes Table . When add) followed a similar rank order as for the unadjusted disability weights derived from the additive model (DWa), being highest for pulpal infection with caries ranked second-highest, but with some re-ordering of the next highest conditions . When adjusted by the percent of time that dental conditions were experienced all disability weights derived from the multiplicative model (DWe) were reduced, with pulpal infection ranked highest, followed by caries, dentinal sensitivity, denture problems, tooth wear and periodontal disease.The disability weights derived from the multiplicative model are presented in Table c) and multiplicative (DWe) models were similar in rank ordering, with pulpal infection, caries, dentinal sensitivity and denture problems ranked highest. While the adjusted disability weights derived from both models were also similar in magnitude those derived from the additive model were lower for all oral conditions except aesthetics, which was identical for both models. In the remainder of the paper the final adjusted disability weights derived from the additive model (DWc) will be presented, as this provided the most conservative estimate.The final adjusted disability weights derived from the additive , with 39.6% of patients reporting symptoms on one or more of the six dimensions . ConversThe findings from this study indicate that oral health conditions may account for a considerably higher level of DALYs than previously thought, due to the lack of quantitative data on the nature of dental conditions. While Australia has not had another national oral health survey since the initial survey of 1987–88, there have been other studies that suggest that dental problems are common ,4, and aCompared to the Australian Burden of Disease and Injury Study the adjusted disability weights for oral health conditions in this study were higher for comparable oral conditions of caries (0.044 versus 0.005 for caries involving a filling and 0.014 for caries involving an extraction), periodontal disease (0.023 versus 0.007) and denture problems (0.026 versus 0.004 for edentulism). In addition there were a range of common oral health problems such as pulpal infection, failed restorations and tooth fracture that were not included in the Australian Burden of Disease and Injury Study which had relatively high disability weights. The inclusion of a fuller range of oral health conditions along with revised disability weights would result in oral health accounting for a much larger amount of disability than originally estimated.None declared.DSB and AJS were chief investigators on the grants obtained to fund the study. DSB performed data collection, analysis and drafting of the manuscript. AJS participated in the design and coordination of the study, and completion of the manuscript. All authors read and approved the manuscript.Appendix 1: algorithm used to calculate disability weights from the additive model. Appendix 2: algorithm used to calculate disability weights from the multiplicative modelClick here for file


Focal segmental glomerulosclerosis (FSGS) made a brief media splash last year when a kidney transplant forced NBA superstar Alonso Mourning into early retirement. Mourning's condition elicited a flood of calls from fans offering their kidneys, but most people with kidney disease are not so lucky. Some 56,000 patients await transplants; many have waited over five years. FSGS, which underlies about 25% of the 60,000 kidney-related deaths each year, causes inflammation and irregular scarring in the glomeruli, clusters of blood vessels in the kidney that filter toxins from the blood. These lesions, which allow protein and blood to escape into the urine, cause progressive kidney failure. FSGS commonly occurs as an outgrowth of various primary disorders, including obesity, HIV infection, diabetes, and hypertension. Though it's not clear what causes FSGS, this form of renal pathology is becoming more common. By using the genes underlying inherited forms of FSGS as probes, scientists hope to uncover the mechanisms that unleash the disease and to find ways to stem the damage.ACTN4 gene, which encodes a protein called α-actinin-4, cause an inherited form of FSGS. The protein normally remodels actin filaments, the primary structural component of muscle and cytoskeleton. Having a single mutated copy of the gene can cause FSGS in humans, though it is unclear how. In this issue of PLoS Biology, Martin Pollak and his colleagues at Brigham and Women's Hospital at Harvard Medical School use a three-pronged approach to figure out how the defective protein wreaks renal havoc and how these physiological changes lead to FSGS. Using biochemical analysis, cell-based studies, and a newly developed “knockin” mouse model, the researchers report that FSGS-related mutations cause α-actinin-4 to engage in various aberrant behaviors that ultimately rob the protein of its function and poison cells.Mutations in the ACTN4. In these individuals, the disease appeared to strike podocytes  first. While engineering mice designed to carry mutations in this gene, the researchers created mice that lacked detectable Actn4 expression. These “knockout” mice developed severely damaged podocytes and progressive glomerular disease. In the current experiments, the researchers returned to their “knockin” mice, which carry two copies of the mutation found in the families with inherited FSGS. They also generated “normal” mice and mice harboring one normal and one mutant copy of the gene.In previous experiments, Pollak's team had discovered that some families with the inherited form of FSGS carried mutations in Actn4 mutation into podocytes, using a variety of methods, to see where in the cells the expressed proteins turned up. They also introduced fluorescently labeled mutant and normal Actn4 genes into podocytes that were grown from the three mouse types: normal proteins were diffused throughout the cytoplasm in each cell type, but the mutant proteins showed an uneven distribution. Analysis of various tissues taken from the knockin mice revealed normal levels of mRNA transcripts—indicating normal gene transcription—but “markedly reduced” α-actinin-4 protein levels. The mutant proteins, it turns out, were manufactured normally but were degraded far more quickly than normal proteins. Electron microscopy showed that podocytes in the kidneys of the knockin mice had structural defects, while the mice themselves had significantly higher levels of protein in their urine than mice with one or two normal copies of the gene did.In the biochemical experiments, the researchers investigated the mutant protein's binding behavior. Typically, two α-actinin-4 proteins form a twosome without incident, but here the mutants behaved badly, assuming improper structural conformations and forming aggregates rather than pairs. Next, Pollak and colleagues introduced the genes with the Actn4 mutations produce α-actinin-4 aggregates with significantly reduced life span, the authors explain, suggests two possible mechanisms of initiating disease: aggregation and the toxic affects of aggregation could injure podocytes, or loss of α-actinin-4 function caused by rapid degradation of the protein could produce injury. Pollak and colleagues argue that both factors likely play a role: Actn4 mutations lead to both reduced α-actinin-4 activity and protein aggregation, and the loss of protein function and the toxic effects of protein aggregation produce glomerular injury. As inherited renal disease typically emerges later in life, it may be that α-actinin-4 aggregation causes incremental but cumulative podocyte damage over time. So what does this mean for patients with progressive renal disease? While these findings may not translate into clinical applications anytime soon, they do suggest that therapies aimed at repairing the structure or expression of these essential cytoskeletal proteins might return the renegade proteins to the fold.The finding that FSGS-associated


Typically, randomization software should allow users to exert control over the different aspects of randomization including block design, provision of unique identifiers and control over the format and type of program output. While some of these characteristics have been addressed by available software, none of them have all of these capabilities integrated into one package. The main objective of the Random Allocation Software project was to enhance the user's control over different aspects of randomization in parallel group trials, including output type and format, structure and ordering of generated unique identifiers and enabling users to specify group names for more than two groups.The program has different settings for: simple and blocked randomizations; length, format and ordering of generated unique identifiers; type and format of program output; and saving sessions for future use. A formatted random list generated by this program can be used directly (without further formatting) by the coordinator of the research team to prepare and encode different drugs or instruments necessary for the parallel group trial.Random Allocation Software enables users to control different attributes of the random allocation sequence and produce qualified lists for parallel group trials. An important aspect of any trial that should be clearly stated in the final report is the method used to assign treatments (or other interventions) to participants . In the Without the use of computer software or Internet services the maintenance of the whole process of randomization and allocation is difficult. In addition, in the case of any necessary restrictions on the process of randomization (i.e. block randomization ) the com1. Independent running on a local computer without any need to access the Internet2. Different types of program output: to file (html or text files), window and system clipboard3. Provisions for different block design4. Capability to deal with a larger number of groups5. Specifying a name for each group6. Control over the format, length and ordering of the generated UIs7. Control over the format of generated sequence8. Saving or loading the randomization settings9. Viewing previously generated randomized sequencesRandom Allocation Software is a program created in Microsoft Visual Basic 6, and it installs in the same way as ordinary Windows software (i.e. running setup.exe and following on screen instructions). Once installed and run, there are some controls in the main window for specifying the number of groups (2 to 16), sample size and the name of each group. It also contains menu items to determine the program output and randomization settings. The default program output is saved into either html or text files, and it may also have output to a window or to the system clipboard. A variety of randomization options can be set in the options window. The length of generated UIs (named as Code in the program) can be between 3 to 10 characters and there are options for different alphanumeric structures. In addition, these UIs can appear in sequential or random order in the generated random list. The program can generate simple or block randomization in different types, including equal size blocks, multiple block lengths with random variation among the specified block sizes and complete randomized blocks (random number and size of blocks). The generated sequence will appear in a multiple columns format and the number of columns (1 to 10) can be changed in the options window. Output to html file will be formatted in the form of one block per table. Borders of the tables may be shown or hidden. By clicking the 'Generate' button in the main window the random sequence will be generated and opened by the default viewer for the output file (e.g. Internet Explorer for html files). Previously created output files can also be viewed from inside the program. Additional options include saving the current randomization settings, loading a previous setting and enabling the program to save the last setting upon program exit.During execution, the program produces a random sequence of allocation using the Rnd function that generates a floating point random number. The Rnd function uses the linear-congruent method for pseudo-random number generation as depicted by the following formula:x1 = (x0 * a + c) MOD (2^24) [12]where:x1 = new valuex0 = previous value a = 1140671485c = 12820163The seed of the Rnd will be the Timer function, which will return the number of seconds elapsed since midnight. Although this version of the program does not produce repeatable lists, it is possible to revise the program in subsequent versions to save the value of the seed to reproduce the same random list. The output consisted of shuffled allocations each of which is a UI, group name pair. The program checks for the uniqueness of the UIs and generates an error message if the specified UI length is insufficient to hold the entire sample size.Runs test was used to check randomness of the output list with sample sizes from 10 to 190  and from 200 to 3000 . Each runs test was carried out for the group number of 2, 3, 5 and 6. SPSS 10 software was used to perform the runs test.The program starts running with the default settings. Users may run the program with the default settings or set the number of groups, the name of each group and the sample size. Clicking the 'Generate' button figure  producesFigure In block randomization the final sample size is usually larger than the specified one.A total of 18 runs test were performed to check the randomness of the program output, which resulted in P values of 0.22 to 0.81.The main use of Random Allocation Software is to produce simple or block randomized sequences for parallel group trials. Its use is restricted to parallel group randomized trials. Compared with similar software, it enables the user to control the length, order and format of the UIs; and the type and format of the output. It allows specifying up to 16 groups for parallel trials.Random Allocation Software has been designed to produce random sequences consisting of UI, group name pairs with additional control over the output format and type. Available randomization software generally has limitations in the number of groups, naming each group, generating UIs and control over the output. Many of these problems have been addressed in the present software. As has been stated in previous sections, the main use of this software is for randomization in parallel group trials. The software can be revised to support crossover and other types of randomized trials. The experienced user may test the randomness of the program output by selecting numeric labels for group names and then exporting the generated list into a statistical software such as SPSS to execute a runs test on the exported data.Project name: Random Allocation SoftwarePublic use access: (Latest version)Operating systems: Windows 98, Me, 2000, XP. It should be noted that on some Windows operating systems  during installation of the program an error message like "Setup Cannot Continue... System Files Are Out of Date" may be displayed. If this happens, click OK and restart the system. Then run the setup.exe again. This is due to a known bug in the installation programs of Microsoft Visual Basic . This prProgramming Language: Visual Basic 6Other requirements: Internet Browser (Internet Explorer 5 or higher is recommended)License: Free for academic use.JIT = Just in TimeUI = Unique IdentifierThe author declares that he has no competing interests.The pre-publication history for this paper can be accessed here:


The goal of much care in chronic childhood illness is to improve quality of life (QOL). However, surveys suggest QOL measures are not routinely included. In addition, there is little consensus about the quality of many QOL measures.To determine the extent to which quality of life (QOL) measures are used in paediatric clinical trials and evaluate the quality of measures used.Systematic literature review.Included paediatric trials published in English between 1994 and 2003 involving children and adolescents up to the age of 20 years, and use of a standardised QOL measure. Data Sources included MEDLINE, CINAHL, EMB Reviews, AMED, BNI, PSYCHINFO, the Cochrane library, Internet, and reference lists from review articles.We identified 18 trials including assessment of QOL . In three trials, parents rated their own QOL but not their child's. Fourteen different QOL measures were used but only two fulfilled our minimal defined criteria for quality.This review confirms previous reports of limited use of QOL measures in paediatric clinical trials. Our review provides information about availability and quality of measures which will be of especial value to trial developers. Chronic disease affects approximately 18% of children  and cystEfforts to measure child QOL have proved complex but a number of generic and disease-specific measures have been reported . GenericThe quality of measures must be evaluated according to performance characteristics. Guidelines suggest good measures of QOL are reliable and valid for the group of patients for whom they are used, include a form for self-report wherever possible, are brief and developmentally appropriate, and allow completion by proxy .There is little evidence that QOL measures are routinely used in clinic practice  or cliniWe report a systematic review drawing on established methodologies  to deterrd quarter 1993, AMED (Allied & Contemporary Medicine) 1985 to December 2003, British Nursing Index (BNI) 1985 – October 2003, EMBASE, PSYCHINFO 1872–2003.The following databases were searched: MEDLINE 1966 to Nov Week 2 2003, CINAHL 1982 to December Week 1 2003, EMB Reviews: Cochrane Central Register of Controlled Trials, Your Journals at OVID, EMB reviews: ACP Journal Club 1991 to July / August 2003, EMB reviews: Database of Abstracts and Reviews of Effects 3Text word and thesaurus searches were used to minimise the chance of missing relevant articles. The following keywords were searched:• child, childhood, children, adolescent, infant, pediatric, paediatric,• quality of life, QOL,• clinical trial, randomised controlled trialSearches were restricted to English language papers.Search engines were used to search the Internet with keywords and Boolean logic. Additional references from articles identified through these searches were also pursued.These included:1) Children and adolescents up to the age of 20 years,2) RCT, formal cross-over trial, or studies evaluating one or more active drug treatment with or without placebo,3) Standardised QOL measure (For these purposes we drew on a previous review  and defi4) Articles published in English between January 1994 and December 2003.1) Samples including both adults and children.2) Comparison of surgical treatment, pain control, palliative medication, or psychological/homeopathic intervention.3) Outcomes evaluated in terms of medical data only, non-standardised measures of QOL or standardised psychological measures including symptom checklists, measures of self-esteem, or coping.Abstracts were reviewed for relevance and full articles obtained where appropriate. A summary sheet was developed and both authors independently reviewed papers to ensure reliability. Data extracted by reviewers was second coded and compared and any discrepancies were resolved through discussion.Of the 917 records retrieved from the databases, initial inspection suggested that 27 abstracts met the inclusion criteria. On reading the full articles, nine failed to meet inclusion criteria. The resulting 18 articles were included in the review -29.Disease: QOL was most frequently included in trials in atopic diseases . Single studies were identified in Cystic fibrosis, Otis media, Amblyopia, Diabetes, Obesity associated with a brain tumour, Idiopathic short stature, and Congenital agranulocytosis.• Location: Seven studies were conducted in the U.S.A, 4 in the U.K, 3 in the Netherlands, one in Taiwan, and one in Israel. Two studies were multi-national.• Child's age: Three studies recruited children across a broad age range (1 to 18 years), 2 focused on pre-school children (1–5 years), 4 on pre-school and middle childhood (2–10 years), 2 on middle childhood (6–12 years), 6 on middle childhood and adolescence (5–18 years), and one on adolescents alone (12–17 years).• Sample size: Sample size ranged from 19 [•  from 19  to 689 [ from 19 . Power cDesign and trial aim: We identified 11 RCTs, 2 cross-over studies, and 5 studies comparing two or more active treatments without placebo or control group. Of the 11 RCTs, 1 was multi-national, 7 multi centre, and 3 single centre studies. Of the 7 non RCTs, 1 was multi-national, 2 were multi centre, and 4 single centre. Nine articles involved comparisons of two or more treatment and the remainder involved comparison of treatments with placebo.• Blinding: Seven RCTs reported blinding procedures.• Parent and caregiver QOL: Fifteen studies measured the impact of the disease on the child's QOL. Three included assessment of the caregivers QOL.• Respondent for child QOL: Of the 15 studies focusing on child QOL, 10 were based on child, and 3 on parent reports. In two studies both children and parents reported the child's QOL and in one of these clinicians also rated child QOL [• hild QOL .Generic or disease specific: In total, 12 disease specific and two generic measures were used [• ere used -38. The ere used ,29.Quality of measure: We assessed quality of measures based on minimal accepted criteria [• criteria  whereby criteria ,38. ThreDespite extensive searches we identified only 18 published reports of paediatric trials including standardised QOL measures. This undoubtedly represents a very small percentage of paediatric trials and supports previous findings that QOL data is seldom reported in paediatric clinical trials . FurtherIn considering why there are relatively few trials including QOL measures, it is important to take into account the aims and purpose of the trial ,41. The Where QOL was measured, disease specific measures were most often used (N = 12) as is normally recommended for use in clinical trials. Only two trials included measures that satisfactorily fulfilled accepted criteria . TypicalSelection of a measure of QOL is dependent on the psychometric properties of the instrument, as well as clinical and demographic variables characteristic of the sample. However, psychometric properties depend upon samples for which the scale has been validated. Hence it is important to ensure measures are used with clinical populations where psychometric data are available.There are some grounds for assuming that QOL changes during childhood, and therefore satisfactory measures target specific age groups . There aIt is also generally recommended that ratings of QOL should be made by children themselves whenever possible . In caseCONSORT  guidelinObjections to inclusion of QOL measures in trials involve anticipated increased costs, extra time needed to gain patient and parent consent, and lack of sophistication of currently available measures . A majorA second problem is that disease specific measures may simply not be available for rare conditions. Attempts to develop such measures are promising and in this review instruments for ambylopia  and agraOther methodological limitations in current work include the lack of power calculations. Where the aim of the trial includes QOL assessment, power calculations must be performed and are an essential element of clinical trial design. In cases where measurement of QOL is a secondary endpoint, sample size calculations are rare and difficult to establish. However attempts should be made to hypothesise expected changes in QOL scores in relation to the agreed sample size prior to the trial .This review supports previous findings of limited use of QOL measures in paediatric cancer trials  and exteThe measurement of QOL provides valuable information about the psychological and social impact of treatment on children especially where no differences in survival rates are anticipated. For this reason, the inclusion of QOL measurement in paediatric trials is becoming increasingly valued and mandatory ,48. TherBoth authors were responsible for planning, conducting and reporting this work and approved the final manuscript.Table 1: Study characteristicsClick here for fileTable 2: Quality of life measuresClick here for file


Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets.Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available.This paper describes the design, implementation and use of a The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation. Bioinformatics tools and techniques depend directly or indirectly upon experimental data. However, interpreting experimental data often requires access to significant amounts of additional information about the sample used in the experiment, the conditions in which measurements were taken, the equipment used to take the measurements, etc. Recent proposals for models that capture such experimental descriptions alongside experimental results include MIAME for transcriptome data  and PEDRIn proteomics, which is rapidly evolving into a high-throughput experimental approach, there is (as yet) no standard representation for experimental data. As a result, limited tool support is available for disseminating, searching, comparing or analysing the results of experiments conducted using different techniques and equipment in different laboratories. Thus, while experimental results can be analysed, often in a labour-intensive manner in-house, the development of bioinformatics techniques for archiving, sharing and wider exploitation of proteomics results is still in its infancy. This paper seeks to contribute to the development of effective and systematic support for proteome data management by:1. Describing a database for storing, searching and disseminating experimental proteomics data. This material should be relevant to the developers of future proteome data management systems in that it discusses and illustrates various design and implementation decisions that have an impact on the role and maintenance of the resulting database.Proteomics Experimental Data Repository) data model [2. Making available data sets from several labs whose data have been included in the initial release of the database. These data sets themselves result from substantial experimental activities, and are representative of the sorts of information that in-house and public proteome data repositories must capture. As the database stores data in an XML format that conforms to the PEDRo  , the StaEstablishing the most appropriate kinds of data to include in a database such as PEDRo is not straightforward, as this depends on the use that is to be made of the data. In a large data repository, users may want to search for results based on widely varying criteria – for example, the proteins identified, the change in the level of a protein over time, the mechanism by which a sample was studied, etc. Furthermore, the users of a proteome data repository may themselves be diverse, and include: experimentalists with minimal direct experience of proteomics, but who are interested in proteins or organisms for which proteome studies have been conducted; proteome scientists who want to identify how successful specific techniques have been in different contexts; or mass-spectrometric analysts who want to compare their results with those of others.This wide range of potential users encourages the creation of a rich repository for proteomics data that provides detailed descriptions of many different aspects of an experiment. However, populating a database such as PEDRo is not a trivial task, as several of the different kinds of data included in PEDRo currently have to be entered manually, which is time-consuming for data providers. Even though a data entry tool has been developed to ease data entry (available from ), experiMany bioinformatics databases, such as UniProt  and PDB The PEDRo database makes extensive use of XML for capturing, transmitting, storing and searching proteomics data. In particular:1. The data-capture process uses a software tool, illustrated in Figure 2. The database stores the XML captured using the data entry tool directly, using Xindice , an open3. The data are presented to users by generating web pages from the stored XML using XSLT , which wThe software components used within PEDRo  are illustrated in Figure sample generation , sample processing , mass spectrometry  and in silico analyses (e.g. database search program used and results obtained). Table in silico data analyses using more than one program. Furthermore, the data captured covers a range of different organisms, including Saccharomyces cerevisiae, Candida albicans, Candida glabrata, Mus musculus, Arabidopsis thaliana and Streptomyces coelicolor.The data stored in the database for each experiment is as described in the PEDRo model , and thuS. cerevisiae and the pathogenic fungus, C. albicans [C. glabrata , whose genome sequence has only just been completed. The Streptomyces coelicolor M600 data set is the largest proteomics time course analysis of this strain in terms of numbers of proteins identified. It adds significantly to our knowledge of expression of some of the 20 gene sets annotated as being determinants of the biosynthesis of secondary metabolites, including antibiotics. Somewhat similar experiments, but differing in many aspects of their metadata, are reported on the SWICZ database [Trichinella spiralis [These PEDRo data are significant in biological terms. For example, they include the first direct comparison of proteomic responses in two fungal species, namely responses to amino-acid starvation in the baker's yeast albicans . In addidatabase . This prspiralis .browsing – interactively listing or navigating through database entries; searching – identifying database entries on the basis of simple restrictions on the values of one or more fields; visualising – presenting a visual representation of the data as a starting point for browsing; or querying – specifying a search that is to be conducted over the database using a query building interface or by providing inputs to pre-written (or "canned") queries. Functional genomics databases tend to emphasise browsing and searching. For example, the Stanford Microarray Database [Web-based interfaces to biological databases tend to support one or more of the following tasks: Database  supportsDatabase  supportsDatabase  supportsS. cerevisiae data from PEDRo will also be made available through GIMS [PEDRo also emphasises browsing and searching. Figures ugh GIMS , for exaA significant motivating factor behind the development of the PEDRo repository has been to allow informed discussion, assisted by concrete examples, into the level of detail and forms of model that are most appropriate for a proteome data repository. As the PEDRo model is being used as the starting point for the HUPO-PSI activity on models for proteome data, early validation of this model is important. The following observations have been made about the PEDRo model during the data capture process:Sample description is neither very precise nor systematic. The effective description of samples is an open issue that spans different kinds of functional genomic data. For example, work is underway on the development of an ontology for characterising microarray experiments, focusing, in particular, on samples [1.  samples . HoweverThere is only limited support for relative protein abundance data (e.g. DIGE and stable isotope labelling strategies). Thus, for example, there is no place in the model to describe an expression ratio for a protein species derived from quantitative experimental strategies, only the ability to capture the 'raw' numbers. In fact, the PEDRo model was not designed to capture expression ratios, partly because such numbers are easily derived from the captured primary data, and partly because the particular method of their derivation may be contentious. It is hoped that the HUPO-PSI model will provide generic constructs for representing relationships between certain kinds of measurement (e.g. relative protein expression readings), to which can be attached the specific detail for individual techniques. However, it also seems important to avoid the pitfalls associated with overly permissive models, as these provide a less stable foundation for the developers of analytical tools than their more proscriptive counterparts.2. The gel model is not particularly detailed. Thus, for example, there is no detailed description of the image analysis software used, the descriptions of individual spots are fairly minimal, and no details are captured on spot excision. An earlier critique of the PEDRo model for gels, and some possible extensions, is provided by [3. vided by . It seemOverall, the appropriate level of detail for a proteomics repository is somewhat subjective, but can usefully be based on guiding principles; agreement as to the principles should then avoid scope-based discussions at a very fine-grained level. The current PEDRo model essentially supports the principle that enough detail should be captured about an experiment to:i. Allow results of different experiments to be analysed/compared.ii. Allow suitability of experiment design and implementation decisions to be assessed.iii. Allow protein identifications to be re-run in the future with new databases or software.There is also an additional negative principle, to the effect that the model itself should not be designed to include dependencies on characteristics relating to the configuration or properties of an individual piece of equipment. Accordingly, we have attempted to allow experimental methods and results to be described in significant detail, but without including parameters and properties that are likely to be superseded rapidly when new models of equipment are introduced, and without including parameters that can only be understood with reference to the documentation of a particular product.in silico analysis. Such design decisions are appropriate for certain categories of user of a proteomics database, but not for others. The UAB database has been designed to provide access to processed experimental results for biomedical researchers, but does not provide enough information to allow detailed comparisons of the ways in which the results were obtained.The data stored in PEDRo is more comprehensive for each experiment than is the case for most existing proteome databases. For example, in the longest established experimental proteomics resource, SWISS-2DPAGE , the empThe ProteomeWeb  providesIn terms of quantities of data, there are fewer data sets in PEDRo than in SWISS-2DPAGE, reflecting the fact that PEDRo is a newly created resource (Release 16 of SWISS-2DPAGE contains 34 reference maps), but somewhat more than in the UAB Proteomics Database. The Open Proteomics Database (OPD) supports the browsing and downloading of comparable amounts of data to those in PEDRo, and also includes mass spectrometry data, although quite a lot of the data are in flat-file format . HoweverThe need for wider and more systematic dissemination of experimental proteomics data is widely recognised, as argued in , and atti. The nature and variety of information that should be recorded about proteomics experiments.ii. The functionality that should be provided by repositories that make large-scale proteomic data available.iii. The computational architecture that should be used to provide the functionality at (ii).iv. The nature of the tools that should be developed for use with such a repository.de jure standard for proteome data representation and sharing. This paper describes a database that includes a rich collection of representative data sets. Furthermore, the paper describes the functionality (issue ii) and architecture (issue iii) of an exploratory system for disseminating such data. In the same way as we see models for representing proteomic data evolving in the light of practical experience, we anticipate that the PEDRo repository, and the overall understanding of the data access and dissemination requirements for proteomic data, will evolve as the opportunities presented by high-throughput experimental techniques and comprehensive data sets become more fully understood.This paper has sought to address issues (i), (ii) and (iii), with a particular emphasis on (i). Following on from  we belie, by following the Database link.The database can be accessed using a web browser at KG and CG implemented the software. SJ, NM and CFT contributed to the development of earlier prototypes. TM coordinated the data capture activity. CK, CE, AW, SH, DS, ZY, AJPB, AH, KC, LH, MM, PG, JH, KSL, SJG conducted or led experimental activities that generated the data in the database, and contributed to feedback on the model. AB, SJH, SJO and NWP oversaw the database design and development activity, and the latter led the write-up.


In order to perform a 3D reconstruction of electron microscopic images of viruses, it is necessary to determine the orientation (Euler angels) of the 2D projections of the virus. The projections containing high resolution information are usually very noisy. This paper proposes a new method, based on weighted-projection matching in wavelet space for virus orientation determination. In order to speed the retrieval of the best match between projections from a model and real virus particle, a hierarchical correlation matching method is also proposed.A data set of 600 HSV-1 capsid particle images in different orientations was used to test the proposed method. An initial model of about 40 Å resolutions was used to generate projections of an HSV-1 capsid. Results show that a significant improvement, in terms of accuracy and speed, is obtained for the initial orientation estimates of noisy herpes virus images. For the bacteriophage (P22), the proposed method gave the correct reconstruction compared to the model, while the classical method failed to resolve the correct orientations of the smooth spherical P22 viruses.This paper introduces a new method for orientation determination of low contrast images and highly noisy virus particles. This method is based on weighted projection matching in wavelet space, which increases the accuracy of the orientations. A hierarchical implementation of this method increases the speed of orientation determination. The estimated number of particles needed for a higher resolution reconstruction increased exponentially. For a 6 Å resolution reconstruction of the HSV virus, 50,000 particles are necessary. The results show that the proposed method reduces the amount of data needed in a reconstruction by at least 50 %. This may result in savings 2 to 3 man-years invested in acquiring images from the microscope and data processing. Furthermore, the proposed method is able to determine orientations for some difficult particles like P22 with accuracy and consistency. Recently a low PH sindbis capsid was determined with the proposed method, where other methods based on the common line fail. Three-dimensional (3D) reconstruction of virus particles like SARS (Severe Acute Respiratory Syndrome) and HSV (Herpes Simplex Virus) using electron microscopy yields crucial information for understanding the assembly and infectivity mechanism. The structural determination begins with acquisition of projection images in an electron-microscope. A major part of data processing is aimed at determining the direction of projection for each particle image (2D projection of virus) so that a 3D reconstruction can be computed. The first step in a virus reconstruction is the detection and selection of the individual particle images from a large area of an electron micrograph.There are different criteria to determine the particle orientation. One criterion is based on the computational search of the common lines in the computed Fourier Transforms of individual or multiple particle images . An imprOne approach is to take two consecutive pictures of the same particles one close-to-focus Fig.  and anotA data set of 600 HSV-1 capsid particle images in different orientations was used to test the HWPM method. The defocus range of herpes particles was chosen to be close to focus between 1.7 μm and 0.4 μm. An initial model of about a 40 Å resolution . A grid A match of the particle into the best 3 of the 200 classes was obtained using the wavelet correlation coefficient (wccf) criterion. Next, the particle was compared to the 39 projections of the best three classes, and the correct orientation was that of the projection giving the highest wccf. The hierarchical implementation wavelet projection matching reduced the time at least by a factor of 10 compared with the classical projection matching method. In the example of 600 particles, by using HWPM it took approximately 3 hours to determine the orientations, instead the 33 hours it took with the classical matching algorithm. Both algorithms were running on the SGI Origin-2000 supercomputer using 10 processors.At this point, each particle had been assigned the orientation of the closest projection. A quality factor was assigned to each orientation, which was the wavelet correlation coefficient. Particles having high wccf coefficients were selected for reconstruction of a first 3D model of the virus.Refinement of initial orientations obtained by HWPM was realized by the same iterative refinement process used in focal pair method . This reIn order to assess the accuracy of the orientations obtained with the HWPM. A comparison with the focal pair method Fig. , which iFig. HWPM was tested on a P22 empty shell capsid which was circular and whose shell is very thin (~40 Angstrom). Twenty micrographs of the P22 empty shell capsid with defocus range [0.5 to 2 μm] were used for testing purpose. The total number of particles is 1340, each image has a size of 300 × 300 pixels, and the dimension of each pixel is 2.8 Å.Concerning the initial orientations determinations using HWPM method, an initial model of around 20 Å resolutions was used to generate projections which uniformly covered the asymmetric triangle of the icosahedrally symmetric model. A grid sampling of 2° in each direction of the asymmetric triangle of icosahedral symmetry was used to obtain an initial orientation, targeting a structure of 30 Å. The number of projections obtained with this grid was about 200 projections. A match of the particle with the projections was obtained by using the wccf criterion. The correct orientation was selected as the one of the projection giving the highest wccf. The better half of the orientations projections (650) according to wccf criterion was chosen for final reconstruction.The initial orientations for the same set of data were determined using the Improved Common Line (ICL) method, with the same input parameters for the software described in . ICL useFig. During the last thirty years the common lines methods were a great method to resolve icoshedral particles up to 7–8 Å . RecentlAt high resolution reconstructions, the number of particles needed increases drastically, and the data with a signal-to-noise ratio valid up to the targeted resolution, tend to be very noisy. For an 8.5 Å structure of HSV-1 it took about 6000 particles for a final reconstruction. For a 6.5 Å structure resolution, the estimated value was about 50,000 particles using the same electron microscope .To further increase the resolution of the HSV virus to 6.5 Å or higher (4 Å), the focal pair method would be impracticable. The focal pair method, for intermediate resolution up to (8 Å) for big viruses like HSV, works well for orientations determinations. The number of particles selected for the final reconstruction about 40% of the original number of particles (taking into account the far-focus and close-focus micrographs). It is necessary to emphasize that results from both methods are very similar in terms of visual resemblance. But, there are two advantages of HWPM over the focal pair method. First, focal pair method uses as much as double the data used for the HWPM. Second, the quality of the density maps shows that HWPM gives a better resolution for the same number of particles ; second most of the data are very close-to-focus with defocus range of 0.5 μm to 1.3 μm. The data was noisy and had a very low contrast. The ICL method was able to give 40% of good orientations for the defocus range between 1.9 and 1.2 μm, here the data was closer to focus, which reduced the percentage of good orientations to less then 22%.The application of the HWPM to the P22 empty shell capsid gave the expected structure Fig. . The wavAnother example of real data reconstruction is the VP5-VP19C recombinant. After long investigation using CL and ICL algorithms, the classical projection matching scheme was also tested in order to determine the orientations, but unfortunately all those methods failed. The wavelet filtering and matching was used during the classification step of the recombinant particle VP5-VP19C ,16, whicThe third examples for low PH sindbis: Three years of investigation using CL and ICL methods failed to obtain the correct density map of the low PH sindbis capsid which is subject to conformational changes and an alteration of the symmetry. Recently the proposed method (HWPM) was tested on low PH sindbis and the correct structure was finally observed and analyzed .Wavelet multi-resolution analysis and processing improves particle detections , classifThis paper describes the development and implementation of a new method for orientation determination for low contrast images of virus particles. This method is based on wavelet filtering, which enhances the contrast of the particles and reduces the noise, and on weighted projection matching in wavelet space. A hierarchical implementation of this method increases the speed of orientation determination. Results show that, HWPM have been able to determine accurately more than 85% of the orientations of low-contrast particles. Compared to the focal pair method (for orientation determination from low contrast data) the HWPM reduced the amount of data required in a reconstruction by at least 50 %. In addition the accuracy of the orientations obtained by the proposed method is higher than those obtained by focal pair method . This imThe choice of wavelet filter bases depends on the signal. Signals coming from different sources have different characteristics. For audio, speech, image and video signals the best choices of wavelet bases are known. The best choice for electron microscopic images is not clear. The problem is to represent typical signals with a small number of convenient computable functions.-1) relevant to data analysis.An investigation to choose the best wavelet bases for electron microscopic images was performed here. During this study, simulated and real electron microscopy images were used. The majority of the wavelets basis existing in Matlab-5 software -24 was tThe principle of the wavelet decomposition is to transform the original raw particle image into several components: one low-resolution component called "approximation" , which iThe approximation component is obtained after applying a bi-orthogonal low-pass wavelet filter in each direction  followed by a sub-sampling of each image by a factor of 2 for each dimension. The details are obtained with the application of a low-pass filter in one direction and a high-pass filter in the other, or a high-pass filter in both directions. The noise is mainly present in the detail components. A higher level of decomposition is obtained by repeating the same filtering operations on the approximation. The wavelet correlation coefficient between two wavelet-transformed images, for a given level, is :1 to Wp are weights given for each components of the wavelet correlation, p is the number of components of wavelet decomposition. A1, A2 are the approximations. ⊗ denote the correlation between two components images. D1i, D2i are the details (Fig. Where WInitial orientation determination is based on model-based projection matching approach . The levThe choice of the number of classes is optimized to give the best tradeoff between speed and accuracy. The classification gives a uniform distribution of projections into the classes. The next step is to compare each wavelet-transformed raw image with the closest projection to the center of each class, and then rank the classes in terms of wccf Fig. . The fin


Biomechatronics is the integration of biological components with artificial devices, in which the biological component confers a significant functional capability to the system, and the artificial component provides specific cellular and tissue interfaces that promote the maintenance and functional adaptation of the biological component. Based upon functional performance, muscle is potentially an excellent mechanical actuator, but the larger challenge of developing muscle-actuated, biomechatronic devices poses many scientific and engineering challenges. As a demonstratory proof of concept, we designed, built, and characterized a swimming robot actuated by two explanted frog semitendinosus muscles and controlled by an embedded microcontroller. Using open loop stimulation protocols, the robot performed basic swimming maneuvers such as starting, stopping, turning (turning radius ~400 mm) and straight-line swimming (max speed >1/3 body lengths/second). A broad spectrum antibiotic/antimycotic ringer solution surrounded the muscle actuators for long term maintenance, ex vivo. The robot swam for a total of 4 hours over a 42 hour lifespan (10% duty cycle) before its velocity degraded below 75% of its maximum. The development of functional biomechatronic prototypes with integrated musculoskeletal tissues is the first critical step toward the long term objective of controllable, adaptive and robust biomechatronic robots and prostheses. Many technological barriers exist for the implementation of life-like mobility in robotic and prosthetic systems. Included among these barriers are (1) the availability of high-energy density storage media, (2) the availability of adequate muscle-like actuators, and (3) the availability of biologically inspired sensory technologies. As a possible resolution to these challenges, we consider in this investigation the use of living muscle tissue as a viable actuator for synthetic devices.Although important research has been conducted to advance a synthetic actuator technology with muscle-like properties, engineering science has not yet produced a motor system that can mimic the contractility, energetics, scalability and plasticity of living muscle tissue ,2. Musclanimal-derived muscle as an actuator for artificial devices in the millimeter to centimeter size scale. Perhaps researchers in the past did not consider muscle tissue a viable mechanical actuator because of tissue maintenance and control difficulties. The objectives of this study are to identify, and to begin to address, the many technical challenges related to maintaining and controlling explanted muscle tissues in the context of a robotic platform. To this end, we construct a hybrid swimming robot comprising a synthetic elastomeric tail actuated by a single pair of whole muscle explants from frog semitendinosus muscle. We anticipate that basic swimming maneuvers such as straight-line swimming and turning can be performed by alternately modulating electrical signals to each muscle actuator across two electrode pairs, one on each muscle near the neuromotor junction. We further anticipate that a multi-day robotic maintenance or lifespan can be achieved by surrounding the muscle actuators with a specific bath of amphibian ringer's solution comprising antibiotic and antimycotic agents. To test these ideas, we construct two robotic build-ups, each comprising a freshly dissected pair of explanted semitendinosus muscles. For each build-up, pilot data are collected to characterize the robot's swimming mechanics and lifespan.In this investigation, we examine the feasibility of using Rana pipiens) were pithed, and both semitendinosus muscles were dissected free and removed with tendons intact. Before removal of the tissues from the animal, the length of each muscle belly was measured at an equilibrium or rest length. The resting length measurement was conducted on the intact muscle specimen with the limb positioned at an anatomically neutral position . Briefly, adult frogs ; MEM Vitamin Mixture, 1:100 dilution (GIBCO # 1120052); Creatine, 1 mM; DL-Carnitine, 1 mM; Ferric Chloride, 0.9 μM; Human Serum Transferrin, 1.35 μM; Insulin, 1 mU/ml; L-Glutamine, 1:100 dilution; Sigma Chemical #A9909, 1:50 dilution (an antibiotic/antimycotic). A broad-spectrum, antibiotic/antimycotic was added out of necessity for long-term maintenance of the muscles, ex vivo. We observed, for periods greater than 24 hours, septic degradation of the muscle specimens in the absence of the antibiotic/antimycotic agents. After each muscle was placed within a Petri dish, a small volume of ringer solution was used to surround each muscle, the balance being used in the test tank for the swimming robot evaluations. The total amount of time between muscle removal from the animal to finalizing the muscle installation into the robotic swimmer was approximately 1 hour.Shortly before harvesting the muscles, two fresh liters of amphibian ringer solution were prepared according to a protocol specifically designed for frog organ culture ,15. The The test tank was constructed from 6 mm (1/4") thick cast acrylic sheet, welded together with methylene chloride, with silicone fish tank adhesive being applied to form a water-tight seal at each joint. The test tank was 30 cm square and 6 cm deep.The robotic platform Figure  was specThe single part silicone RTV (Dow Corning type 734 flowable silicone) tails were cast using a 5-part virgin Teflon mold machined to form a single solid tail assembly with all of the features shown in Figure The onboard electronics were based upon a previously published design for an implantable muscle stimulator , and thuStimulation was controlled remotely via a unidirectional infra red (IR) link from a hand-held command module. The on-board fixed stimulation parameters were: amplitude = 5.8 V  , frequenThe electrodes were fashioned from medical grade TFE coated 40 AWG stainless steel multi-strand electrode wire (Cooner Wire). The distal ends were stripped to allow the electrode wire to be wrapped around each muscle, as described previously . The finDuring robotic swimming operations, the fuel sources were a glucose-bearing ringer solution (~2 g/L glucose), and lithium batteries to power the embedded microcontroller and stimulator system. Due to the micro-power electronic design, the estimated battery life for the system was ~21 days (assuming a 10% stimulation duty cycle) ,17.The semitendinosus muscle was selected primarily due to its convenient size and tendon anatomy. It is easily dissected with both proximal and distal tendons attached. The proximal tendons of each semitendinosus muscle were sutured to the rigid Delrin head piece, and the distal tendons were sutured to the lateral mounting flange on each side of the tail base using 5-0 braided silk suture Figure . The musTwo robotic platforms were evaluated in terms of muscle actuator performance, swimming efficiency and locomotory maneuverability. Each robotic platform was designated "B1x", where "x" indicated the build-up, serialized as "a, b, c, ..." for each subsequent pair of explanted frog muscles. Two build-ups were constructed, B1a and B1b, each with a separate pair of freshly explanted frog semitendinosus muscles.Muscle Removal and Maintenance) were poured into the test tank, providing a fluid depth of approximately 2.1 cm, enough for the robot to swim without touching the bottom of the tank. The tank temperature was measured but not controlled, and was allowed to stabilize at room temperature, approximately 22°C for the duration of each experiment. The ringer solution was aerated with unfiltered room air using 4 standard porous stone fish tank aerators, one placed at each corner of the tank, and connected to an aquarium aeration pump via silicone tubing. Aeration was discontinued briefly before each test run to minimize turbulence in the test tank. For each robotic build-up, or for each pair of explanted semitendinosus muscles, the test tank ringer solution was not replaced or replenished for the entirety of the robotic experimental session.Prior to swimming evaluations, two liters of ringer solution . After installation was complete, the muscles were allowed to acclimate for a period of approximately 5 minutes before stimulation. The robot was manually placed to allow forward motion through the bath, and muscle stimulus parameters, specifically stimulus train duration and dwell time, were varied manually until the maximum swimming velocity was achieved. To increase swimming speed, dwell period was decreased and train duration was increased until further decreases in dwell time or further increases in train duration did not result in additional increases in forward swimming speed. During experimentation, swimming speed was determined by measuring the amount of time required for the robot to swim across a known, fixed distance. Once the maximum swimming speed was achieved, the ventral view of the swimming robot was filmed , and the film was then digitized to determine tail-beat frequency, tail amplitude, and the wave speed and wave length of the propulsive body wave. In addition to forward straight-line swimming, muscle stimulus parameters were varied to investigate turning maneuvers. At a maximum forward swimming speed, the robot's open loop, alternating stimulation pattern between the antagonistic actuators was switched to a continuous one-sided muscle activation for steering control, causing the robot to turn in the direction of the single stimulated muscle . Here again, the ventral view of the swimming robot was filmed, and the film was then digitized to determine the maximum turning radius.For each tail-beat period, at least 10 video frames were captured, separated in time by 33 ms, depending on the swimming speed of the robot. A customized software program was used to digitize 10 points on each side of the outline of the ventral silhouette of the robot, for a total of 20 points for each image. A series of cubic spline functions were used to draw the best-fit line along these points ,19, and To estimate the overall mechanical swimming efficiency of each robotic build-up, we calculated the robot's slip value, a dimensionless velocity . A high Muscle Removal and Maintenance). Still further, to estimate muscle-shortening velocity at the maximum swimming speed, the measured linear-distance change between muscle attachment points was divided by the time required for the tail to re-position from a neutral, straight position to the tail amplitude posture measured during straight-line swimming. This time period was measured from the digitized films and was equal to approximately one quarter of a tail-beat period.To estimate muscle actuator performance at the maximum swimming speed, muscle strain and shortening velocity were estimated using the tail-beat frequency and amplitude measurements taken from the digitized films. After the swimming experiments were finalized, the change in linear distance between the robot's muscle attachment points was measured when the robot's tail was re-positioned from a neutral, straight position to the tail amplitude posture measured during straight-line swimming. As an estimate of peak muscle shortening strain, this linear-distance change was then divided by the muscle's resting length, or the muscle belly length when the tail was held straight  and isotonic contraction experiments  were conFor the B1a and B1b robotic swimmers, the locomotory performance parameters at maximum swimming velocity are summarized in Table Each robotic build-up was capable of the following controlled maneuvers: forward accelerations, decelerations, steady state gliding, and turning to the right or left. The robot was capable of surface swimming only, so all maneuvers were restricted to 2-dimensions. Turning was accomplished after forward momentum had been established by continuously activating only one actuator. The minimum gliding turn radius was 400 mm as estimated from the digitized video images of the robot's midpoint trajectory.After swimming the full length of the test tank, the robot was manually repositioned to the opposite end of the tank where it began, once again, to swim across the tank width. Typically, a period of swimming activity (~3 min) was followed by a period of swimming inactivity (~30 min). Due to muscle fatigue, periods of inactivity were required to restore the robot's peak swimming velocity to at least 75% of its maximum value measured during the first session of robotic swimming (first 10 minutes of the robot's lifespan). Robot B1a swam for a sum total of 45 minutes over a 7.5 hour lifespan (10% duty cycle), after which its swimming velocity degraded below 75% of its maximum value even after a 30 minute period of swimming inactivity. In distinction, robot B1b swam for a much longer period – a sum total of 4 hours over a 42 hour lifespan (10% duty cycle) before its velocity degraded below 75% of its maximum value following a 30 minute period of swimming inactivity.To compare the overall swimming efficiency of each robotic build-up, we calculated the propeller efficiency using the measure of slip (swimming velocity/ propulsive wave speed) Table . In a stmax, of 78 ± 3 mm s-1  in isotonic contractions. At the maximum swimming speed, the muscle actuators within robots B1a and B1b experienced a shortening velocity of 25 mm s-1  produced a maximum shortening velocity, Vanimal-derived muscle as an actuator for artificial devices. We construct a simple robotic platform powered by explanted living amphibian muscle and controlled by an embedded microcontroller via an infra red data link. Using an open loop control and a simple interface design, we present preliminary data that suggests that living muscle might one day be employed as a practical, controllable actuator. Hybrid robot B1b remained active for up to 42 hours, and during that time, performed basic swimming maneuvers such as starting, stopping, turning and straight-line swimming at speeds exceeding 1/3 body lengths per second. The muscle-actuated swimming robot also offered a reasonable swimming efficiency, as indicated by a slip value of 0.32 , both for controllability and for tissue phenotype maintenance.The frog semitendinosus muscles employed in the robot were comprised predominantly of fast-twitch muscle fibers, and therefore provided higher mechanical power, at the expense of being considerably more fatigable, than would have been achievable using a slow-twitch muscle of comparable size. Ideally, a biomechatronic swimming robot would incorporate several muscle fiber types to permit both explosive as well as low-power locomotion and maneuvering. For the robotic platform of this investigation, it is important to note that the stimulation was non-physiologic in many ways. Each muscle was stimulated in bulk, with all fibers being subjected to approximately the same electric field. In living muscle in vivo, individual motor axons innervate one or more muscle fibers, establishing the fundamental neuromotor functional unit: a in vitro generally fall into one of the following categories: (1) core necrosis due to lack of oxygenation/capillary perfusion and large diffusion distances, (2) sepsis, (3) exogenous toxicity, (4) electro-chemical damage resulting from excessive electrical stimulation, (5) accumulated contraction-induced injury, (6) sarcomeres heterogeneity leading to loss of thick and thin filament overlap in regions of muscle fibers , and (7) direct mechanical damage to the muscle from external sources, such as the robot frame, attachment hardware, or electrodes.In this study, the performance of the muscle actuators eventually degraded to the point where they were no longer effective mechanical actuators. Several factors contributed to the observed tissue degradation. To begin with, explanted muscle generally has a very finite functional life expectancy ,15, usuaex vivo tissue maintenance are necessary. These include loss of muscle excitability and mass, phenotypic drift, and de-differentiation of the muscle from desired adult muscle phenotypes.For the tissue-actuated device of this investigation, several design considerations were made to minimize many of these failure modes. The bath was aerated to assist oxygen delivery to the tissues, although this strategy would only be helpful to the outer shell of muscle fibers no greater than ~200 μm from the surface. In addition, the level of muscle cell depolarization was kept to a minimum in order to limit electro-chemical damage . Still fEven though organogenic mechanisms are poorly understood, it is nonetheless possible to engineer functional muscle organs from individual cells in culture -26, but The results of this investigation, although preliminary, suggest that some degree of ex vivo robustness and longevity is possible for natural muscle actuators if adequate chemical and electromechanical interventions are supplied from a host robotic environment. Clearly, an important area of future research will be to establish processes by which optimal intervention strategies are defined for a given hybrid-machine task objective. Another important area of research will be tissue control. It has been established that natural muscle changes in size and strength depending on environmental work-load, and when supplied with appropriate signals, changes frequency characteristic or fiber type -11. HencIn this paper, we ask whether muscle tissue explants can be employed as mechanical actuators for robots in the millimeter to centimeter size scale. Using a very simple control and interface design, we present preliminary data that suggests that living muscle might one day be employed as a practical, controllable actuator. The robot of this investigation remained active for up to 42 hours, and during that time, performed basic swimming maneuvers such as starting, stopping, turning and straight-line swimming at speeds exceeding 1/3 body lengths per second. It is our hope that this work will lead to further studies of tissue actuated robots and prostheses that will result in an even wider range of biomechatronic machine capabilities.


Another study casts doubt on the value of early treatment and treatment interruptions. What are the implications of this study for our understanding of HIV pathogenesis, treatment, and vaccine development? The devastating effects of HIV infection worldwide are reason enough for AIDS researchers to grasp at thin rays of hope. But seldom has a single anecdotal case stimulated as much hope as the 1999 report of an acutely infected patient who appeared to control HIV replication after two short treatment interruptions [Consistent with this hypothesis was the prior finding that early antiretroviral therapy led to induction of HIV-specific proliferative responses similar to those that had been observed in patients with long-term, non-progressing HIV . This leA series of discoveries from clinical trials began to chip away at the enthusiasm for both early treatment of HIV infection and supervised treatment interruptions (STIs) as a way to boost the immune response.Several small trials of STIs in chronically infected patients were carried out , buoyed Larger trials clearly showed that STIs were of little if any benefit in chronic infection and that when therapy was stopped, viral loads invariably returned to pre-treatment levels . Other sPLoS Medicine that found that in 14 patients who were treated early and who had controlled viral loads for at least 90 days, the virologic control was only transient [Now comes a study in this month's ransient . While oThere was a disconnect between the low viral loads and an unexpectedly high rate of CD4+ T cell decline in several patients. While the small number of patients and the single-arm nature of the study preclude definitive comparisons, it is possible that the early treatment and STIs did not result in a delay in CD4+ T cell decline  beyond what would have occurred had the patients received no early treatment.This study raises important questions in our understanding of HIV pathogenesis, treatment, and vaccine development.First, why is it that early antiretroviral treatment, even if it does lead to better control of viral replication, does not protect against CD4+ T cell depletion? It is possible that by the time patients present with acute retroviral syndrome their CD4+ T cell reserves (in gut and lymphoid tissues) have been severely depleted, despite the fairly normal CD4+ profile of their peripheral blood. Thus, even low-level viral replication is then sufficient to deplete the remaining central and peripheral reserves .Second, how do these findings affect treatment guidelines during acute infection? None of the current treatment guidelines in either resource-rich or resource-poor settings recommend early antiretroviral therapy. In the light of these new data , there dbefore any HIV replication (a prophylactic vaccine) might be better able to control virus replication. Far be it for us to stop grasping at rays of hope.Finally, is this good or bad news for HIV vaccine development? Since most current vaccine strategies are based upon the hypothesis that induction of T cell immunity will lead to control of viral replication, it is difficult to be optimistic when a strong and broad immune response is unable to prevent disease progression. However, one must recall that phenotypic and functional assessments of HIV-specific T cell responses, even in antiretroviral-treated patients, show that these responses clearly differ from responses against viruses that are normally cleared or controlled by the immune system . Therefo


As human beings, aging and death are an inevitable part of our lives. As we pass through each decade, the concrete signs of aging—greying hair, aches and pains, the gradual failure of one organ system after another—and the realization that we are mortal increasingly occupies our thoughts.Saccharomyces cerevisiae (baker's yeast), for example, the function of individual cells gradually declines with time, and each yeast cell has a finite life span. In organisms like this, it has been proposed that reproduction by asymmetric division is a prerequisite for aging. In other words, for a unicellular organism to age, when it divides, it must give rise to a “parent” cell and a smaller offspring cell (as in yeast), which then has to go through a juvenile phase of growth or differentiation before it divides. At each cell division, the parent cell becomes older until it reaches its natural life span and dies.All other multicellular animals and plants also show clear signs of aging, as do some single-celled organisms. In the yeast Escherichia coli, a bacteria that reproduces without a juvenile phase and with an apparently symmetric division.But what about organisms that produce two apparently identical cells when they divide? Do such organisms age? The assumption has been for some years that cells that divide symmetrically do not age and are functionally immortal. Eric Stewart and colleagues have now tested this idea by analyzing repeated cycles of reproduction in E. coli is a rod-shaped organism that reproduces by dividing in the middle. Each resultant cell inherits an old end or pole and a new pole, which is made during the division. The new and the old pole contain slightly different components, so although they look the same, they are physiologically asymmetrical. At the next division, one cell inherits the old pole again (plus a brand new pole), while the other cell inherits, a not-quite-so-old pole and a new pole. Thus, Stewart and co-workers reasoned, an age in divisions can be assigned to each pole and hence to each cell.E. coli cell. In all, the researchers built up a lineage for 35,049 cells in terms of which pole—old or new—each cell had inherited at each division during its history. They found that the cells inheriting old poles had a reduced growth rate, decreased rate of offspring formation, and increased risk of dying compared with the cells inheriting new poles. Thus, although the cells produced when E. coli divide look identical, they are functionally asymmetric, and the “old pole” cell is effectively an aging parent repeatedly producing rejuvenated offspring.The researchers used automated time-lapse microscopy to follow all the cell divisions in 94 colonies, each grown from a single fluorescently labeled E. coli should now provide an excellent genetic platform for the study of the fundamental mechanisms of cellular aging and so could provide information that might ameliorate some of the unpleasantness of the human aging process.Stewart and his colleagues conclude that no life strategy is immune to the effects of aging and suggest that this may be because immortality is too costly or is mechanistically impossible. This may be bad news for people who had hoped that advances in science might eventually lead to human immortality. Nevertheless,


Fatigue is a crucial sensation that triggers rest, yet its underlying neuronal mechanisms remain unclear. Intense long-term fatigue is a symptom of chronic fatigue syndrome, which is used as a model to study the mechanisms underlying fatigue.Using magnetic resonance imaging, we conducted voxel-based morphometry of 16 patients and 49 age-matched healthy control subjects.We found that patients with chronic fatigue syndrome had reduced gray-matter volume in the bilateral prefrontal cortex. Within these areas, the volume reduction in the right prefrontal cortex paralleled the severity of the fatigue of the subjects.These results are consistent with previous reports of an abnormal distribution of acetyl-L-carnitine uptake, which is one of the biochemical markers of chronic fatigue syndrome, in the prefrontal cortex. Thus, the prefrontal cortex might be an important element of the neural system that regulates sensations of fatigue. Chronic fatigue is common and is reported in more than 20% of people seen in primary care . HoweverCFS is a clinically defined condition characterized by severe disabling fatigue and a combination of symptoms, the prominent features being self-reported impairments in concentration and short-term memory, sleep disturbances and musculoskeletal pain . The diaSixteen CFS patients  and 49 age-matched healthy control subjects  were enrolled in the study. They were recruited from the outpatient fatigue clinic in Osaka University Hospital  where more than 430 CFS patients, who met the diagnostic criteria of CFS [Voxel-based morphometry (VBM)  was perf2 = 0.46, P = 0.004; Figure We observed a significant reduction in gray-matter volume in the bilateral prefrontal areas of CSF patients Figure . The affThe present study provides the first report of focal gray-matter atrophy in the prefrontal cortex of CFS patients. Previous MRI studies of CFS revealed non-specific abnormalities: hyperintense small punctuated subcortical white-matter foci were observed predominantly in the frontal lobes  and theiPrefrontal pathology has been reported in MS with pathological fatigue . RoelckeIn the present study, right dorsolateral prefrontal-cortex atrophy was significantly correlated with the severity of fatigue, as measured by the performance-status scores. As the performance status rates the daily activities that trigger or aggravate fatigue, this correlated volume reduction might reflect a functional deficiency that makes patients susceptible to fatigue.A single site in the dorsolateral prefrontal cortex revealed the parallel between volume reduction and fatigue severity. This does not necessarily mean that it is fatigue-specific; instead, this area might be the part of the network that, when functioning sub-normally, results in pathological fatigue. Fatigue is also a symptom of diseases that affect the basal ganglia, and that interrupt the connection between the prefrontal cortex and thalamus . Hence, The dorsolateral prefrontal cortex has dense widespread subcortical and cortical connections . A serieThe dorsolateral prefrontal cortex also has widespread reciprocal corticocortical connections with posterior temporal, parietal and occipital association areas . FurtherThese anatomical and functional characteristics of the frontal-subcortical circuits suggest that the large decrease in acetyl-L-carnitine uptake in the dorsolateral prefrontal, anterior cingulate and temporal cortices  represenThe results of the present study suggest that the dorsolateral prefrontal cortex might be an important component of the neural substrates that regulate the sensation of fatigue.BA, Brodmann's area; CMRGlu, cerebral metabolic rate of glucose; CFS, chronic fatigue syndrome; MRI, magnetic resonance imaging; VBM, voxel-based morphometryThe author(s) declare that they have no competing interests.TO carried out the MRI scanning, data analysis and drafted the manuscript. MT conducted MRI scanning and participants' coordination. HK conducted the medical evaluation of the participants. YW and NS participated in the study design. All authors read and approved the final manuscript.The pre-publication history for this paper can be accessed here: