Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken; Kyrpides, Nikos C.
A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.
M.C. Traub (Myriam); J.R. van Ossenbruggen (Jacco); J. He (Jiyin); L. Hardman (Lynda); M. de Rijke (Maarten); T Kentner; A.P. de Vries (Arjen); F.M.G. de Jong (Franciska); C. Zhai (ChengXiang ); K. Hofmann (Katja); K. Radinsky
htmlabstractTasks that require users to have expert knowledge are diffi- cult to crowdsource. They are mostly too complex to be carried out by non-experts and the available experts in the crowd are difficult to target. Adapting an expert task into a non-expert user task, thereby enabling the
Full Text Available Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.
Full Text Available It is a challenging problem to efficiently interpret the large volumes of remotely sensed image data being collected in the current age of remote sensing “big data”. Although human visual interpretation can yield accurate annotation of remote sensing images, it demands considerable expert knowledge and is always time-consuming, which strongly hinders its efficiency. Alternatively, intelligent approaches (e.g., supervised classification and unsupervised clustering can speed up the annotation process through the application of advanced image analysis and data mining technologies. However, high-quality expert-annotated samples are still a prerequisite for intelligent approaches to achieve accurate results. Thus, how to efficiently annotate remote sensing images with little expert knowledge is an important and inevitable problem. To address this issue, this paper introduces a novel active clustering method for the annotation of high-resolution remote sensing images. More precisely, given a set of remote sensing images, we first build a graph based on these images and then gradually optimize the structure of the graph using a cut-collect process, which relies on a graph-based spectral clustering algorithm and pairwise constraints that are incrementally added via active learning. The pairwise constraints are simply similarity/dissimilarity relationships between the most uncertain pairwise nodes on the graph, which can be easily determined by non-expert human oracles. Furthermore, we also propose a strategy to adaptively update the number of classes in the clustering algorithm. In contrast with existing methods, our approach can achieve high accuracy in the task of remote sensing image annotation with relatively little expert knowledge, thereby greatly lightening the workload burden and reducing the requirements regarding expert knowledge. Experiments on several datasets of remote sensing images show that our algorithm achieves state
Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias
An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147
Ames, L.L.; Rai, D.; Serne, R.J.
The annotated bibliography is divided into sections on chemistry and geochemistry, migration and accumulation, cultural distributions, natural distributions, and bibliographies and annual reviews. (LK)
Irshad, H; Montaser-Kouhsari, L; Waltz, G; Bucur, O; Nowak, J A; Dong, F; Knoblauch, N W; Beck, A H
The development of tools in computational pathology to assist physicians and biomedical scientists in the diagnosis of disease requires access to high-quality annotated images for algorithm learning and evaluation. Generating high-quality expert-derived annotations is time-consuming and expensive. We explore the use of crowdsourcing for rapidly obtaining annotations for two core tasks in com- putational pathology: nucleus detection and nucleus segmentation. We designed and implemented crowdsourcing experiments using the CrowdFlower platform, which provides access to a large set of labor channel partners that accesses and manages millions of contributors worldwide. We obtained annotations from four types of annotators and compared concordance across these groups. We obtained: crowdsourced annotations for nucleus detection and segmentation on a total of 810 images; annotations using automated methods on 810 images; annotations from research fellows for detection and segmentation on 477 and 455 images, respectively; and expert pathologist-derived annotations for detection and segmentation on 80 and 63 images, respectively. For the crowdsourced annotations, we evaluated performance across a range of contributor skill levels (1, 2, or 3). The crowdsourced annotations (4,860 images in total) were completed in only a fraction of the time and cost required for obtaining annotations using traditional methods. For the nucleus detection task, the research fellow-derived annotations showed the strongest concordance with the expert pathologist- derived annotations (F-M =93.68%), followed by the crowd-sourced contributor levels 1,2, and 3 and the automated method, which showed relatively similar performance (F-M = 87.84%, 88.49%, 87.26%, and 86.99%, respectively). For the nucleus segmentation task, the crowdsourced contributor level 3-derived annotations, research fellow-derived annotations, and automated method showed the strongest concordance with the expert pathologist
From reading texts to annotating web pages, grade 6-8 students rely on group cooperation and individual reading and writing skills in this research project that spans six 50-minute lessons. Student objectives for this project are that they will: read, discuss, and keep a journal on a book in literature circles; understand the elements of and…
Students have social and personal needs to fulfill and communicate these needs in different ways. This annotated bibliographic review examined communication studies to provide educators of diverse classrooms with ideas to build an environment that contributes to student well-being. Participants in the studies ranged in age, ability, and cultural…
Kiselev, N. N.; Kiseleva, E. V.
An analysis of pedagogical expert reviews at children's therapeutic recreation camps in Novosibirsk Region shows that it is necessary to implement an expert review system that plays a supporting and developmental role. Such a system should allow teams of teachers to submit their work to expert review and to move forward by reflecting on their…
Full Text Available Background. The Latin American region is undergoing a demographic and epidemiological transition, which is leading to an increase in chronic and degenerative diseases. Osteoporosis (OP and fragility fractures (FF are emerging as main causes of disease burden with great impact on health institutions. Purpose. This review article provides an updated overview of trends in the epidemiology and economic impact of OP and FF, as well as in diagnosis and available treatments in Latin America, including calcium, vitamin D and prevention programs. Methods. Expert panel. Conclusions. According to this review, there is a lack of epidemiological and economic information in the region. It is desirable to obtain information regarding quality of life in OP and FF as well as to highlight prevention as a tool to reduce FF.
Hwang, Wu-Yuin; Chen, Nian-Shing; Shadiev, Rustam; Li, Jin-Sing
Previous studies have demonstrated that making annotations can be a meaningful and useful learning method that promote metacognition and enhance learning achievement. A web-based annotation system, Virtual Pen (VPEN), which provides for the creation and review of annotations and homework solutions, has been developed to foster learning process…
Full text: Senior nuclear experts today offered several recommendations on how the International Atomic Energy Agency (IAEA) can further develop its operational safety review services. The IAEA hosted a technical meeting on the Evaluation of Effectiveness of Operational Safety Review Services and their Future Evolution at the Agency's headquarters in Vienna from 1 to 4 November 2011. Representatives from nuclear regulatory bodies, nuclear utilities, nuclear power plants and technical support organisations from 19 IAEA Member States and the World Association of Nuclear Operators (WANO) took part in the meeting. It provided a platform for the exchange of information, experience and lessons learned from the operational safety review missions performed during 2008-2011. The meeting also included discussion of expectations for the future evolution of these services. ''This week's meeting demonstrated the response of the IAEA's Member States to the lessons learned from the Fukushima accident. Nations must constantly strive to improve their nuclear safety practices, and the IAEA review services provide an excellent tool to assess their progress,'' said Miroslav Lipar, head of the IAEA's Operational Safety Section. The IAEA's operational safety review services assess the operational safety performance of nuclear power plants by conducting peer reviews using the requirements of IAEA Safety Standards. The longest running safety review service, the Operational Safety Review Team (OSART) programme, was established in 1982 and has provided advice and assistance to Member States in 165 missions to enhance the safety of nuclear power plants during commissioning and operation. Other review services available in the area of operations evaluate operating experience feedback, safe long-term operation and safety culture. The IAEA Action Plan on Nuclear Safety includes actions focused towards strengthening the existing IAEA peer reviews by incorporating lessons learned and improving
Zheng, Jiaping; Yu, Hong
Background Many health organizations allow patients to access their own electronic health record (EHR) notes through online patient portals as a way to enhance patient-centered care. However, EHR notes are typically long and contain abundant medical jargon that can be difficult for patients to understand. In addition, many medical terms in patients’ notes are not directly related to their health care needs. One way to help patients better comprehend their own notes is to reduce information overload and help them focus on medical terms that matter most to them. Interventions can then be developed by giving them targeted education to improve their EHR comprehension and the quality of care. Objective We aimed to develop a supervised natural language processing (NLP) system called Finding impOrtant medical Concepts most Useful to patientS (FOCUS) that automatically identifies and ranks medical terms in EHR notes based on their importance to the patients. Methods First, we built an expert-annotated corpus. For each EHR note, 2 physicians independently identified medical terms important to the patient. Using the physicians’ agreement as the gold standard, we developed and evaluated FOCUS. FOCUS first identifies candidate terms from each EHR note using MetaMap and then ranks the terms using a support vector machine-based learn-to-rank algorithm. We explored rich learning features, including distributed word representation, Unified Medical Language System semantic type, topic features, and features derived from consumer health vocabulary. We compared FOCUS with 2 strong baseline NLP systems. Results Physicians annotated 90 EHR notes and identified a mean of 9 (SD 5) important terms per note. The Cohen’s kappa annotation agreement was .51. The 10-fold cross-validation results show that FOCUS achieved an area under the receiver operating characteristic curve (AUC-ROC) of 0.940 for ranking candidate terms from EHR notes to identify important terms. When including term
Williamson, Joyce E.; Haj, Adel E.; Stamm, John F.; Valder, Joshua F.; Prautzch, Vicki L.
The U.S. Geological Survey has evaluated and adopted various field methods for collecting real-time sediment and nutrient data. These methods have proven to be valuable representations of sediment and nutrient concentrations and loads but are not able to accurately identify specific source areas. Recently, more advanced data collection and analysis techniques have been evaluated that show promise in identifying specific source areas. Application of field methods could include studies of sources of fluvial sediment, otherwise referred to as sediment “fingerprinting.” The identification of sediment is important, in part, because knowing the primary sediment source areas in watersheds ensures that best management practices are incorporated in areas that maximize reductions in sediment loadings. This report provides a literature review and annotated bibliography of existing methodologies applied in the field of fluvial sediment fingerprinting. This literature review provides a bibliography of publications where sediment fingerprinting methods have been used; however, this report is not assumed to provide an exhaustive listing. Selected publications were categorized by methodology with some additional summary information. The information contained in the summary may help researchers select methods better suited to their particular study or study area, and identify methods in need of more testing and application.
This annotated bibliography describes the key literature relevant to the elicitation of expert judgements in radioactive waste management. The bibliography is divided into seven sections; section 2 lists the literature exploring the proper interpretation of probabilities used in Probabilistic Risk Analysis (PRA). Section 3 lists literature describing other calculi for handling uncertainty in a numerical fashion. In section 4 comments are given on how to elicit probabilities from individuals as a measure of subjective degrees of belief and section 5 lists the literature concerning how expert judgements can be combined. Sections 6 and 7 list literature giving an overview of the issues involved in PRA for radioactive waste repositories. (author)
Ball, Elaine C
of annotation influences student learning and assessment or, indeed, helps tutors to employ better annotative practices [Juwah, C., Macfarlane-Dick, D., Matthew, B., Nicol, D., Ross, D., Smith, B., 2004. Enhancing student learning through effective formative feedback. The Higher Education Academy, 1-40; Jewitt, C., Kress, G., 2005. English in classrooms: only write down what you need to know: annotation for what? English in Education, 39(1), 5-18]. There is little evidence on ways to heighten students' self-awareness when their essays are returned with annotated feedback [Storch, N., Tapper, J., 1997. Student annotations: what NNS and NS university students say about their own writing. Journal of Second Language Writing, 6(3), 245-265]. The literature review clarifies forms of annotation as feedback practice and offers a summary of the challenges and usefulness of annotation. Copyright 2009. Published by Elsevier Ltd.
Linde, K.; ter Riet, G.; Hondras, M.; Vickers, A.; Saller, R.; Melchart, D.
OBJECTIVE: To provide a comprehensive collection and a summary of systematic reviews of clinical trials on herbal medicines. METHODS: Potentially relevant reviews were searched through the register of the Cochrane Complementary Medicine Field, the Cochrane Library, Medline, and bibliographies of
Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
Lippmann, Richard; Ingols, K. W
This report reviews past research papers that describe how to construct attack graphs, how to use them to improve security of computer networks, and how to use them to analyze alerts from intrusion detection systems...
Ratz, Joan M.; Conk, Shannon J.
The U.S. Fish and Wildlife Service National Conservation Training Center requested a literature review product that would serve as a resource to natural resource professionals interested in using webcams to connect people with nature. The literature review focused on the effects on the public of viewing wildlife through webcams and on information regarding installation and use of webcams. We searched the peer reviewed, published literature for three topics: wildlife cameras, virtual tourism, and technological nature. Very few publications directly addressed the effect of viewing wildlife webcams. The review of information on installation and use of cameras yielded information about many aspects of the use of remote photography, but not much specifically regarding webcams. Aspects of wildlife camera use covered in the literature review include: camera options, image retrieval, system maintenance and monitoring, time to assemble, power source, light source, camera mount, frequency of image recording, consequences for animals, and equipment security. Webcam technology is relatively new and more publication regarding the use of the technology is needed. Future research should specifically study the effect that viewing wildlife through webcams has on the viewers' conservation attitudes, behaviors, and sense of connectedness to nature.
Whisman, M.L.; Anderson, R.P.; Woodward, P.W.; Giles, H.N.
A state-of-the-art review and assessment of storage effects on crude oil and product quality was undertaken through a literature search by computer accessing several data base sources. Pertinent citations from that literature search are tabulated for the years 1980 to the present. This 1990 revision supplements earlier reviews by Brinkman and others which covered stability publications through 1979 and an update in 1983 by Goetzinger and others that covered the period 1952--1982. For purposes of organization, citations are listed in the current revision chronologically starting with the earliest 1980 publications. The citations have also been divided according to primary subject matter. Consequently 11 sections appear including: alternate fuels, gasoline, distillate fuel, jet fuel, residual fuel, crude oil, biodegradation, analyses, reaction mechanisms, containment, and handling and storage. Each section contains a brief narrative followed by all the citations for that category.
Altaf, Farhaan; Weber, Michael; Dea, Nicolas; Boriani, Stefano; Ames, Christopher; Williams, Richard; Verlaan, Jorrit-Jan; Laufer, Ilya; Fisher, Charles G.
STUDY DESIGN.: Systematic review and consensus expert opinion. OBJECTIVE.: To provide surgeons and other health care professionals with guidelines for surgical reconstruction of metastatic spine disease based on evidence and expert opinion. SUMMARY OF BACKGROUND DATA.: The surgical treatment of
Maremmani, Icro; Rolland, Benjamin; Somaini, Lorenzo; Roncero, Carlos; Reimer, Jens; Wright, Nat; Littlewood, Richard; Krajci, Peter; Alho, Hannu; D'Agnone, Oscar; Simon, Nicolas
Treatment of opioid dependence with buprenorphine improves outcomes. Typical dosing ranges for all patients from clinical evidence and as defined in the product information are wide. For specific groups with complex clinical scenarios, there is no clear consensus on dosing choices to achieve best possible outcomes. The doses of buprenorphine used in 6 European countries was reviewed. A review of published evidence supported rapid induction with buprenorphine and the benefits of higher doses but did not identify clearly useful guidance on dosing choices for groups with complex clinical scenarios. An expert group of physicians with experience in addiction care participated in a discussion meeting to share clinical practice experience and develop a consensus on dosing choices. There was general agreement that treatment outcomes can be improved by optimising buprenorphine doses in specific subgroups. Specific groups in whom buprenorphine doses may be too low and who could have better outcomes with optimised dosing were identified on the basis of clinical practice experience. These groups include people with severe addiction, high tolerance to opioids, and psychiatric comorbidities. In these groups it is recommended to review dosing choices to ensure buprenorphine dosing is sufficient.
.... Training and military doctrine has been evolving to reflect this emphasis on teamwork. The purpose of this annotated bibliography is to review literature published over the last ten years concerning team and small group performance...
Hunger, Theresa; Schnell-Inderst, Petra; Sahakyan, Narine; Siebert, Uwe
External experts can be consulted at different stages of an HTA. When using vague information sources, it is particularly important to plan, analyze, and report the information processing in a standardized and transparent way. Our objective was to search and analyze recommendations regarding where and how to include expert data in HTA. We performed a systematic database search and screened the Internet pages of seventy-seven HTA organizations for guidelines, recommendations, and methods papers that address the inclusion of experts in HTA. Relevant documents were downloaded, and information was extracted in a standard form. Results were merged in tables and narrative evidence synthesis. From twenty-two HTA organizations, we included forty-two documents that consider the use of expert opinion in HTA. Nearly all documents mention experts in the step of preparation of the evidence report. Six documents address their role for priority setting of topics, fifteen for scoping, twelve for the appraisal of evidence and results, another twelve documents mention experts when considering the dissemination of HTA results. During the assessment step, experts are most often asked to amend the literature search or to provide expertise for special data analyses. Another issue for external experts is to appraise the HTA results and refer them back to a clinical and social context. Little is reported on methods of expert elicitation when their input substitutes study data. Despite existing recommendations on the use of expert opinion in HTA, common standards for elicitation are scarce in HTA guidelines.
Full Text Available Purpose: This paper proposes an expert assignment method for scientific project review that considers both accuracy and impartiality. As impartial and accurate peer review is extremely important to ensure the quality and feasibility of scientific projects, enhanced methods for managing the process are needed. Design/methodology/approach: To ensure both accuracy and impartiality, we design four criteria, the reviewers’ fitness degree, research intensity, academic association, and potential conflict of interest, to express the characteristics of an appropriate peer review expert. We first formalize the expert assignment problem as an optimization problem based on the designed criteria, and then propose a randomized algorithm to solve the expert assignment problem of identifying reviewer adequacy. Findings: Simulation results show that the proposed method is quite accurate and impartial during expert assignment. Research limitations: Although the criteria used in this paper can properly show the characteristics of a good and appropriate peer review expert, more criteria/conditions can be included in the proposed scheme to further enhance accuracy and impartiality of the expert assignment. Practical implications: The proposed method can help project funding agencies (e.g. the National Natural Science Foundation of China find better experts for project peer review. Originality/value: To the authors’ knowledge, this is the first publication that proposes an algorithm that applies an impartial approach to the project review expert assignment process. The simulation results show the effectiveness of the proposed method.
Young, Ryan; Maga, A Murat
Here we present an application of advanced registration and atlas building framework DRAMMS to the automated annotation of mouse mandibles through a series of tests using single and multi-atlas segmentation paradigms and compare the outcomes to the current gold standard, manual annotation. Our results showed multi-atlas annotation procedure yields landmark precisions within the human observer error range. The mean shape estimates from gold standard and multi-atlas annotation procedure were statistically indistinguishable for both Euclidean Distance Matrix Analysis (mean form matrix) and Generalized Procrustes Analysis (Goodall F-test). Further research needs to be done to validate the consistency of variance-covariance matrix estimates from both methods with larger sample sizes. Multi-atlas annotation procedure shows promise as a framework to facilitate truly high-throughput phenomic analyses by channeling investigators efforts to annotate only a small portion of their datasets.
Expert system validationthat is, testing systems to ascertain whether they achieve acceptable performance levelshas with few exceptions been ad hoc, informal, and of dubious value. Very few efforts have been made in this regard in the transport...
Routson, R.C.; Bean, R.M.
This review covers the available literature concerning ground-disposed wastes and effluents of a potential oil shale industry. Ground disposal has been proposed for essentially all of the solid and liquid wastes produced (Pfeffer, 1974). Since an oil shale industry is not actually in operation, the review is anticipatory in nature. The section, Oil Shale Technology, provides essential background for interpreting the literature on potential shale oil wastes and the topics are treated more completely in the section entitled Environmental Aspects of the Potential Disposal of Oil Shale Wastes to Ground. The first section of the annotated bibliography cites literature concerning potential oil shale wastes and the second section cites literature concerning oil shale technology. Each section contains references arranged historically by year. An index is provided.
The paper summarizes the research accomplishments of the past year for the artificial intelligence and expert systems areas. Most projects have been underway for only a short time; however, overall progress within the areas has been steady and worthwhile. Several projects have already attained their major objectives.
Muller, Sean; Abernethy, Bruce
Expert performers in striking sports can hit objects moving at high speed with incredible precision. Exceptionally well developed anticipation skills are necessary to cope with the severe constraints on interception. In this paper, we provide a review of the empirical evidence regarding expert interception in striking sports and propose a…
Kirschenbaum, Daniel S.; Gierut, Kristen
Objective: To compare and contrast 5 sets of expert recommendations about the treatment of childhood and adolescent obesity. Method: We reviewed 5 sets of recent expert recommendations: 2007 health care organizations' four stage model, 2007 Canadian clinical practice guidelines, 2008 Endocrine Society recommendations, 2009 seven step model, and…
Eric J. Gustafson
This volume perfectly illustrates the truism"we don't know what it is that we don't know." I have been a landscape ecologist for over 20 years, and have even used expert knowledge many times in my own research. Yet I learned something profoundly new in almost every chapter of this collection of primers and case studies focused on the use...
Yokota, M; Kusama, M; Matsuki, N; Ono, S
External experts play an important role in shaping regulatory decisions in the new drug review process in the United States, Europe and Japan. No rigorous study has been performed addressing how and to what extent external experts, in contrast to internal reviewers in the agency, influence the regulatory decisions during new drug reviews. We examined their contributions in Japanese regulatory reviews in contrast to the internal reviewers, focusing on the labelling decision on therapeutic indications. With the data set of 219 new molecular entities (NMEs) approved in Japan from 2000 to 2009, we observed how proposed indications in labelling were modified in a stepwise manner during the review process and conducted multinomial logistic analysis to examine the possible mechanism behind. We found that interim assessment of indications by the internal reviewers was modified substantially by the influence of the external experts in about 20% of the 219 NMEs. Our analysis suggested that internal reviewers provided their opinion mainly based on strict review discipline, whereas external experts added flexibility and reality to their reviews. Our analysis revealed different evaluations between internal reviewers and external experts during regulatory discussions in new drug reviews and how the external panel contributes to changing internal decisions. This study provides a new and quantitative approach to better label setting by emphasizing the contributions of each stakeholder in new drug reviews, which would improve the efficiency, quality and transparency of new drug reviews to enhance public health. © 2013 John Wiley & Sons Ltd.
... expert review process, which occurs in parallel with the U.S. government review. More information on the... DEPARTMENT OF STATE [Public Notice 8042] Call for Expert Reviewers to the U.S. Government Review... both experts and governments. The Second Order Draft of the Working Group I contribution to the 5th...
Жанна Васильевна Пузанова
Full Text Available Patriotism is designated as a national idea in Russia; nowadays the questions the relevance of patriotic education of the most reactive of social groups - young people - is especially acute. Round table in the format of focus groups with 20 experts working with young people, among them - professors, teachers, veterans, employees public authorities to work with youth was held on the 27th of May 2016 on the basis of the museum-panorama “Battle of Stalingrad” in Volgograd, with the assistance of the Peoples’ Friendship University of Russia. During the two-hour round table were discussed issues of civil and patriotic education of youth, including the theme - “Ultrapatriotizm-Patriotism-pseudo-patriotism” (ratio of the concepts, their similarities and differences, manifestations in modern Russian society among young people, “Today's youth and moral conflicts” (spiritually-moral development of today's youth, its values, “infantilism - the scourge of modern youth?” (problem of infantilism as a barrier in the way of civic and patriotic education, “Does extremist views attractive for young people?” (the attitude of youth to extremism and terrorism, effective countermeasures of youth involvement in extremist groups.
Colby, D.; Lipscomb, D.M.; McCunney, R.J.; Seilo, M.T.; Sondergaard, B.
This paper presented the results of a study conducted to review the current literature available on the perceived health effects of wind turbines. The review was conducted by a multidisciplinary panel comprised of audiologists, medical doctors, and acoustical professionals from throughout the world. The document was prepared as a reference point for legislators, regulators and other stakeholders in need of information about wind turbine sounds. A large body of peer-reviewed literature on sound and health effects in general were reviewed in order to assess the plausible biological effects of exposure to wind turbine sound. A review of potential environmental exposures associated with wind turbine operations was conducted. Results of the study indicated that there is no evidence that the sounds emitted by wind turbines have any direct adverse physiological effects, and that the ground-borne vibrations from wind turbines are too weak to be detected or to affect humans. The panel concluded that the sounds from wind turbines can not plausibly have direct adverse health consequences. 126 refs., 3 tabs., 4 figs., 5 appendices.
The role of sensitivity and uncertainty analyses for radioactive waste disposal assessments is reviewed. The report covers a description of the these concepts were applied in the authorities' review of the safety report SR 97. With regard to the use of expert knowledge, the most significant weakness of SR 97 is absence of any standards, procedures, and even definitions for expert judgment. This situation needs to be dealt with by SKB in the near future as it denigrates the portions of the study that are well done. In developing expert judgment processes, SSI should ensure that SKB creates procedures that guarantee traceability and transparency. This will become very important as the repository system matures and receives greater public scrutiny. Both in the area of scenario creation and expert judgement, there are processes that have gained international acceptance. It would be in the best interest of SKB, and the public, to adhere these accepted approaches
The role of sensitivity and uncertainty analyses for radioactive waste disposal assessments is reviewed. The report covers a description of the these concepts were applied in the authorities' review of the safety report SR 97. With regard to the use of expert knowledge, the most significant weakness of SR 97 is absence of any standards, procedures, and even definitions for expert judgment. This situation needs to be dealt with by SKB in the near future as it denigrates the portions of the study that are well done. In developing expert judgment processes, SSI should ensure that SKB creates procedures that guarantee traceability and transparency. This will become very important as the repository system matures and receives greater public scrutiny. Both in the area of scenario creation and expert judgement, there are processes that have gained international acceptance. It would be in the best interest of SKB, and the public, to adhere these accepted approaches.
Full Text Available OBJECTIVE: To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers. METHODS AND MATERIALS: Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact. RESULTS: Shortly after publication, 62 (9% of the 687 research papers were determined to describe at least a 'major addition to knowledge' -6 were thought to be 'landmark' papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications. CONCLUSION: When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.
Full Text Available The aim of this study is to formulate the best clinical practice in the diagnosis and management of chronic pruritus (CP. We searched PubMed, EMBASE, Scopus, Web of Science, and the WHO's regional databases, for studies on “Diagnosis and management of chronic pruritus” from January 1, 2014, to July 31, 2015. We included programmatic reports and hand-searched references of published reviews and articles. Two independent reviewers screened articles and extracted data. We screened 87 of 95 studies that contained qualitative data. Avoid: Dry climate, heat, alcohol compress, ice packs, frequent bathing and washing, intake of very hot and spicy food, intake of alcohol, contact with irritant substances, excitement, strain and stress, and allergens. Using: Mild nonalkaline soaps, moisturizers, bathing oils, lukewarm water while bathing, soft cotton clothing and night creams/lotions, relaxation therapy, autogenic training, psychosocial education, educating patients to cope with itching and scratching, and educational programs. Especially use of moisturizers is considered important. In addition, symptomatic treatment options include systemic H1 antihistamines and topical corticosteroids. Symptomatic therapy directed toward the cause (hepatic, renal, atopic, polycythemia, etc.. If refractory or cause is unknown, consider capsaicin, calcineurin inhibitors for localized pruritus and naltrexone, pregabalin, ultraviolet therapy, Cyclosporine for generalized itching. CP is quite frequent finding associated with skin and systemic diseases in the overall population. It is known to significantly affect quality life score of an individual and also adds burden on the health-care cost. A specific recommendation for treatment of CP is difficult as a result of varied and diverse possibility of underlying diseases associated with CP.
Subhi, Yousif; Bube, Sarah Hjartbro; Rolskov Bojsen, Signe; Skou Thomsen, Ann Sofia; Konge, Lars
Both clinicians and patients use medical mobile phone apps. Anyone can publish medical apps, which leads to contents with variable quality that may have a serious impact on human lives. We herein provide an overview of the prevalence of expert involvement in app development and whether or not app contents adhere to current medical evidence. To systematically review studies evaluating expert involvement or adherence of app content to medical evidence in medical mobile phone apps. We systematically searched 3 databases (PubMed, The Cochrane Library, and EMBASE), and included studies evaluating expert involvement or adherence of app content to medical evidence in medical mobile phone apps. Two authors performed data extraction independently. Qualitative analysis of the included studies was performed. Based on inclusion criteria, 52 studies were included in this review. These studies assessed a total of 6520 apps. Studies dealt with a variety of medical specialties and topics. As much as 28 studies assessed expert involvement, which was found in 9-67% of the assessed apps. Thirty studies (including 6 studies that also assessed expert involvement) assessed adherence of app content to current medical evidence. Thirteen studies found that 10-87% of the assessed apps adhered fully to the compared evidence (published studies, recommendations, and guidelines). Seventeen studies found that none of the assessed apps (n=2237) adhered fully to the compared evidence. Most medical mobile phone apps lack expert involvement and do not adhere to relevant medical evidence.
The traditional role of health librarians as expert searchers is under challenge. The purpose of this review is to establish health librarians' views, practices and educational processes on expert searching. The search strategy was developed in LISTA and then customised for ten other databases: ALISA, PubMed, Embase, Scopus, Web of Science, CINAHL, ERIC, PsycINFO, Cochrane Library and Google Scholar. The search terms were (expert search* OR expert retriev* OR mediated search* OR information retriev*) AND librar*. The searches, completed in December 2010 and repeated in May 2011, were limited to English language publications from 2000 to 2011 (unless seminal works). Expert searching remains a key role for health librarians, especially for those supporting systematic reviews or employed as clinical librarians answering clinical questions. Although clients tend to be satisfied with searches carried out for them, improvements are required to effectively position the profession. Evidence-based guidelines, adherence to transparent standards, review of entry-level education requirements and a commitment to accredited, rigorous, ongoing professional development will ensure best practice. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.
Sheikhtaheri, Abbas; Sadoughi, Farahnaz; Hashemi Dehaghi, Zahra
Complicacy of clinical decisions justifies utilization of information systems such as artificial intelligence (e.g. expert systems and neural networks) to achieve better decisions, however, application of these systems in the medical domain faces some challenges. We aimed at to review the applications of these systems in the medical domain and discuss about such challenges. Following a brief introduction of expert systems and neural networks by representing few examples, the challenges of these systems in the medical domain are discussed. We found that the applications of expert systems and artificial neural networks have been increased in the medical domain. These systems have shown many advantages such as utilization of experts' knowledge, gaining rare knowledge, more time for assessment of the decision, more consistent decisions, and shorter decision-making process. In spite of all these advantages, there are challenges ahead of developing and using such systems including maintenance, required experts, inputting patients' data into the system, problems for knowledge acquisition, problems in modeling medical knowledge, evaluation and validation of system performance, wrong recommendations and responsibility, limited domains of such systems and necessity of integrating such systems into the routine work flows. We concluded that expert systems and neural networks can be successfully used in medicine; however, there are many concerns and questions to be answered through future studies and discussions.
Pereira-Azevedo, N. (Nuno); Carrasquinho, E. (Eduardo); De Oliveira, E.C. (Eduardo Cardoso); Cavadas, V. (Vitor); Osório, L. (Luís); Fraga, A. (Avelino); Castelo-Branco, M. (Miguel); Roobol, M.J. (Monique J.)
textabstractIntroduction: Smartphones are increasingly playing a role in healthcare and previous studies assessing medical applications (apps) have raised concerns about lack of expert involvement and low content accuracy. However, there are no such studies in Urology. We reviewed Urology apps with
What happens to the body when we are near cell phones, base stations and wireless networks are questions that are much debated in the media. A panel of experts appointed by the Health and transport authorities have reviewed research results, test results and management in this field and concludes that the large number of studies that are considered, not provide evidence that these devices can cause adverse health effects. This information leaflet shows the main conclusions from the review. (eb)
Full Text Available The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM2, comprised 60,770 full-length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein-coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full-length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web-based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full-length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding (including partial or truncated transcripts, providing to our knowledge the greatest current coverage of the mouse proteome by full-length cDNAs. The total number of distinct non-protein-coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and final expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.
... ENVIRONMENTAL PROTECTION AGENCY [FRL-9508-2] Request for Nominations of Experts for the Review of... nominations for technical experts to form an SAB panel to review the agency's approaches for a deriving... actions. As a Federal Advisory Committee, the SAB conducts business in accordance with the Federal...
... Nominations of Experts for the Review of Great Lakes Restoration Initiative Action Plan AGENCY: Environmental... requesting public nominations for technical experts to form an SAB panel to review the interagency Great... Administrator on the technical basis for EPA actions. As a Federal Advisory Committee, the SAB conducts business...
Bonet, Mercedes; Nogueira Pileggi, Vicky; Rijken, Marcus J; Coomarasamy, Arri; Lissauer, David; Souza, João Paulo; Gülmezoglu, Ahmet Metin
There is a need for a clear and actionable definition of maternal sepsis, in order to better assess the burden of this condition, trigger timely and effective treatment and allow comparisons across facilities and countries. The objective of this study was to review maternal sepsis definitions and identification criteria and to report on the results of an expert consultation to develop a new international definition of maternal sepsis. All original and review articles and WHO documents, as well as clinical guidelines providing definitions and/or identification criteria of maternal sepsis were included. A multidisciplinary international panel of experts was surveyed through an online consultation in March-April 2016 on their opinion on the existing sepsis definitions, including new definition of sepsis proposed for the adult population (2016 Third International Consensus Definitions for Sepsis and Septic Shock) and importance of different criteria for identification of maternal sepsis. The definition was agreed using an iterative process in an expert face-to-face consensus development meeting convened by WHO and Jhpiego. Standardizing the definition of maternal sepsis and aligning it with the current understanding of sepsis in the adult population was considered a mandatory step to improve the assessment of the burden of maternal sepsis by the expert panel. The literature review and expert consultation resulted in a new WHO consensus definition "Maternal sepsis is a life-threatening condition defined as organ dysfunction resulting from infection during pregnancy, child-birth, post-abortion, or post-partum period". Plans are in progress to validate the new WHO definition of maternal sepsis in a large international population. The operationalization of the new maternal sepsis definition requires generation of a set of practical criteria to identify women with sepsis. These criteria should enable clinicians to focus on the timely initiation of actionable elements of
Thoma, Brent; Chan, Teresa; Desouza, Natalie; Lin, Michelle
Emergency physicians are leaders in the ''free open-access meducation'' (FOAM) movement. The mandate of FOAM is to create open-access education and knowledge translation resources for trainees and practicing physicians (e.g., blogs, podcasts, and vodcasts). Critics of FOAM have suggested that because such resources can be easily published online without quality control mechanisms, unreviewed FOAM resources may be erroneous or biased. We present a new initiative to incorporate open, expert, peer review into an established academic medical blog. Experts provided either pre- or postpublication reviews that were visible to blog readers. This article outlines the details of this initiative and discusses the potentially transformative impact of this educational innovation.
Over the past years, several fish passage models have been developed to examine the downstream survival of salmon during their annual migration through the Columbia River reservoir system to below Bonneville Dam. More recently, models have been created to simulate the survival of salmon throughout the entire life cycle. The models are used by various regional agencies and native American tribes to assess impacts of dam operation, harvesting, and predation on salmonid abundance. These models are now also being used to assess extinction probabilities and evaluate restoration alternatives for threatened and endangered salmonid stocks. Oak Ridge National Laboratory (ORNL) coordinated an initial evaluation of the principal models by a panel of outside, expert reviewers. None of the models were unequivocally endorsed by any reviewer. Significant strengths and weaknesses were noted for each with respect to reasonability of assumptions and equations, adequacy of documentation, adequacy of supporting data, and calibration procedures. Although the models reviewed differ in some important respects, all reflect a common conceptual basis in classical population dynamic theory and a common empirical basis consisting of the available time series of salmonid stock data, hydrographic records, experimental studies of dam passage parameters, and measurements of reservoir mortality. The results of this initial review are not to be construed as a comprehensive scientific peer review of existing Columbia River Basin (CRB) salmon population models and data. The peer review process can be enhanced further by a dynamic exchange regional modelers and scientific panel experts involving interaction and feedback
Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.
Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images
The expert system is a computer system that emulates the decision-making ability of a human expert, which aims to solve complex problems by reasoning knowledge. It is an important branch of artificial intelligence. In this paper, firstly, we briefly introduce the development and basic structure of the expert system. Then, from the perspective of the enabling technology, we classify the current expert systems and elaborate four expert systems: The Rule-Based Expert System, the Framework-Based Expert System, the Fuzzy Logic-Based Expert System and the Expert System Based on Neural Network.
Robbins, Matthew S; Kuruvilla, Deena; Blumenfeld, Andrew; Charleston, Larry; Sorrell, Michael; Robertson, Carrie E; Grosberg, Brian M; Bender, Steven D; Napchan, Uri; Ashkenazi, Avi
To review the existing literature and describe a standardized methodology by expert consensus for the performance of trigger point injections (TPIs) in the treatment of headache disorders. Despite their widespread use, the efficacy, safety, and methodology of TPIs have not been reviewed specifically for headache disorders by expert consensus. The Peripheral Nerve Blocks and Other Interventional Procedures Special Interest Section of the American Headache Society over a series of meetings reached a consensus for nomenclature, indications, contraindications, precautions, procedural details, outcomes, and adverse effects for the use of TPIs for headache disorders. A subcommittee of the Section also reviewed the literature. Indications for TPIs may include many types of episodic and chronic primary and secondary headache disorders, with the presence of active trigger points (TPs) on physical examination. Contraindications may include infection, a local open skull defect, or an anesthetic allergy, and precautions are necessary in the setting of anticoagulant use, pregnancy, and obesity with unclear anatomical landmarks. The most common muscles selected for TPIs include the trapezius, sternocleidomastoid, and temporalis, with bupivacaine and lidocaine the agents used most frequently. Adverse effects are typically mild with careful patient and procedural selection, though pneumothorax and other serious adverse events have been infrequently reported. When performed in the appropriate setting and with the proper expertise, TPIs seem to have a role in the adjunctive treatment of the most common headache disorders. We hope our effort to characterize the methodology of TPIs by expert opinion in the context of published data motivates the performance of evidence-based and standardized treatment protocols. © 2014 American Headache Society.
Raymond, J.R.; Eddy, P.A.; Wallace, R.W.; Foley, M.G.; Bierschenk, W.H.; Harrison, R.P. (Pacific Northwest Lab., Richland, WA (USA); IT Corp., Richland, WA (USA); Pacific Northwest Lab., Richland, WA (USA))
The purpose of this report is to provide information on changes in the state of knowledge on the hydrology and radionuclide migration that have occurred at the Nevada Test Site (NTS) since 1976. In the present study, a literature review was conducted to examine information published since 1976 about the various activities that have occurred at the NTS. Information was collected from the literature on the site's geological, hydrological, geochemical, and geomorphic characteristics related to the impacts on the ground water from weapons testing and the disposal of waste at the NTS. This information was used to identify the state of knowledge about the NTS and the potential impacts of NTS activities on the ground water. More than 250 reports were reviewed, of which about 200 contained information pertinent to the subject of this report. Because the reports have never been collected in a single location, only those that were supplied by the US Department of Energy and other cooperating organizations could be reviewed, and some pertinent documents may have been missed. Appendix A contains an annotated bibliography of the reports reviewed. 149 refs., 28 figs., 2 tabs.
Full Text Available Smartphones are increasingly playing a role in healthcare and previous studies assessing medical applications (apps have raised concerns about lack of expert involvement and low content accuracy. However, there are no such studies in Urology. We reviewed Urology apps with the aim of assessing the level of participation of healthcare professionals (HCP and scientific Urology associations in their development.A systematic search was performed on PubMed, Apple's App Store and Google's Play Store, for Urology apps, available in English. Apps were reviewed by three graders to determine the app's platform, target customer, developer, app type, app category, price and the participation of a HCP or a scientific Urology association in the development.The search yielded 372 apps, of which 150 were specific for Urology. A fifth of all apps had no HCP involvement (20.7% and only a third had been developed with a scientific Urology association (34.7%. The lowest percentage of HCP (13.4% and urological association (1.9% involvement was in apps designed for the general population. Furthermore, there was no contribution from an Urology society in "Electronic Medical Record" nor in "Patient Information" apps. A limitation of the study is that only Android and iOS apps were reviewed.Despite the increasing Mobile Health (mHealth market, this is the first study that demonstrates the lack of expert participation in the design of Urology apps, particularly in apps designed for the general public. Until clear regulation is enforced, the urological community should help regulate app development. Maintaining a register of certified apps or issuing an official scientific seal of approval could improve overall app quality. We propose that urologists become stakeholders in mHealth, shaping future app design and promoting peer-review app validation.
Pereira-Azevedo, Nuno; Carrasquinho, Eduardo; Cardoso de Oliveira, Eduardo; Cavadas, Vitor; Osório, Luís; Fraga, Avelino; Castelo-Branco, Miguel; Roobol, Monique J
Smartphones are increasingly playing a role in healthcare and previous studies assessing medical applications (apps) have raised concerns about lack of expert involvement and low content accuracy. However, there are no such studies in Urology. We reviewed Urology apps with the aim of assessing the level of participation of healthcare professionals (HCP) and scientific Urology associations in their development. A systematic search was performed on PubMed, Apple's App Store and Google's Play Store, for Urology apps, available in English. Apps were reviewed by three graders to determine the app's platform, target customer, developer, app type, app category, price and the participation of a HCP or a scientific Urology association in the development. The search yielded 372 apps, of which 150 were specific for Urology. A fifth of all apps had no HCP involvement (20.7%) and only a third had been developed with a scientific Urology association (34.7%). The lowest percentage of HCP (13.4%) and urological association (1.9%) involvement was in apps designed for the general population. Furthermore, there was no contribution from an Urology society in "Electronic Medical Record" nor in "Patient Information" apps. A limitation of the study is that only Android and iOS apps were reviewed. Despite the increasing Mobile Health (mHealth) market, this is the first study that demonstrates the lack of expert participation in the design of Urology apps, particularly in apps designed for the general public. Until clear regulation is enforced, the urological community should help regulate app development. Maintaining a register of certified apps or issuing an official scientific seal of approval could improve overall app quality. We propose that urologists become stakeholders in mHealth, shaping future app design and promoting peer-review app validation.
Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália
Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Full text: An international team of nuclear safety experts today completed an IAEA mission to review the effectiveness of Iran's safety regulation of its first nuclear power plant and to identify possible improvements before the plant begins operation. Upon invitation of the Islamic Republic of Iran, the International Atomic Energy Agency (IAEA) assembled a team of senior regulators from seven Member States for an Integrated Regulatory Review Service (IRRS) mission. The scope of the mission was limited to the safety regulation of Bushehr nuclear power plant (BNPP-1). The IRRS review took place from 20 February to 2 March at the INRA offices in Tehran and included a technical visit to the BNPP-1 site. The mission was an objective peer review based on IAEA safety standards, and was neither an inspection, nor an audit. Ms. Olena Mykolaichuk, IRRS Team Leader and Head of the State Nuclear Regulatory Committee of Ukraine, commended her INRA counterparts: 'The regulatory work performed on the Bushehr construction and in preparation for commissioning has demonstrated significant progress of INRA as a nuclear regulatory authority,' she said. Philippe Jamet, Director of the IAEA's Nuclear Installation Safety Division, added: 'Through this IRRS mission, both Iran and the international experts contribute to the enhancement of nuclear safety and worldwide experience sharing.' In the course of its review the IRRS team identified the following strengths: - INRA has a dedicated, conscientious staff, demonstrating clear commitments to further improvements. - INRA clearly recognizes the value of peer reviews and international cooperation regarding nuclear safety. - Despite a shortage of staff, INRA demonstrated strong leadership while performing both review and assessment and inspection tasks during the BNPP-1 construction and pre-commissioning. - INRA has developed an excellent computerized documentation control system. Recommendations and suggestions to improve INRA's regulatory
Fonagy, Peter; Speranza, Mario; Luyten, Patrick; Kaess, Michael; Hessels, Christel; Bohus, Martin
Borderline personality disorder (BPD) has onset in adolescence, but is typically first diagnosed in young adulthood. This paper provides a narrative review of the current evidence on diagnosis, comorbidity, phenomenology and treatment of BPD in adolescence. Instruments available for diagnosis are reviewed and their strengths and limitations discussed. Having confirmed the robustness of the diagnosis and the potential for its reliable clinical assessment, we then explore current understandings of the mechanisms of the disorder and focus on neurobiological underpinnings and research on psychological mechanisms. Findings are accumulating to suggest that adolescent BPD has an underpinning biology that is similar in some ways to adult BPD but differs in some critical features. Evidence for interventions focuses on psychological therapies. Several encouraging research studies suggest that early effective treatment is possible. Treatment development has just begun, and while adolescent-specific interventions are still in the process of evolution, most existing therapies represent adaptations of adult models to this developmental phase. There is also a significant opportunity for prevention, albeit there are few data to date to support such initiatives. This review emphasizes that there can be no justification for failing to make an early diagnosis of this enduring and pervasive problem.
Full Text Available Abstract Background Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy. This article is dealing with acupuncture. Potentially relevant reviews were searched through the register of the Cochrane Complementary Medicine Field, the Cochrane Library, Medline, and bibliographies of articles and books. To be included articles had to review prospective clinical trials of acupuncture; had to describe review methods explicitly; had to be published; and had to focus on treatment effects. Information on conditions, interventions, methods, results and conclusions was extracted using a pretested form and summarized descriptively. Results From a total of 48 potentially relevant reviews preselected in a screeening process 39 met the inclusion criteria. 22 were on various pain syndromes or rheumatic diseases. Other topics addressed by more than one review were addiction, nausea, asthma and tinnitus. Almost unanimously the reviews state that acupuncture trials include too few patients. Often included trials are heterogeneous regarding patients, interventions and outcome measures, are considered to have insufficient quality and contradictory results. Convincing evidence is available only for postoperative nausea, for which acupuncture appears to be of benefit, and smoking cessation, where acupuncture is no more effective than sham acupuncture. Conclusions A large number of systematic reviews on acupuncture exists. What is most obvious from these reviews is the need for (the funding of well-designed, larger clinical trials.
Full Text Available Abstract Background Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy. This article is dealing with herbal medicine. Potentially relevant reviews were searched through the register of the Cochrane Complementary Medicine Field, the Cochrane Library, Medline, and bibliographies of articles and books. To be included articles had to review prospective clinical trials of herbal medicines; had to describe review methods explicitly; had to be published; and had to focus on treatment effects. Information on conditions, interventions, methods, results and conclusions was extracted using a pre-tested form and summarized descriptively. Results From a total of 79 potentially relevant reviews pre-selected in the screening process 58 met the inclusion criteria. Thirty of the reports reviewed ginkgo (for dementia, intermittent claudication, tinnitus, and macular degeneration, hypericum (for depression or garlic preparations (for cardiovascular risk factors and lower limb atherosclerosis. The quality of primary studies was criticized in the majority of the reviews. Most reviews judged the available evidence as promising but definitive conclusions were rarely possible. Conclusions Systematic reviews are available on a broad range of herbal preparations prescribed for defined conditions. There is very little evidence on the effectiveness of herbalism as practised by specialist herbalists who combine herbs and use unconventional diagnosis.
Linde, Klaus; Hondras, Maria; Vickers, Andrew; Riet, Gerben ter; Melchart, Dieter
Background Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with homeopathy. Potentially relevant reviews were searched through the register of the Cochrane Complementary Medicine Field, the Cochrane Library, Medline, and bibliographies of articles and books. To be included articles had to review prospective clinical trials of homeopathy; had to describe review methods explicitly; had to be published; and had to focus on treatment effects. Information on conditions, interventions, methods, results and conclusions was extracted using a pretested form and summarized descriptively. Results Eighteen out of 22 potentially relevant reviews preselected in the screening process met the inclusion criteria. Six reviews addressed the question whether homeopathy is effective across conditions and interventions. The majority of available trials seem to report positive results but the evidence is not convincing. For isopathic nosodes for allergic conditions, oscillococcinum for influenza-like syndromes and galphimia for pollinosis the evidence is promising while in other areas reviewed the results are equivocal. Interpretation Reviews on homeopathy often address general questions. While the evidence is promising for some topics the findings of the available reviews are unlikely to end the controversy on this therapy. PMID:11527508
Background Literature on scoliosis screening is vast, however because of the observational nature of available data and methodological flaws, data interpretation is often complex, leading to incomplete and sometimes, somewhat misleading conclusions. The need to propose a set of methods for critical appraisal of the literature about scoliosis screening, a comprehensive summary and rating of the available evidence appeared essential. Methods To address these gaps, the study aims were: i) To propose a framework for the assessment of published studies on scoliosis screening effectiveness; ii) To suggest specific questions to be answered on screening effectiveness instead of trying to reach a global position for or against the programs; iii) To contextualize the knowledge through expert panel consultation and meaningful recommendations. The general methodological approach proceeds through the following steps: Elaboration of the conceptual framework; Formulation of the review questions; Identification of the criteria for the review; Selection of the studies; Critical assessment of the studies; Results synthesis; Formulation and grading of recommendations in response to the questions. This plan follows at best GRADE Group (Grades of Recommendation, Assessment, Development and Evaluation) requirements for systematic reviews, assessing quality of evidence and grading the strength of recommendations. Conclusions In this article, the methods developed in support of this work are presented since they may be of some interest for similar reviews in scoliosis and orthopaedic fields. PMID:23883346
Wilmot, R.D.; Crawford, M.B.
The Swedish Nuclear Fuel and Waste Management Company (SKB) recently published its latest performance assessment for deep disposal of spent nuclear fuel, based on the KBS-3 concept. This assessment, SR 97, uses three hypothetical repository sites (known as Aberg, Beberg and Ceberg) to provide a range of geological settings and hydrogeological conditions for the assessment. The long-term performance of these sites is compared for several sets of assumptions relating to canister lifetimes, climate evolution, and patterns of human behaviour. This report is a review of SR 97 conducted by Galson Sciences Ltd on behalf of the Swedish Nuclear Power Inspectorate (SKI). The review focussed on the use of expert judgement in the assessment and on the treatment of uncertainty and the use of probability in assessment calculations. The review of SR 97 concluded that SKB had identified many of the judgements made in developing and implementing the assessment and modelling approaches, but that a more formal documentation of the assumptions involved would add to the clarity and transparency of the use of judgements. Similarly, explicit acknowledgement of the basis for making judgements about the treatment of FEPs would improve confidence in the assessment. There are a number of tools that can be useful in justifying the judgements made in an assessment. The review concluded that more use of dialogue with stake holders, peer review and expert elicitation could all be of value in SKB's assessment programme. Recently introduced regulations in Sweden have established an individual risk criterion for the long-term performance of repositories. SKB has previously identified 'pessimistic' and 'reasonable' values for a number of model parameters, and used these in a range of deterministic calculations to calculate dose and to illustrate system performance. To allow for the calculation of risk, SKB introduced probabilistic analyses into the SR 97 assessment by assigning probabilities of 10
Arrowood, L.F.; Tonn, B.E.
This report presents recommendations relative to the use of expert systems and machine learning techniques by the Bureau of Labor Statistics (BLS) to substantially automate product substitution decisions associated with the Consumer Price Index (CPI). Thirteen commercially available, PC-based expert system shells have received in-depth evaluations. Various machine learning techniques were also reviewed. Two recommendations are given: (1) BLS should use the expert system shell LEVEL5 OBJECT and establish a software development methodology for expert systems; and (2) BLS should undertake a small study to evaluate the potential of machine learning techniques to create and maintain the approximately 350 ELI-specific knowledge bases to be used in CPI product substitution review.
Sangro, Bruno; Martínez-Urbistondo, Diego; Bester, Lourens; Bilbao, Jose I; Coldwell, Douglas M; Flamen, Patrick; Kennedy, Andrew; Ricke, Jens; Sharma, Ricky A
Selective internal radiation therapy (or radioembolization) by intra-arterial injection of radioactive yttrium-90-loaded microspheres is increasingly used for the treatment of patients with liver metastases or primary liver cancer. The high-dose beta-radiation penetrates an average of only 2.5 mm from the source, thus limiting its effects to the site of delivery. However, the off-target diversion of yttrium-90 microspheres to tissues other than the tumor may lead to complications. The most prominent of these complications include radiation gastritis and gastrointestinal ulcers, cholecystitis, radiation pneumonitis, and radioembolization-induced liver disease, which may occur despite careful pretreatment planning. Thus, selective internal radiation therapy demands an expert multidisciplinary team approach in order to provide comprehensive care for patients. This review provides recommendations to multidisciplinary teams on the optimal medical processes in order to ensure the safe delivery of selective internal radiation therapy. Based on the best available published evidence and expert opinion, we recommend the most appropriate strategies for the prevention, early diagnosis, and management of potential radiation injury to the liver and to other organs. (Hepatology 2017;66:969-982). © 2017 by the American Association for the Study of Liver Diseases.
Shields, Carolyn M.; LaRocque, Linda J.
This paper reviews research literature on year-round schools (YRS) for the British Columbia Ministry of Education. The literature review is organized around the goals of the British Columbia Ministry of Education: (1) impact on student in terms of academic achievement, attitudes, and behavior; (2) costs and benefits; (3) facility use; (4) impact…
8217 "Functional MRI of EMDR in Peacekeepers" a review of the EMDR literature and an annotated bibliography Megan M. Thompson Luigi Pasto DISTRIBUTION...025 July 2002 Canad 20021023 098 "- Empirical assessment of Lanius et al.s’ ’Functional MRI of EMDR in Peacekeepers’, a review of the EMDR ...functional MRI (Magnetic Resonance Imaging), and to determine whether an Eye Movement Desensitization and Reprocessing ( EMDR ) intervention causes
... Advisory Board Panel To Review EPA's Web-Based Report on the Environment AGENCY: Environmental Protection... nominations of technical experts to form an SAB panel to review the Agency's Web-based Report on the... are requested including: (a) Environmental scientists and engineers with knowledge of the sources...
Blome, Christine; Sondermann, Hanno; Augustin, Matthias
Background: This systematic review aimed to extract recommendations from expert opinion articles on how to give a medical research presentation on a scientific conference and to determine whether the experts agree on what makes an effective or poor presentation. Methods: Presentation-related terms were searched within article titles listed in PubMed, restricting the search to English-language articles published from January 1975 to July 2015. Recommendations were extracted from the articles...
Kitajima, Shinichi; En, Junichiro; Kitajima, Shiori; Barua, Sumana; Goto, Masamichi
In 2012 the WHO Expert Committee on Leprosy published its 8th report, 14 years after the publication of its 7th report in 1998. This report, the first since the leprosy reduction goal was met in 2000, highlights key points such as improvements in the quality of various services available to patients and the efforts of individuals and societies, in addition to medical progress in diagnosis and treatment. This review will mainly describe the changes made since the 7th report. Some of the main modifications are the deletion of single lesion paucibacillary type, elongated treatment of patients with high bacterial indices, the introduction of promising new drugs, and a shift from reducing the statistical number of patients to a new target for disability prevention.
Beatty, Mark E.; Beutels, Philippe; Meltzer, Martin I.; Shepard, Donald S.; Hombach, Joachim; Hutubessy, Raymond; Dessis, Damien; Coudeville, Laurent; Dervaux, Benoit; Wichmann, Ole; Margolis, Harold S.; Kuritsky, Joel N.
Dengue vaccines are currently in development and policymakers need appropriate economic studies to determine their potential financial and public health impact. We searched five databases (PubMed, EMBASE, LILAC, EconLit, and WHOLIS) to identify health economics studies of dengue. Forty-three manuscripts were identified that provided primary data: 32 report economic burden of dengue and nine are comparative economic analyses assessing various interventions. The remaining two were a willingness-to-pay study and a policymaker survey. An expert panel reviewed the existing dengue economic literature and recommended future research to fill information gaps. Although dengue is an important vector-borne disease, the economic literature is relatively sparse and results have often been conflicting because of use of inconsistent assumptions. Health economic research specific to dengue is urgently needed to ensure informed decision making on the various options for controlling and preventing this disease. PMID:21363989
Linde, K.; Vickers, A.; Hondras, M.; ter Riet, G.; Thormählen, J.; Berman, B.; Melchart, D.
BACKGROUND: Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with acupuncture.
Linde, K.; ter Riet, G.; Hondras, M.; Vickers, A.; Saller, R.; Melchart, D.
BACKGROUND: Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with herbal medicine.
Linde, K.; Hondras, M.; Vickers, A.; ter Riet, G.; Melchart, D.
BACKGROUND: Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with homeopathy.
Full text: An international expert team has today completed a two-week IAEA review of Germany's nuclear regulatory system. The team identified good practices within the system and gave advice on some areas for further improvement. The IAEA has conveyed the initial findings to German authorities but the final report will be submitted within two months. At the request of the Government of the Federal Republic of Germany, the International Atomic Energy Agency (IAEA) assembled a team of 14 experts to conduct an Integrated Regulatory Review Service (IRRS) mission. This is a peer review based on IAEA Standards. It is not an inspection, nor an audit. The scope of the mission was limited to the safety regulation of nuclear power plants. Experts from Canada, the Czech Republic, Finland, France, Japan, the Netherlands, Republic of Korea, Spain, Switzerland, the UK, the US and from the IAEA took part in the mission, which was conducted from 7 to 19 September in Bonn, Stuttgart and Berlin. The main basis for the review was a well-prepared self-assessment made by the Federal Ministry of Environment, Nature Conservation and Nuclear Safety (BMU) and the Ministry of Environment of the federal state of Baden-Wuerttemberg (UM BW). 'The team members were impressed by the extensive preparation and dedication of the staff both at BMU and UM BW to excellence in nuclear safety,' said Mike Weightman, IRRS Team Leader and Chief Inspector of the UK nuclear regulatory body, the Nuclear Directorate of the Health and Safety Executive. 'We hope the IRRS mission will facilitate further improvements in the safety regulation of nuclear power in Germany and throughout the world.' 'Germany's invitation to undergo such a detailed review is a clear demonstration of its openness and commitment to continuously improve nuclear safety regulation,' said Philippe Jamet, Director of the IAEA's Nuclear Installation Safety Division. Among the particular strengths of BMU and UM BW associated with their
Constenla, Dagna; Garcia, Cristina; Lefcourt, Noah
The economics of dengue is complex and multifaceted. We performed a systematic review of the literature to provide a critical overview of the issues related to dengue economics research and to form a background with which to address the question of cost. Three literature databases were searched [PubMed, Embase and Latin American and Caribbean Health Sciences Literature (LILACS)], covering a period from 1980 to 2013, to identify papers meeting preset inclusion criteria. Studies were reviewed for methodological quality on the basis of a quality checklist developed for this purpose. An expert survey was designed to identify priority areas in dengue economics research and to identify gaps between the methodology and actual practice. Survey responses were combined with the literature review findings to determine stakeholder priorities in dengue economics research. The review identified over 700 papers. Forty-two of these papers met the selection criteria. The studies that were reviewed presented results from 32 dengue-endemic countries, underscoring the importance of dengue as a global public health problem. Cost analyses were the most common, with 21 papers, followed by nine cost-effectiveness analyses and seven cost-of-illness studies, indicating a relatively strong mix of methodologies. Dengue annual overall costs (in 2010 values) ranged from US$13.5 million (in Nicaragua) to $56 million (in Malaysia), showing cost variations across countries. Little consistency exists in the way costs were estimated and dengue interventions evaluated, making generalizations around costs difficult. The current evidence suggests that dengue costs are substantial because of the cost of hospital care and lost earnings. Further research in this area will broaden our understanding of the true economic impact of dengue.
Full text: International safety experts last week concluded a two-week International Atomic Energy Agency (IAEA) mission to review the regulatory framework for nuclear and radiation safety in Poland. In its preliminary report, the Integrated Regulatory Review Service (IRRS) mission team found that Poland's nuclear regulator, Panstwowa Agencja Atomistyki (PAA), has a clear commitment to safety, a high level of transparency, competent staff and leadership, and a good recognition of challenges ahead related to Poland's efforts to develop nuclear power. ''Poland's regulatory framework and the work of PAA give high confidence of strong radiation protection for the Polish people. Further, there has been significant progress in the development of Poland's regulatory framework in preparation for the challenge of regulating nuclear power,'' said team leader Robert Lewis, a senior executive in the US Nuclear Regulatory Commission. The mission was conducted at the request of the Government of Poland from 15-25 April. The team was made up of 11 regulatory experts from Belgium, the Czech Republic, Finland, France, the Republic of Korea, Slovakia, Slovenia, Sweden, the United Arab Emirates, the United Kingdom and the United States, as well as five IAEA staff members. The IRRS review team was very thorough in its review, and we welcome its advice on how to continue to improve our programmes to protect people and the environment , said Janusz Wlodarski, President of PAA. The team interviewed members of PAA and officials from various ministries, as well as key players in the Polish safety framework. Such IRRS missions are peer reviews based on IAEA Safety Standards, not inspections or audits. Among its main observations the IRRS review team identified the following good practices: Applying the considerable experience of PAA's senior management to regulatory issues; The introduction of changes to Poland's laws and regulations following broad public consultation at an early stage in
Full text: Nuclear and radiation safety experts today concluded an eight-day mission to review the Australian Radiation Protection and Nuclear Safety Agency (ARPANSA), the country's nuclear regulator. At the request of the Australian Government, the International Atomic Energy Agency (IAEA) assembled a peer-review team of five regulatory experts from as many nations and three IAEA staff members to conduct a follow-up assessment of an Integrated Regulatory Review Service (IRRS) mission conducted in 2007. This follow-up IRRS mission examined ARPANSA's progress in acting upon the recommendations and suggestions made during the 2007 IRRS mission and reviewed the areas of significant regulatory changes since that review. Both reviews covered safety regulatory aspects of all facilities and activities regulated by ARPANSA. IRRS team leader Kaare Ulbak, Chief Advisor of Denmark's National Institute of Radiation Protection, said: ''ARPANSA should be commended for the significant amount of efforts in addressing all the findings identified in the 2007 mission and for inviting this follow-up review.'' The review team found that ARPANSA has made significant progress toward improving its regulatory activities, as most of the findings identified in the 2007 report have been effectively addressed and therefore can be considered closed. Complementing the ARPANSA strengths identified during the 2007 mission, the 2011 IRRS team noted the following strengths: Response to the Tepco Fukushima Dai-ichi accident; High level of in-house technical expertise in radiation safety; Recognition of the need and willingness to re-organize ARPANSA; Timely development of the national sealed source register in good coordination with other relevant organizations; and Creation of the Australian clinical dosimetry service and the national dose reference levels database. The 2011 IRRS team also made recommendations and suggestions to further strengthen ARPANSA's regulatory system, including: Making full
Full text: A team of international nuclear safety experts today completed a two-week International Atomic Energy Agency (IAEA) review of the regulatory framework for nuclear safety in Switzerland. The Integrated Regulatory Review Service (IRRS) mission noted good practices in the Swiss system and also made recommendations for the nation's nuclear regulatory authority, the Swiss Federal Nuclear Safety Inspectorate (ENSI). ''Our team developed a good impression of the independent Swiss regulator - ENSI - and the team considered that ENSI deserves particular credit for its actions to improve Swiss safety capability following this year's nuclear accident in Japan,'' said IRRS Team Leader Jean-Christophe Niel of France. The mission's scope covered the Swiss nuclear regulatory framework for all types of nuclear-related activities regulated by ENSI. The mission was conducted from 20 November to 2 December, mainly at ENSI headquarters in Brugg. The team held extensive discussions with ENSI staff and visited many Swiss nuclear facilities. IRRS missions are peer reviews, not inspections or audits, and are conducted at the request of host nations. For the Swiss review, the IAEA assembled a team of 19 international experts from 14 countries. The experts came from Belgium, Brazil, the Czech Republic, Finland, France, Germany, Italy, the Republic of Korea, Norway, Russia, Slovakia, Sweden, the United Kingdom, and the United States. ''The findings of the IRRS mission will help us to further improve our work. That is part of our safety culture,'' said ENSI Director General Hans Wanner. ''As Switzerland argued at international nuclear safety meetings this year for a strengthening of the international monitoring of nuclear power, we will take action to fulfil the recommendations.'' The IRRS team highlighted several good practices of the Swiss regulatory system, including the following: ENSI requires Swiss nuclear operators to back-fit their facilities by continuously upgrading
Full text: Nuclear safety experts today concluded a 10-day mission to peer-review the UK Nuclear Regulator: Health and Safety Executive (HSE), Nuclear Directorate (ND). At the request of the UK Government, the International Atomic Energy Agency assembled a team of ten high-level regulatory experts from eight nations to conduct the Integrated Regulatory Review Service (IRRS) mission. The mission was the second of three planned IRRS missions for the United Kingdom. The first was held in March 2006 to begin a process to assess the nation's readiness to regulate and license new reactor designs, considered as a result of the Energy Policy review initiated by the British Prime Minister and the Secretary of State for Trade and Industry (DTI) in 2005. The IRRS team leader Mr. William Borchardt, Executive Director of Operations from the US Nuclear Regulatory Commission, stated, ''The IAEA IRRS serves an important role in both benchmarking against its safety standards and in promoting dialogue between nuclear safety regulators from around the world.'' During the 2nd mission the IRRS the team reviewed HSE/ND progress since the first IRRS mission and recent regulatory developments, the regulation of operating power plants and fuel cycle facilities, the inspection and enforcement programme for nuclear power plants and fuel cycle facilities, and the emergency preparedness and response programme. The IAEA found that HSE/ND has made significant progress toward improving its effectiveness in regulating existing nuclear power plants and in preparing to license new nuclear reactors designs. Many of the findings identified in the 2006 report had been fully addressed and therefore could be considered closed, the others are being addressed in accordance with a comprehensive action plan. IRRS team members visited the Heysham 1 Nuclear Power Plant near Lancaster, the Sellafield site at Cumbria and the Strategic Control Centre at Hutton, and they met senior managers from HSE and a UK
Full text: The IAEA today completed its expert review mission to investigate the 10 April fuel cleaning incident at the Paks nuclear power plant in Hungary. The mission was requested by the Hungarian Government to provide an independent assessment of the causes and actions taken by the plant and Hungarian authorities. The team was composed of nuclear and radiation experts from the IAEA, Austria, Canada, Finland, Slovakia, the United Kingdom and the United States. In a press conference, team leader Miroslav Lipar highlighted the team's findings in five areas: On management, the team concluded that the Hungarian Atomic Energy Authority and Paks are committed to improving the safety of the plant. They noted that as a result of steam generator decontamination in previous years, deposits became attached to the fuel assemblies. A decision was made to clean the fuel and contract an outside company to develop and operate a fuel cleaning process. The team found that the design and operation of the fuel cleaning tank and system was not accomplished in the manner prescribed by the IAEA Safety Standards. Neither the Hungarian Atomic Energy Authority nor Paks used conservative decision-making in their safety assessments for this unproven fuel cleaning system. The team determined that there was an over-reliance on the contractor that had been selected for the design, management and operation of the fuel cleaning system. Time pressure related to a prescribed fuel outage schedule, combined with confidence generated by previous successful fuel cleaning operations, contributed to a weak assessment of a new design and operation, which involved fuel directly removed from the reactor following a planned shutdown. On regulatory oversight, the IAEA team concluded that the Hungarian Atomic Energy Authority underestimated the safety significance of the proposed designs for the fuel cleaning system, which resulted in a less than rigorous review and assessment than should have been necessary
In this manuscript, empirical research on performance of various types of financial experts is reviewed. Financial experts are used as the umbrella term for financial analysts, stockbrokers, money managers, investors, and day-traders etc. The goal of the review is to find out about the abilities of financial experts to produce accurate forecasts, to issue profitable stock recommendations, as well as to make successful investments and trades. On the whole, the reviewed studies show discouragin...
Full text: An international team of senior experts on nuclear safety regulation today completed a two-week International Atomic Energy Agency (IAEA) review of the governmental and regulatory framework for nuclear safety in the People's Republic of China. The team identified good practices within the system and gave advice on areas for future improvements. The IAEA has conveyed the team's main conclusions to the Government of the People's Republic of China. The final report will be submitted to China by Autumn 2010. At the request of Chinese authorities, the IAEA assembled a team of 22 experts to conduct an Integrated Regulatory Review Service (IRRS) mission. This mission is a peer review based on the IAEA Safety Standards . It is not an inspection, nor an audit. The experts came from 15 different countries: Australia, Canada, the Czech Republic, Finland, France, Hungary, Japan, Pakistan, the Republic of Korea, Slovenia, South Africa, Sweden, the United Kingdom, Ukraine and the United States. Mike Weightman, the United Kingdom's Head of Nuclear Directorate, HSE and HM Chief Inspector of Nuclear Installations said: ''I was honoured and pleased to lead such a team of senior regulatory experts from around the world, and I was impressed by their commitment, experience and hard work to provide their best advice possible. We had very constructive interactions with the Chinese authority to maximize the beneficial impact of the mission.'' The scope of the mission included the regulation of nuclear and radiation safety of the facilities and activities regulated by the Ministry of Environmental Protection (MEP) National Nuclear Safety Administration (NNSA). The mission was conducted from 18 to 30 July, mainly in Beijing. To observe Chinese regulatory activities, the IRRS team visited several nuclear facilities, including a nuclear power plant, a manufacturer of safety components for nuclear power plants, a research reactor, a fuel cycle facility, a waste management facility
Full Text Available The number of valid of pathogen and non-pathogen species of Entamoeba has continuously increased in human and animals. This review is performed to provide an update list and some summarized information on Entamoeba species, which were identified up to the 2014.We evaluated the Entamoeba genus with a broad systematic review of the literature, books and electronic databases until February 2014. The synonyms, hosts, pathogenicity and geographical distribution of valid species were considered and recorded. Repeated and unrelated cases were excluded.Totally 51 defined species of Entamoeba were found and arranged by the number of nuclei in mature cyst according to Levin's grouping. Seven of these species within the 4 nucleate mature cysts group and 1 species with one nucleate mature cyst are pathogen. E. histolytica, E. invadence, E. rananrum and E. anatis causes lethal infection in human, reptiles, amphibians and brides respectively, four species causes non-lethal mild dysentery. The other species were non-pathogen and are important to differential diagnosis of amoebiasis.There are some unknown true species of Entamoeba that available information on the morphology, hosts, pathogenicity and distribution of them are still very limited and more considerable investigation will be needed in order to clarify the status of them.
HOOSHYAR, Hossein; ROSTAMKHANI, Parvin; REZAEIAN, Mostafa
Background: The number of valid of pathogen and non-pathogen species of Entamoeba has continuously increased in human and animals. This review is performed to provide an update list and some summarized information on Entamoeba species, which were identified up to the 2014. Methods: We evaluated the Entamoeba genus with a broad systematic review of the literature, books and electronic databases until February 2014. The synonyms, hosts, pathogenicity and geographical distribution of valid species were considered and recorded. Repeated and unrelated cases were excluded. Results: Totally 51 defined species of Entamoeba were found and arranged by the number of nuclei in mature cyst according to Levin’s grouping. Seven of these species within the 4 nucleate mature cysts group and 1 species with one nucleate mature cyst are pathogen. E. histolytica, E. invadence, E. rananrum and E. anatis causes lethal infection in human, reptiles, amphibians and brides respectively, four species causes non-lethal mild dysentery. The other species were non-pathogen and are important to differential diagnosis of amoebiasis. Conclusion: There are some unknown true species of Entamoeba that available information on the morphology, hosts, pathogenicity and distribution of them are still very limited and more considerable investigation will be needed in order to clarify the status of them. PMID:26246811
Hovy, Dirk; Plank, Barbara; Søgaard, Anders
Crowdsourcing lets us collect multiple annotations for an item from several annotators. Typically, these are annotations for non-sequential classification tasks. While there has been some work on crowdsourcing named entity annotations, researchers have assumed that syntactic tasks such as part......-of-speech (POS) tagging cannot be crowdsourced. This paper shows that workers can actually annotate sequential data almost as well as experts. Further, we show that the models learned from crowdsourced annotations fare as well as the models learned from expert annotations in downstream tasks....
The document reproduces the opening remarks made by the Director General of the IAEA on 23 March 1998 at the first meeting of the Senior Expert Group for the review of the Agency's programme and activities. The Director General explains his considerations in establishing the group, and the major challenges facing the safe use of nuclear energy and technologies
Wolters, Anna; de Wert, Guido; van Schayck, Onno C P; Horstman, Klasien
The ongoing development of novel nicotine vaccines makes it urgent to identify the normative questions around this innovative health technology against smoking. A qualitative thematic analysis of peer-reviewed papers on nicotine vaccination published between 2001 and 2013. In the scientific discourse, nicotine vaccination is presented in a neurobiological frame as a potent concept for (long-term) smoking cessation. Nicotine vaccination is also considered a hypothetical strategy to prevent nicotine addiction in minors. Ethical assessments are conducted for the use of nicotine vaccination in public health and clinical medicine. Whereas vaccination for primary prevention is usually associated with public health, the hypothetical case of nicotine prevention in minors is also assessed for individualized protection. Therapeutic and preventive applications are given uneven attention: the classic goal of vaccination (primary prevention in minors) receives methodical consideration and invokes lively debate. The unprecedented use of vaccination, namely smoking cessation, is left largely unattended in the ethical analyses. While health innovations such as nicotine vaccination need broad reflection to guide decisions on their further development and possible future implementations, only a small part of the ethical and social issues of this innovative technology has been discussed. For a debate to come into existence, a 'neurobio-psycho-socio-cultural' frame of smoking and quitting appears fruitful. Important topics for reflection are the human activities and social processes in a vaccine-supported quit attempt, next to respect for individuals, possible harms and questions of (global) justice and research ethics. © 2014 Society for the Study of Addiction.
Giménez-Arnau, Ana M
Chronic spontaneous urticaria (CSU) is characterized by the recurrence of itchy hives and/or angioedema for greater than six weeks, with no known external trigger. Omalizumab, a humanized, recombinant, monoclonal anti-IgE antibody, is the only approved add-on therapy for H1-antihistamine refractory CSU patients. Areas covered: The objective of this article is to discuss the mechanism of action, pharmacokinetics and pharmacodynamics of omalizumab for the treatment of CSU. The review also summarizes efficacy and safety data from proof-of-concept, phase II (X-CUISITE, MYSTIQUE), and pivotal phase III omalizumab studies (ASTERIA I, ASTERIA II, and GLACIAL). Expert opinion: Omalizumab is a clinically effective and safe biological therapy for treating H1-antihistamine refractory CSU patients. It significantly reduces CSU symptoms (hives, itch and angioedema), and improves patient health-related quality of life. While omalizumab is already integral to the treatment of antihistamine refractory CSU, widespread use will depend on legal and economic factors, as well as improvements in the early and accurate diagnosis of CSU patients who would benefit from treatment.
Geard, Amy; Pule, Gift D; Chelo, David; Bitoungui, Valentina Josiane Ngo; Wonkam, Ambroise
Sickle cell disease (SCD) vastly impacts the African continent and is associated with cardiovascular diseases. Stroke, kidney disease, and pulmonary hypertension are considered as proxies of severity in SCD with several genomic loci implicated in their heritability. The present expert review examined the current data on epidemiology and genetic risk factors of stroke, pulmonary hypertension, and kidney disease associated with SCD, as indexed in PubMed ® and Google Scholar ® . Studies collectively show that stroke and kidney disease each affect ∼10% of SCD patients, with pulmonary hypertension displaying a higher prevalence of 30% among adults with SCD. There is some evidence that these epidemiology figures may be an underestimate in SCD patients living in Africa. A modest number of publications have identified genetic factors involved in pathways regulating inflammation, coagulation, cell adhesion, heme degradation, α-globin and γ-globin production, and others, which contribute to the development risk of targeted cardiovascular phenotypes. However, in most cases, these studies have not been validated across populations. There is therefore an urgent need for large-scale genome-wide association, whole-exome and whole-genome studies, and multiomics research on cardiovascular diseases associated with SCD, particularly in Africa, to allow for proportional investment of global research funding on diseases that greatly impact the African continent. Ultimately, this will cultivate socially responsible research investments and identification of at-risk individuals with improved preventive medicine, which should be a cornerstone of global precision medicine.
Full text: An international team of nuclear safety experts today completed a two-week IAEA review of the regulatory framework and effectiveness of the Canadian Nuclear Safety Commission (CNSC). The team identified good practices within the system and gave advice on some areas for improvement. The IAEA has conveyed initial findings to Canadian authorities; the final report will be submitted by autumn. The International Atomic Energy Agency (IAEA) assembled a team of nuclear, radiation, and waste safety experts at the request of the Government of Canada, to conduct an Integrated Regulatory Review Service (IRRS) mission. The mission from 31 May to 12 June was a peer review based on IAEA Standards, not an inspection, nor an audit. The scope of the mission included sources, facilities and activities regulated by the CNSC: the operation of nuclear power plants (NPPs), research reactors and fuel cycle facilities; the refurbishment or licensing of new NPPs; uranium mining; radiation protection and environmental protection programmes; and the implementation of IAEA Code of Conduct on Safety and Security of Radioactive Sources. The 21-member team from 13 IAEA States and from the IAEA itself reviewed CNSC's work in all relevant areas: legislative and governmental responsibilities; responsibilities and functions; organization; activities of the regulatory body, including the authorization process, review and assessment, inspection and enforcement, the development of regulations, as well as guides and its the management system of CNSC. The basis for the review was a well-prepared self-assessment by the CNSC, including an evolution of its strengths and proposed actions to improve its regulatory effectiveness. Mr. Shojiro Matsuura, IRRS Team Leader and President of the Japanese Nuclear Safety Research Association, said the team 'was impressed by the extensive preparation at all CNSC staff levels.' 'We identified a number of good practices and made recommendations and suggestions
Intended for potential business users, this paper describes the main characteristics of expert systems; discusses practical use considerations; presents a taxonomy of the systems; and reviews several expert system development projects in business and industry. (MBR)
Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners
Reidsma, Dennis; op den Akker, Hendrikus J.A.; Artstein, R.; Boleda, G.; Keller, F.; Schulte im Walde, S.
Many interesting phenomena in conversation can only be annotated as a subjective task, requiring interpretative judgements from annotators. This leads to data which is annotated with lower levels of agreement not only due to errors in the annotation, but also due to the differences in how annotators
Full text: Nuclear safety experts concluded a seven-day mission to review the German Regulatory System, conducted from 4-10 September in Bonn, Stuttgart and Berlin. At the request of the Government of the Federal Republic of Germany, the International Atomic Energy Agency assembled a peer-review team of six high-level regulatory experts from six nations (Finland, France, the Netherlands, Switzerland, the UK, the US and three IAEA senior staff members) to conduct a follow-up assessment of an Integrated Regulatory Review Service (IRRS) mission conducted in 2008. This follow-up IRRS mission examined the progress in acting upon the recommendations and suggestions made during the 2008 IRRS mission and reviewed the areas of significant regulatory changes since that review at both the Federal Ministry of Environment, Nature Conservation and Nuclear Safety (BMU) and the Ministry of Environment of the federal state of Baden-Wurttemberg (UM BW). The first mission reviewed Germany's regulatory framework against IAEA Safety Standards and fostered the exchange of information and experience on safety regulation. This is a peer review based on IAEA Standards. It is not an inspection, nor an audit. The scope of the mission was limited to the safety regulation of nuclear power plants. IRRS team leader, Mr. McCree, of the US Nuclear Safety Commission (USNRC), said, ''This was an important IRRS mission, particularly given the recent Fukushima Daiichi Nuclear Power Plant accident and the related insights which underscore the importance of having an independent, credible nuclear safety regulator.'' ''The IRRS team identified several strengths of the German nuclear safety regulators, including the prompt and coordinated incident response activities of BMU and UM BW to the Fukushima accident. Some suggestions were also made to further strengthen nuclear safety regulations concerning the future work of BMU,'' he said. The review team found that important progress has been made toward
Full Text Available The rapid development of the internet has led to the accumulation of massive amounts of data, and thus we find ourselves entering the age of big data. Obtaining useful information from these big data is a crucial issue. The aim of this article is to solve the problem of recommending experts to provide peer reviews for universities and other scientific research institutions. Our proposed recommendation method has two stages. An information filtering method is first offered to identify proper experts as a candidate set. Then, an aggregation model with various constraints is suggested to recommend appropriate experts for each applicant. The proposed method has been implemented in an online research community, and the results exhibit that the proposed method is more effective than existing ones.
The right annotation tool does not always exist for processing a particular natural language task. In these scenarios, researchers are required to build new annotation tools to fit the tasks at hand. However, developing new annotation tools is difficult and inefficient. There has not been careful consideration of software complexity in current annotation tools. Due to the problems of complexity, new annotation tools must reimplement common annotation features despite the availability of imple...
This study seeks to provide an overview of the current state of development in the application of expert system in technology in the field of library and information science. The study starts briefly looking into the capabilities of Artificial Intelligence (AI) in general and then its relevance to LIS (Library Information System) work. A basic introduction to expert system technology and outgrowth of AI research is given. The major components of a generalized expert system are discussed in some detail, and the ways in which system development can be approached are looked at. The main area of expert system applications in library and information science are discussed, looking at cataloguing, classification, reference work and library management etc. (author)
Coplen, Tyler B.; Holden, Norman E.
The Commission on Isotopic Abundances and Atomic Weights uses annotations given in footnotes that are an integral part of the Tables of Standard Atomic Weights to alert users to the possibilities of quite extraordinary occurrences, as well as sources with abnormal atomic-weight values outside an otherwise acceptable range. The basic need for footnotes to the Standard Atomic Weights Table and equivalent annotations to the Table of Isotopic Compositions of the Elements arises from the necessity to provide users with information that is relevant to one or more elements, but that cannot be provided using numerical data in columns. Any desire to increase additional information conveyed by annotations to these Tables is tempered by the need to preserve a compact format and a style that can alert users, who would not be inclined to consult either the last full element-by-element review or the full text of a current Standard Atomic Weights of the Elements report. Since 1989, the footnotes of the Tables of Standard Atomic Weights and the annotations in column 5 of the Table of Isotopic Compositions of the Elements have been harmonized by use of three lowercase footnotes, “g”, “m”, and “r”, that signify geologically exceptionally specimens (“g”), modified isotopic compositions in material subjected to undisclosed or inadvertent isotopic fractionation (“m”), and the range in isotopic composition of normal terrestrial material prevents more precise atomic-weight value being given (“r”). As some elements are assigned intervals for their standard atomic-weight values (applies to 12 elements since 2009), footnotes “g” and “r” are no longer needed for these elements.
Fromreide, Hege; Hovy, Dirk; Søgaard, Anders
We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a......) language drift on Twitter is significant, and while off-the-shelf systems have been reported to perform well on in-sample data, they often perform poorly on new samples of tweets, (b) state-of-the-art performance across various datasets can beobtained from crowdsourced annotations, making it more feasible...
Jovanović, Jelena; Bagheri, Ebrahim
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing. This process is widely known as semantic annotation, and the tools that perform it are known as semantic annotators.Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology. Aiming to establish grounds for further developments in this area, we review a selected set of state of the art biomedical semantic annotators, focusing particularly on general purpose annotators, that is, semantic annotation tools that can be customized to work with texts from any area of biomedicine. We also examine potential directions for further improvements of today's annotators which could make them even more capable of meeting the needs of real-world applications. To motivate and encourage further developments in this area, along the suggested and/or related directions, we review existing and potential practical applications and benefits of semantic annotators.
Valentini, Vincenzo; Glimelius, Bengt; Haustermans, Karin; Marijnen, Corrie A.M.; Rödel, Claus; Gambacorta, Maria Antonietta; Boelens, Petra G.; Aristei, Cynthia; Velde, Cornelis J.H. van de
Background and Purpose: Although rectal and colon cancer management has progressed greatly in the last few decades clinical outcomes still need to be optimized. Furthermore, consensus is required on several issues as some of the main international guidelines provide different recommendations. The European Registration of Cancer Care (EURECCA) drew up documents to standardize management and care in Europe and aid in decision-making. Material and Methods: In the present section the panel of experts reviews and discusses data from the literature on rectal cancer, focusing on recommendations for selecting between short-course radiotherapy (SCRT) and long-course radio-chemotherapy (LCRTCT) as preoperative treatment as well as on the controversies about adjuvant treatment in patients who had received a pre-operative treatment. Results: The starting-point of the present EURECCA document is that adding SCRT or LCRTCT to TME improved loco-regional control but did not increase overall survival in any single trial which, in any case, had improved with the introduction of total mesorectal excision (TME) into clinical practice. Moderate consensus was achieved for cT3 anyNM0 disease. In this frame, agreement was reached on either SCRT followed by immediate surgery or LCRTCT with delayed surgery for mesorectal fascia (MRF) negative tumors at presentation. LCRTCT was recommended for tumor shrinkage in MRF+ at presentations but if patients were not candidates for chemotherapy, SCRT with delayed surgery is an option/alternative. LCRTCT was recommended for cT4 anycNM0. SCRT offers the advantages of less acute toxicity and lower costs, and LCRTCT tumor shrinkage and down-staging, with 13–36% pathological complete response (pCR) rates. To improve the efficacy of preoperative treatment both SCRT and LCRTCT have been, or are being, associated with diverse schedules of chemotherapy and even new targeted therapies but without any definitive evidence of benefit. Nowadays, standard
Neubauer, Markus; Schoberwalter, Dieter; Cenik, Fadime; Keilani, Mohammad; Crevenna, Richard
Literature about lymphedema and its influence on the ability to work and employability is limited. The aim of the present study was to investigate the opinion of Austrian experts on factors influencing the ability to work and employability in patients suffering from lymphedema. A self-administered questionnaire consisting of 6 questions was sent to 12 Austrian lymphedema experts with 6 different specializations from May to August 2016. These experts were asked about suitable and unsuitable professions, the possible influence of lymphedema on the ability to work and employability as well as about existing and additional measures to improve the return to work. The reply rate was 100% (12 out of 12). All experts agreed that lymphedema can restrict the ability to work and employability. The leading reason for limited ability to work and employability was restricted mobility or function of the affected limb along with time-consuming therapeutic modalities, pain and psychological stress. The most suitable job named was teacher and the most unsuitable job named was cook. As easements for return to work, early rehabilitation, self-management, coping strategies, patient education, employer's goodwill and employer's cooperation were reported. Furthermore, experts stressed the need for an adjustment of the legal framework as well as low-barrier and more therapy offers. Adjusted work demands seem to be of greater importance to support the ability to work and employability than recommendations for specific job profiles alone. Experts suggest an adjustment of the legal framework for affected patients, claiming a right for early rehabilitation as well as for life-long therapy. Even though some clinically useful conclusions may be drawn from this article, further research in the field is warranted.
Brister, James Rodney; Bao, Yiming; Kuiken, Carla; Lefkowitz, Elliot J; Le Mercier, Philippe; Leplae, Raphael; Madupu, Ramana; Scheuermann, Richard H; Schobel, Seth; Seto, Donald; Shrivastava, Susmita; Sterk, Peter; Zeng, Qiandong; Klimke, William; Tatusova, Tatiana
Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
Full Text Available Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.
Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony
To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.
Stillwell, W.G.; Seaver, D.A.; Schwartz, J.P.
This report reviews probability assessment and psychological scaling techniques that could be used to estimate human error probabilities (HEPs) in nuclear power plant operations. The techniques rely on expert opinion and can be used to estimate HEPs where data do not exist or are inadequate. These techniques have been used in various other contexts and have been shown to produce reasonably accurate probabilities. Some problems do exist, and limitations are discussed. Additional topics covered include methods for combining estimates from multiple experts, the effects of training on probability estimates, and some ideas on structuring the relationship between performance shaping factors and HEPs. Preliminary recommendations are provided along with cautions regarding the costs of implementing the recommendations. Additional research is required before definitive recommendations can be made
Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard
The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation.
Full Text Available Despite the structure and objectivity provided by the Gene Ontology (GO, the annotation of proteins is a complex task that is subject to errors and inconsistencies. Electronically inferred annotations in particular are widely considered unreliable. However, given that manual curation of all GO annotations is unfeasible, it is imperative to improve the quality of electronically inferred annotations. In this work, we analyze the full GO molecular function annotation of UniProtKB proteins, and discuss some of the issues that affect their quality, focusing particularly on the lack of annotation consistency. Based on our analysis, we estimate that 64% of the UniProtKB proteins are incompletely annotated, and that inconsistent annotations affect 83% of the protein functions and at least 23% of the proteins. Additionally, we present and evaluate a data mining algorithm, based on the association rule learning methodology, for identifying implicit relationships between molecular function terms. The goal of this algorithm is to assist GO curators in updating GO and correcting and preventing inconsistent annotations. Our algorithm predicted 501 relationships with an estimated precision of 94%, whereas the basic association rule learning methodology predicted 12,352 relationships with a precision below 9%.
Sarkar, Rashmi; Aurangabadkar, Sanjeev; Salim, T; Das, Anupam; Shah, Swapnil; Majid, Imran; Singh, Mohan; Ravichandran, G; Godse, Kiran; Arsiwala, Shehnaz; Arya, Latika; Gokhale, Narendra; Sarma, Nilendu; Torsekar, R G; Sonthalia, Sidharth; Somani, V K
Lasers have come up as the newest therapeutic modality in dermatological conditions including melasma. In this article, as a group of experts from Pigmentary Disorders Society in collaboration with South Asian Pigmentary Disorders Forum (SPF), we have tried to discuss the lasers which have been used in melasma and formulate simple consensus guidelines. Following thorough literature search, we have summarised the rationale of using the lasers and the supporting evidences have also been provided. It is clear that laser cannot be the first line treatment for melasma. However, it can be used as an adjuvant therapy in resistant cases, provided the selection of patient and counselling has been done properly. PMID:29263531
Oral contraception and menstrual bleeding during treatment of venous thromboembolism: Expert opinion versus current practice: Combined results of a systematic review, expert panel opinion and an international survey
Klok, F. A.; Schreiber, K.; Stach, K.; Ageno, W.; Middeldorp, S.; Eichinger, S.; Delluc, A.; Blondon, M.; Ay, C.
The optimal management of oral contraception and menstrual bleeding during treatment of venous thromboembolism (VTE) is largely unknown. We aimed to elicit expert opinion and compare that to current practice as assessed by a world-wide international web-based survey among physicians. 10
Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C
The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of
Full Text Available Melasma is one of the most common hyperpigmentary disorders found mainly in women and dark-skinned patients. Sunlight, hormones, pregnancy, and genetics remain the most implicated in the causation of melasma. Although rather recalcitrant to treatment, topical agents such as hydroquinone, modified Kligman's Regime, azelaic acid, kojic acid, Vitamin C, and arbutin still remain the mainstay of therapy with sun protection being a cornerstone of therapy. There are several new botanical and non botanical agents and upcoming oral therapies for the future. There is a lack of therapeutic guidelines, more so in the Indian setup. The article discusses available evidence and brings forward a suggested treatment algorithm by experts from Pigmentary Disorders Society (PDS in a collaborative discussion called South Asian Pigmentary Forum (SPF.
Daniels, V. R.; Bayuse, T. M.; Mulcahy, R. A.; McGuire, R. K. M.; Antonsen, E. L.
Exploration spaceflight poses several challenges to the provision of a comprehensive medication formulary. This formulary must accommodate the size and space limitations of the spacecraft, while addressing individual medication needs and preferences of the crew, consequences of a degrading inventory over time, the inability to resupply used or expired medications, and the need to forecast the best possible medication candidates to treat conditions that may occur. The Exploration Medical Capability (ExMC) Element's Pharmacy Project Team has developed a research plan (RP) that is focused on evidence-based models and theories as well as new diagnostic tools, treatments, or preventive measures aimed to ensure an available, safe, and effective pharmacy sufficient to manage potential medical threats during exploration spaceflight. Here, we will discuss the ways in which the ExMC Pharmacy Project Team pursued expert evaluation and guidance, and incorporated acquired insight into an achievable research pathway, reflected in the revised RP.
Lindstrøm, Bo; Wells, Lisa Marie
a method which makes it possible to associate auxiliary information, called annotations, with tokens without modifying the colour sets of the CP-net. Annotations are pieces of information that are not essential for determining the behaviour of the system being modelled, but are rather added to support...... a certain use of the CP-net. We define the semantics of annotations by describing a translation from a CP-net and the corresponding annotation layers to another CP-net where the annotations are an integrated part of the CP-net....
The definitions of the terms 'artificial intelligence' and 'expert systems', the methodology, areas of employment and limits of expert systems are discussed. The operation of an expert system is described, especially the presentation and organization of knowledge as well as interference and control. Methods and tools for expert system development are presented and their application in nuclear energy are briefly addressed. 7 figs., 2 tabs., 6 refs
Errami, Mounir; Wren, Jonathan D.; Hicks, Justin M.; Garner, Harold R.
Authors, editors and reviewers alike use the biomedical literature to identify appropriate journals in which to publish, potential reviewers for papers or grants, and collaborators (or competitors) with similar interests. Traditionally, this process has either relied upon personal expertise and knowledge or upon a somewhat unsystematic and laborious process of manually searching through the literature for trends. To help with these tasks, we report three utilities that parse and summarize the...
Wöste, Marius; Dugas, Martin
Wahyono, T Y M; Nealon, J; Beucher, S; Prayitno, A; Moureau, A; Nawawi, S; Thabrany, H; Nadjib, M
Routine, passive surveillance systems tend to underestimate the burden of communicable diseases such as dengue. When empirical methods are unavailable, complimentary opinion-based or extrapolative methods have been employed. Here, an expert Delphi panel estimated the proportion of dengue captured by the Indonesian surveillance system, and associated health system parameters. Following presentation of medical and epidemiological data and subsequent discussions, the panel made iterative estimates from which expansion factors (EF), the ratio of total:reported cases, were calculated. Panelists estimated that of all symptomatic Indonesian dengue episodes, 57·8% (95% confidence interval (CI) 46·6-59·8) enter healthcare facilities to seek treatment; 39·3% (95% CI 32·8-42·0) are diagnosed as dengue; and 20·3% (95% CI 16·1-24·3) are subsequently reported in the surveillance system. They estimated most hospitalizations occur in the public sector, while ~55% of ambulatory episodes are seen privately. These estimates gave an overall EF of 5·00; hospitalized EF of 1·66; and ambulatory EF of 34·01 which, when combined with passive surveillance data, equates to an annual average (2006-2015) of 612 005 dengue cases, and 183 297 hospitalizations. These estimates are lower than those published elsewhere, perhaps due to case definitions, local clinical perceptions and treatment-seeking behavior. These findings complement global burden estimates, support health economic analyses, and can be used to inform decision-making.
Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam
User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.
Blome, Christine; Sondermann, Hanno; Augustin, Matthias
Background: This systematic review aimed to extract recommendations from expert opinion articles on how to give a medical research presentation on a scientific conference and to determine whether the experts agree on what makes an effective or poor presentation. Methods: Presentation-related terms were searched within article titles listed in PubMed, restricting the search to English-language articles published from January 1975 to July 2015. Recommendations were extracted from the articles, grouped by content, and analyzed for frequency. Ninety-one articles were included. Among 679 different recommendations, 29 were given in more than 20% of articles each. The five most frequent recommendations were to keep slides simple, adjust the talk to the audience, rehearse, not read the talk from slides or a manuscript, and make eye contact. Results: No article gave advice that was the complete opposite of the 29 most frequent recommendations with the exception of whether a light or dark background should be used for slides. Conclusions: Researchers should comply with these widely accepted standards to be perceived as effective presenters. PMID:28293678
Full Text Available Background: This systematic review aimed to extract recommendations from expert opinion articles on how to give a medical research presentation on a scientific conference and to determine whether the experts agree on what makes an effective or poor presentation. Methods: Presentation-related terms were searched within article titles listed in PubMed, restricting the search to English-language articles published from January 1975 to July 2015. Recommendations were extracted from the articles, grouped by content, and analyzed for frequency. Ninety-one articles were included. Among 679 different recommendations, 29 were given in more than 20% of articles each. The five most frequent recommendations were to keep slides simple, adjust the talk to the audience, rehearse, not read the talk from slides or a manuscript, and make eye contact. Results: No article gave advice that was the complete opposite of the 29 most frequent recommendations with the exception of whether a light or dark background should be used for slides. Conclusions: Researchers should comply with these widely accepted standards to be perceived as effective presenters.
Bonet, Mercedes; Nogueira Pileggi, Vicky; Rijken, Marcus J.; Coomarasamy, Arri; Lissauer, David; Souza, João Paulo; Gülmezoglu, Ahmet Metin
Background: There is a need for a clear and actionable definition of maternal sepsis, in order to better assess the burden of this condition, trigger timely and effective treatment and allow comparisons across facilities and countries. The objective of this study was to review maternal sepsis
Andersen, F Alan; Bergfeld, Wilma F; Belsito, Donald V; Hill, Ronald A; Klaassen, Curtis D; Liebler, Daniel C; Marks, James G; Shank, Ronald C; Slaga, Thomas J; Snyder, Paul W
Calendula officinalis extract, C officinalis flower, C officinalis flower extract, C officinalis flower oil, and C officinalis seed oil are cosmetic ingredients derived from C officinalis. These ingredients may contain minerals, carbohydrates, lipids, phenolic acids, flavonoids, tannins, coumarins, sterols and steroids, monoterpenes, sesquiterpenes, triterpenes, tocopherols, quinones, amino acids, and resins. These ingredients were not significantly toxic in single-dose oral studies using animals. The absence of reproductive/developmental toxicity was inferred from repeat-dose studies of coriander oil, with a similar composition. Overall, these ingredients were not genotoxic. They also were not irritating, sensitizing, or photosensitizing in animal or clinical tests but may be mild ocular irritants. The Cosmetic Ingredient Review (CIR) Expert Panel concluded that these ingredients are safe for use in cosmetics in the practices of use and concentration given in this amended safety assessment.
Full Text Available Trauma related haemorrhagic anaemia is rarely diagnosed by physical examination alone but typically includes measurement of blood haemoglobin, one of the most frequently ordered laboratory tests. Recently, noninvasive technologies have been developed that allow haemoglobin to be measured immediately without the need for intravenous access or having to take venous, arterial, or capillary blood. Moreover, with these technologies haemoglobin can be continuously measured in patients with active bleeding, to guide the start and stop of blood transfusions and to detect occult bleeding. Recent studies on the accuracy of the devices showed promising results in terms of accuracy of hemoglobin measurement compared to laboratory determination. The present review gives an overview on the technology itself and reviews the current literature on the subject.
Wagg, Adrian S; Newman, Diane K; Leichsenring, Kai; van Houten, Paul
Global demographic trends suggest that the incidence of both urinary and faecal incontinence will rise in the coming years, bringing significant health and economic implications for both patients and payers. There is limited organisational evidence to guide payers and providers about service configuration which will deliver efficient guideline-compliant, high-quality patient care. To create, using evidence from a systematic review, qualitative data and expert consensus an internationally applicable service specification for continence care. Evidence was obtained from a systematic and grey literature review of published randomised controlled trials and quasi-experimental studies reporting efficacy of continence service design at the level of the community dwelling patient with either bladder or bowel incontinence, governmental reports and policy frameworks supplemented by data from 47 semi-structured interviews with clinicians, patients, patient-representatives and policy experts from four geographies broadly representative of different healthcare systems. A number of themes related to current and potential future organisation of continence care were identified from the data. A modular service specification with eight core components was created including case detection, initial assessment and treatment, case co-ordination, caregiver support, community-based support, specialist assessment and treatment, use of containment products, and use of technology. Within this framework important key recommendations are: ensure robust referral pathways, shift assessment for case coordination to nurses specializing in continence care, promote self-management and technology, use comprehensive assessment tools and service performance targets based on outcome and operational measures. This study has defined practice gaps in the provision of continence services and described eight core components of a service specification for incontinence that commissioners and payers of health
Adrian S Wagg
Full Text Available Global demographic trends suggest that the incidence of both urinary and faecal incontinence will rise in the coming years, bringing significant health and economic implications for both patients and payers. There is limited organisational evidence to guide payers and providers about service configuration which will deliver efficient guideline-compliant, high-quality patient care.To create, using evidence from a systematic review, qualitative data and expert consensus an internationally applicable service specification for continence care.Evidence was obtained from a systematic and grey literature review of published randomised controlled trials and quasi-experimental studies reporting efficacy of continence service design at the level of the community dwelling patient with either bladder or bowel incontinence, governmental reports and policy frameworks supplemented by data from 47 semi-structured interviews with clinicians, patients, patient-representatives and policy experts from four geographies broadly representative of different healthcare systems.A number of themes related to current and potential future organisation of continence care were identified from the data. A modular service specification with eight core components was created including case detection, initial assessment and treatment, case co-ordination, caregiver support, community-based support, specialist assessment and treatment, use of containment products, and use of technology. Within this framework important key recommendations are: ensure robust referral pathways, shift assessment for case coordination to nurses specializing in continence care, promote self-management and technology, use comprehensive assessment tools and service performance targets based on outcome and operational measures.This study has defined practice gaps in the provision of continence services and described eight core components of a service specification for incontinence that commissioners and
Full text: A team of international nuclear safety experts today completed a review of Japan's two-stage process for assessing nuclear safety at the nation's nuclear power plants. The team began its work on 23 January and delivered a Preliminary Summary Report to Japanese officials today and plans to finish the final report by the end of February. National safety assessments and their peer review by the IAEA are a key component of the IAEA's Action Plan on Nuclear Safety, which was approved by the Agency's 152 Member States following last year's nuclear accident at Fukushima Daiichi Nuclear Power Station. At the request of the Government of Japan, the International Atomic Energy Agency (IAEA) organized a 10-person team to review the Japanese Nuclear and Industrial Safety Agency's (NISA) approach to the Comprehensive Assessments for the Safety of Existing Power Reactor Facilities and how NISA examines the results submitted by nuclear operators. The IAEA safety review mission consisted of five IAEA and three international nuclear safety experts. To help its review, the team held meetings in Tokyo with officials from NISA, the Japanese Nuclear Energy Safety (JNES) Organization, and the Kansai Electric Power Company (KEPCO), and the team visited the Ohi Nuclear Power Station to see an example of how Japan's Comprehensive Safety Assessment is being implemented by nuclear operators. 'We concluded that NISA's instructions to power plants and its review process for the Comprehensive Safety Assessments are generally consistent with IAEA Safety Standards', said team leader James Lyons, director of the IAEA's Nuclear Installation Safety Division. In its Preliminary Summary Report delivered today, the team highlighted a number of good practices and identified some improvements that would enhance the overall effectiveness of the Comprehensive Safety Assessment process. Good practices identified by the mission team include: Based on NISA instructions and commitments of the
Hansen, Frank Allan
Ubiquitous annotation systems allow users to annotate physical places, objects, and persons with digital information. Especially in the field of location based information systems much work has been done to implement adaptive and context-aware systems, but few efforts have focused on the general...... requirements for linking information to objects in both physical and digital space. This paper surveys annotation techniques from open hypermedia systems, Web based annotation systems, and mobile and augmented reality systems to illustrate different approaches to four central challenges ubiquitous annotation...... systems have to deal with: anchoring, structuring, presentation, and authoring. Through a number of examples each challenge is discussed and HyCon, a context-aware hypermedia framework developed at the University of Aarhus, Denmark, is used to illustrate an integrated approach to ubiquitous annotations...
Georgiana Marin; Mihai Catalin Andrei
In recent decades IT and computer systems have evolved rapidly in economic informatics field. The goal is to create user friendly information systems that respond promptly and accurately to requests. Informatics systems evolved into decision assisted systems, and such systems are converted, based on gained experience, in expert systems for creative problem solving that an organization is facing. Expert systems are aimed at rebuilding human reasoning on the expertise obtained from experts, sto...
Andrew H Lin
Full Text Available Introduction: The Health Experts onLine at Portsmouth teleconsultation system is designed to connect health providers in the Navy Medicine East Region to specialists at Naval Medical Center Portsmouth. Methods: A review of the first year of the Health Experts onLine at Portsmouth system was performed. Data on each teleconsultation were extracted from the Health Experts onLine at Portsmouth system database and analyzed. Results: From June 2014 to May 2015 there have been 585 teleconsultations. Providers stationed on 36 ships/submarines and at 28 remote military treatment facilities have utilized the Health Experts onLine at Portsmouth system. Over 280 specialists in 34 different specialties were consulted. The median time to first response from a specialist was 6 h and 8 min, with 75% of all consults being addressed within 24 h. Eighteen medevacs were recommended. Thirty-nine potential medevacs were prevented, and 100 potential civilian network deferrals were prevented, resulting in an estimated savings of over US$580,000. Discussion: Based on the 1-year metrics, Health Experts onLine at Portsmouth has provided improved access and quality of care to service members and their families throughout the Navy Medicine East Region. It has helped avoid over US$580,000 in unnecessary cost burden. Further review at the 2-year time interval will demonstrate the continued growth and effectiveness of the Health Experts onLine at Portsmouth system.
Lin, Andrew H; Cole, Jacob H; Chin, John C; Mahnke, Chirstopher Becket
The Health Experts onLine at Portsmouth teleconsultation system is designed to connect health providers in the Navy Medicine East Region to specialists at Naval Medical Center Portsmouth. A review of the first year of the Health Experts onLine at Portsmouth system was performed. Data on each teleconsultation were extracted from the Health Experts onLine at Portsmouth system database and analyzed. From June 2014 to May 2015 there have been 585 teleconsultations. Providers stationed on 36 ships/submarines and at 28 remote military treatment facilities have utilized the Health Experts onLine at Portsmouth system. Over 280 specialists in 34 different specialties were consulted. The median time to first response from a specialist was 6 h and 8 min, with 75% of all consults being addressed within 24 h. Eighteen medevacs were recommended. Thirty-nine potential medevacs were prevented, and 100 potential civilian network deferrals were prevented, resulting in an estimated savings of over US$580,000. Based on the 1-year metrics, Health Experts onLine at Portsmouth has provided improved access and quality of care to service members and their families throughout the Navy Medicine East Region. It has helped avoid over US$580,000 in unnecessary cost burden. Further review at the 2-year time interval will demonstrate the continued growth and effectiveness of the Health Experts onLine at Portsmouth system.
Sagar, Budhi; Egan, Michael; Roehlig, Klaus-Juergen; Chapman, Neil; Wilmot, Roger
In 2006, SKB published a safety assessment (SR-Can) as part of its work to support a licence application for the construction of a final repository for spent nuclear fuel. The purposes of the SR-Can project were stated in the main project report to be: 1. To make a first assessment of the safety of potential KBS-3 repositories at Forsmark and Laxemar to dispose of canisters as specified in the application for the encapsulation plant. 2. To provide feedback to design development, to SKB's research and development (R and D) programme, to further site investigations and to future safety assessments. 3. To foster a dialogue with the authorities that oversee SKB's activities, i.e. the Swedish Nuclear Power Inspectorate, SKI, and the Swedish Radiation Protection Authority, SSI, regarding interpretation of applicable regulations, as a preparation for the SR-Site project. To help inform their review of SKB's proposed approach to development of the longterm safety case, the authorities appointed three international expert review teams to carry out a review of SKB's SR-Can safety assessment report. Comments from one of these teams - the Safety Assessment Methodology (SAM) review team - are presented in this document. The SAM review team's scope of work included an examination of SKB's documentation of the assessment ('Long-term safety for KBS-3 Repositories at Forsmark and Laxemar - a first evaluation' and several supporting reports) and hearings with SKB staff and contractors, held in March 2007. As directed by SKI and SSI, the SAM review team focused on methodological aspects and sought to determine whether SKB's proposed safety assessment methodology is likely to be suitable for use in the future SR-Site and to assess its consistency with the Swedish regulatory framework. No specific evaluation of long-term safety or site acceptability was undertaken by any of the review teams. SKI and SSI's Terms of Reference for the SAM review team requested that consideration be given
Loes C M Bertens
Full Text Available BACKGROUND: In diagnostic studies, a single and error-free test that can be used as the reference (gold standard often does not exist. One solution is the use of panel diagnosis, i.e., a group of experts who assess the results from multiple tests to reach a final diagnosis in each patient. Although panel diagnosis, also known as consensus or expert diagnosis, is frequently used as the reference standard, guidance on preferred methodology is lacking. The aim of this study is to provide an overview of methods used in panel diagnoses and to provide initial guidance on the use and reporting of panel diagnosis as reference standard. METHODS AND FINDINGS: PubMed was systematically searched for diagnostic studies applying a panel diagnosis as reference standard published up to May 31, 2012. We included diagnostic studies in which the final diagnosis was made by two or more persons based on results from multiple tests. General study characteristics and details of panel methodology were extracted. Eighty-one studies were included, of which most reported on psychiatry (37% and cardiovascular (21% diseases. Data extraction was hampered by incomplete reporting; one or more pieces of critical information about panel reference standard methodology was missing in 83% of studies. In most studies (75%, the panel consisted of three or fewer members. Panel members were blinded to the results of the index test results in 31% of studies. Reproducibility of the decision process was assessed in 17 (21% studies. Reported details on panel constitution, information for diagnosis and methods of decision making varied considerably between studies. CONCLUSIONS: Methods of panel diagnosis varied substantially across studies and many aspects of the procedure were either unclear or not reported. On the basis of our review, we identified areas for improvement and developed a checklist and flow chart for initial guidance for researchers conducting and reporting of studies
Hildebrandt, Thomas Troels; Cattani, Gian Luca
An expert system is a computer system for inferring knowledge from a knowledge base, typically by using a set of inference rules. When the concept of expert systems was introduced at Stanford University in the early 1970s, the knowledge base was an unstructured set of facts. Today the knowledge...... base of expert systems is often given in terms of an ontology, extracted and built from various data sources by employing natural language-processing and statistics. To emphasize such capabilities, the term “expert” is now often replaced by “cognitive,” “knowledge,” “knowledge-based,” or “intelligent......” system. With very few exceptions, general-purpose expert systems have failed to emerge so far. However, expert systems are applied in specialized domains, particularly in healthcare. The increasing availability of large quantities of data to organizations today provides a valuable opportunity...
Hofmeister, Alan M.; Ferrara, Joseph M.
The article discusses the characteristics of expert systems (computer programs designed to replicate human expertise in a variety of areas), describes recently available expert system development tools, suggests applications within the field of special education, and reviews recent efforts to apply expert systems technology to special education…
Shadbolt, N. R.
This paper examines the origins, current state and future prospects for expert systems. The origins are traced from the schism with classic Artificial Intelligence. The characteristics of early expert systems are described and contrasted with more recent developments. A number of influential forces operating on present day systems are reviewed. The future trends in the evolution of expert systems are discussed.
Karayannis Nicholas V
Full Text Available Abstract Background Several classification schemes, each with its own philosophy and categorizing method, subgroup low back pain (LBP patients with the intent to guide treatment. Physiotherapy derived schemes usually have a movement impairment focus, but the extent to which other biological, psychological, and social factors of pain are encompassed requires exploration. Furthermore, within the prevailing 'biological' domain, the overlap of subgrouping strategies within the orthopaedic examination remains unexplored. The aim of this study was "to review and clarify through developer/expert survey, the theoretical basis and content of physical movement classification schemes, determine their relative reliability and similarities/differences, and to consider the extent of incorporation of the bio-psycho-social framework within the schemes". Methods A database search for relevant articles related to LBP and subgrouping or classification was conducted. Five dominant movement-based schemes were identified: Mechanical Diagnosis and Treatment (MDT, Treatment Based Classification (TBC, Pathoanatomic Based Classification (PBC, Movement System Impairment Classification (MSI, and O'Sullivan Classification System (OCS schemes. Data were extracted and a survey sent to the classification scheme developers/experts to clarify operational criteria, reliability, decision-making, and converging/diverging elements between schemes. Survey results were integrated into the review and approval obtained for accuracy. Results Considerable diversity exists between schemes in how movement informs subgrouping and in the consideration of broader neurosensory, cognitive, emotional, and behavioural dimensions of LBP. Despite differences in assessment philosophy, a common element lies in their objective to identify a movement pattern related to a pain reduction strategy. Two dominant movement paradigms emerge: (i loading strategies (MDT, TBC, PBC aimed at eliciting a phenomenon
Background Several classification schemes, each with its own philosophy and categorizing method, subgroup low back pain (LBP) patients with the intent to guide treatment. Physiotherapy derived schemes usually have a movement impairment focus, but the extent to which other biological, psychological, and social factors of pain are encompassed requires exploration. Furthermore, within the prevailing 'biological' domain, the overlap of subgrouping strategies within the orthopaedic examination remains unexplored. The aim of this study was "to review and clarify through developer/expert survey, the theoretical basis and content of physical movement classification schemes, determine their relative reliability and similarities/differences, and to consider the extent of incorporation of the bio-psycho-social framework within the schemes". Methods A database search for relevant articles related to LBP and subgrouping or classification was conducted. Five dominant movement-based schemes were identified: Mechanical Diagnosis and Treatment (MDT), Treatment Based Classification (TBC), Pathoanatomic Based Classification (PBC), Movement System Impairment Classification (MSI), and O'Sullivan Classification System (OCS) schemes. Data were extracted and a survey sent to the classification scheme developers/experts to clarify operational criteria, reliability, decision-making, and converging/diverging elements between schemes. Survey results were integrated into the review and approval obtained for accuracy. Results Considerable diversity exists between schemes in how movement informs subgrouping and in the consideration of broader neurosensory, cognitive, emotional, and behavioural dimensions of LBP. Despite differences in assessment philosophy, a common element lies in their objective to identify a movement pattern related to a pain reduction strategy. Two dominant movement paradigms emerge: (i) loading strategies (MDT, TBC, PBC) aimed at eliciting a phenomenon of centralisation of
Savage, David (Quintessa Limited, Henley-on-Thames (GB)); Bennett, David (TerraSalus Limited, Oakham (GB)); Apted, Mick (Monitor Scientific LLC, Denver, CO (US)); Saellfors, Goeran (Chalmers Univ. of Technology, Goeteborg (SE)); Saario, Timo (VTT Materials and Building (FI)); Segle, Peter (Inspecta, Stockholm (SE))
The Swedish Nuclear Fuel and Waste Management Company (SKB) has recently submitted a license application for the construction of a spent fuel encapsulation plant. SKB plans to submit a further license application in 2009 for the construction of a repository for the disposal spent nuclear fuel. In connection with the first of these applications, SKB published a safety report, known as SR-Can, which assessed the safety of a spent-fuel repository. The Swedish Nuclear Power Inspectorate (SKI) and the Swedish Radiation Protection Authority (SSI) (the Authorities) will make formal reviews of the licence applications, and have, therefore, jointly commissioned a team of independent experts to assess and provide comments on SKB's safety reports. The Authorities will consider the views of the independent review team in completing their own reviews. This document presents the comments and findings of the Engineered Barrier System (EBS) review group on SR-Can. The SR-Can safety report includes an examination of EBS design and performance for a range of scenarios, including expected repository evolution and possible variant scenarios, that together address processes and events that might result in the loss of certain repository safety functions. Furthermore, a series of sensitivity analyses is also presented that provides helpful insights into the relative importance of many key parameters and processes related to the EBS. In general, the explanatory text of the SR-Can safety report is clear, and the cited references provide adequate technical justifications for the assumptions, models, and data that are abstracted into the SR-Can safety report. The review group considers, therefore, that SKB's development of SR-Can has been a very valuable exercise, and that SKB should be congratulated on the breadth, depth and general clarity of its research and development and safety assessment programmes. Notwithstanding these successes, the EBS review group has identified a range
Karimi, Sarvnaz; Metke-Jimenez, Alejandro; Kemp, Madonna; Wang, Chen
CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.(1). Copyright © 2015 Elsevier Inc. All rights reserved.
A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.
Full Text Available Over the past two decades many checklists of reptiles of India and adjacent countries have been published. These publications have furthered the growth of knowledge on systematics, distribution and biogeography of Indian reptiles, and the field of herpetology in India in general. However, the reporting format of most such checklists of Indian reptiles does not provide a basis for direct verification of the information presented. As a result, mistakes in the inclusion and omission of species have been perpetuated and the exact number of reptile species reported from India still remains unclear. A verification of the current listings based on distributional records and review of published checklists revealed that 199 species of lizards (Reptilia: Sauria are currently validly reported on the basis of distributional records within the boundaries of India. Seventeen other lizard species have erroneously been included in earlier checklists of Indian reptiles. Omissions of species by these checklists have been even more numerous than erroneous inclusions. In this paper, I present a plea to report species lists as annotated checklists which corroborate the inclusion and omission of species by providing valid source references or notes.
Howe, Kevin; Davis, Paul; Paulini, Michael; Tuli, Mary Ann; Williams, Gary; Yook, Karen; Durbin, Richard; Kersey, Paul; Sternberg, Paul W
WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE.
Noyes, Jane; Brenner, Maria; Fox, Patricia; Guerin, Ashleigh
To report a novel review to develop a health systems model of successful transition of children with complex healthcare needs from hospital to home. Children with complex healthcare needs commonly experience an expensive, ineffectual and prolonged nurse-led discharge process. Children gain no benefit from prolonged hospitalization and are exposed to significant harm. Research to enable intervention development and process evaluation across the entire health system is lacking. Novel mixed-method integrative review informed by health systems theory. DATA CINAHL, PsychInfo, EMBASE, PubMed, citation searching, personal contact. REVIEW Informed by consultation with experts. English language studies, opinion/discussion papers reporting research, best practice and experiences of children, parents and healthcare professionals and purposively selected policies/guidelines from 2002-December 2012 were abstracted using Framework synthesis, followed by iterative theory development. Seven critical factors derived from thirty-four sources across five health system levels explained successful discharge (new programme theory). All seven factors are required in an integrated care pathway, with a dynamic communication loop to facilitate effective discharge (new programme logic). Current health system responses were frequently static and critical success factors were commonly absent, thereby explaining ineffectual discharge. The novel evidence-based model, which reconceptualizes 'discharge' as a highly complex longitudinal health system intervention, makes a significant contribution to global knowledge to drive practice development. Research is required to develop process and outcome measures at different time points in the discharge process and future trials are needed to determine the effectiveness of integrated health system discharge models. © 2013 John Wiley & Sons Ltd.
Ruxton, C H S
The increased availability of caffeinated drinks raises questions about the level of caffeine that is appropriate for children, as well as the benefits and risks associated with their consumption. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, this systematic review evaluates evidence from randomised controlled trials investigating the effects of caffeine on cognition, behaviour, mood and exercise performance in children. Observational studies and expert panel guidelines are also discussed. One hundred and nine studies were found, with 11 randomised controlled trials and 13 observational studies meeting the criteria. High caffeine intakes (e.g. >5 mg kg(-1) body weight day(-1)) were associated with an increased risk of anxiety and withdrawal symptoms. However, smaller amounts were not linked with such effects and may benefit cognitive function and sports performance based on adult studies. The evidence suggests that children and adolescents should limit daily caffeine consumption to 2.5 mg kg(-1) body weight day(-1), equating to one or two cups of tea or one small cup of coffee. Lower contributors of caffeine, such as tea, may be more appropriate for children because they contribute to daily fluid intakes and provide flavonoids. By contrast, caffeinated soft drinks may be less suitable options for children as a result of their acidity, higher caffeine content, presence of added sugar (in some cases) and absence of bioactive compounds. More studies are needed to determine the intakes that represent a risk and whether there may be benefits for alertness and sports performance with moderate intakes of caffeine. © 2013 The British Dietetic Association Ltd.
Koch, Lisa M; Rajchl, Martin; Bai, Wenjia; Baumgartner, Christian F; Tong, Tong; Passerat-Palmbach, Jonathan; Aljabar, Paul; Rueckert, Daniel
Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation.
Barrios, Ernie, Ed.
More than 300 books and articles published from 1920 to 1971 are reviewed in this annotated bibliography of literature on the Chicano. The citations and reviews are categorized by subject area and deal with contemporary Chicano history, education, health, history of Mexico, literature, native Americans, philosophy, political science, pre-Columbian…
Hartung, Thomas; Blaauboer, Bas J; Bosgra, Sieto
The European cosmetics legislation foresees a review in 2011 and possible postponement of the 2013 marketing ban to enforce the testing ban for systemic and repeated-dose animal tests. For this purpose, a 119-page report commissioned by the European Commission was published recently. Here, a group...... of 17 independent experts from the US, Europe, and Japan was brought together to evaluate the report. The expert panel strongly endorsed the report and its conclusions. A number of important options not considered were identified; these do not, however, affect the overall conclusions regarding...
van de Velde, C J H; Boelens, P G; Tanis, P J; Espin, E; Mroczkowski, P; Naredi, P; Pahlman, L; Ortiz, H; Rutten, H J; Breugom, A J; Smith, J J; Wibe, A; Wiggers, T; Valentini, V
The first multidisciplinary consensus conference on colon and rectal cancer was held in December 2012, achieving a majority of consensus for diagnostic and treatment decisions using the Delphi Method. This article will give a critical appraisal of the topics discussed during the meeting and in the consensus document by well-known leaders in surgery that were involved in this multidisciplinary consensus process. Scientific evidence, experience and opinions are collected to support multidisciplinary teams (MDT) with arguments for medical decision-making in diagnosis, staging and treatment strategies for patients with colon or rectal cancer. Surgery is the cornerstone of curative treatment for colon and rectal cancer. Standardizing treatment is an effective instrument to improve outcome of multidisciplinary cancer care for patients with colon and rectal cancer. In this article, a review of the following focuses; Perioperative care, age and colorectal surgery, obstructive colorectal cancer, stenting, surgical anatomical considerations, total mesorectal excision (TME) surgery and training, surgical considerations for locally advanced rectal cancer (LARC) and local recurrent rectal cancer (LRRC), surgery in stage IV colorectal cancer, definitions of quality of surgery, transanal endoscopic microsurgery (TEM), laparoscopic colon and rectal surgery, preoperative radiotherapy and chemoradiotherapy, and how about functional outcome after surgery? Copyright © 2013 Elsevier Ltd. All rights reserved.
Deal, Shanley B; Stefanidis, Dimitrios; Brunt, L Michael; Alseidi, Adnan
We sought to determine the feasibility of developing a multimedia educational tutorial to teach learners to assess the critical view of safety using input from expert surgeons, non-surgeons and crowd-sourcing. We intended to develop a tutorial that would teach learners how to identify the basic anatomy and physiology of the gallbladder, identify the components of the critical view of safety criteria, and understand its significance for performing a safe gallbladder removal. Using rounds of assessment with experts, laypersons and crowd-workers we developed an educational video with improving comprehension after each round of revision. We demonstrate that the development of a multimedia educational tool to educate learners of various backgrounds is feasible using an iterative review process that incorporates the input of experts and crowd sourcing. When planning the development of an educational tutorial, a step-wise approach as described herein should be considered. Copyright © 2017 Elsevier Inc. All rights reserved.
demonstrated that, on the balance of probabilities, a correct diagnosis at that time would not have altered the course of the illness. Quantum. Where it appears likely that the claimant may have a strong case on both breach of duty and causation, MPS may seek the opinion of a quantum expert to assist in determining the size.
Robert A Morris
Full Text Available Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.
Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins
Duval, Beverly K.; Main, Linda
Describes expert systems and discusses their use in libraries. Highlights include parts of an expert system; expert system shells; an example of how to build an expert system; a bibliography of 34 sources of information on expert systems in libraries; and a list of 10 expert system shells used in libraries. (Contains five references.) (LRW)
DeShaw, Dana; Mullin, Joan; DeCiccio, Albert C.
Presents an annotated bibliography tracing 20 years of "Writing Center Journal" scholarship covering a variety of issues which include teacher training, critical thinking, writing apprehension, peer tutoring, Internet sources and individual instruction. Contains annotations of all the articles and reviews published in this journal's…
The purpose of the IAEA Safety Review Mission was to review the safety aspects of the Kozloduy 5/6 modernization programme, and to advise on the completeness and adequacy of the safety improvements proposed. The IAEA draft report ''Ranking of Safety Issues for WWER-1000 Model 320 NPPs'', WWER-SC-104, 1995-05-29 (referred to as the Issue Book in the subsequent text) was the basis for the experts' review. The IAEA NUSS standards and guides, and internationally accepted safety concepts and practices and national standards, complemented by the Russian safety rules in force, were used in the preparation of the issue book. The scope of the review covered the plant design and operational safety aspects as proposed in the modernization programme. The upgrading measures, which are only related to the improvement of plant availability, were not included in the review
Torkamani, Ali; Scott-Van Zeeland, Ashley A; Topol, Eric J; Schork, Nicholas J
Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. Copyright © 2011 Elsevier Inc. All rights reserved.
Torkamani, Ali; Scott-Van Zeeland, Ashley A.; Topol, Eric J.; Schork, Nicholas J.
Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for doing so. It is arguable that, in the foreseeable future, DNA sequencing of individual genomes will become routine for clinical, research, forensic, and personal purposes. We therefore also consider directions and areas for further research in annotating genomic variants. PMID:21839162
Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)
The following annotated bibliography was developed as part of the geospatial algorithm verification and validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Verification and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following five topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models. Many other papers were studied during the course of the investigation including. The annotations for these articles can be found in the paper "On the verification and validation of geospatial image analysis algorithms".
Minnesota Univ., Minneapolis. National Center for Youth with Disabilities.
This Spanish-language annotated bibliography describes English-language resources covering a wide range of issues related to disabled youth and their families. The 38 bibliographic citations date from 1980 to 1989 and are grouped into the following categories: psychosocial issues, health issues, educational issues, and community living.…
Bishop, Wendy; And Others
Focusing on pedagogical issues in creative writing, this annotated bibliography reviews 149 books, articles, and dissertations in the fields of creative writing and composition, and, selectively, feminist and literary theory. Anthologies of original writing and reference books are not included. (MM)
Richard Eugene Frye
Full Text Available Despite the fact that seizures are commonly associated with autism spectrum disorder (ASD, the effectiveness of treatments for seizures has not been well studied in individuals with ASD. This manuscript reviews both traditional and novel treatments for seizures associated with ASD. Studies were selected by systematically searching major electronic databases and by a panel of experts that treat ASD individuals. Only a few anti-epileptic drugs (AEDs have undergone carefully controlled trials in ASD, but these trials examined outcomes other than seizures. Several lines of evidence point to valproate, lamotrigine and levetiracetam as the most effective and tolerable AEDs for individuals with ASD. Limited evidence supports the use of traditional non-AED treatments, such as the ketogenic and modified Atkins diet, multiple subpial transections and immunomodulation and neurofeedback treatments. Although specific treatments may be more appropriate for specific genetic and metabolic syndromes associated with ASD and seizures, there are few studies which have documented the effectiveness of treatments for seizures for specific syndromes. Limited evidence supports L-carnitine, multivitamins and N-acetyl-L-cysteine in mitochondrial disease and dysfunction, folinic acid in cerebral folate abnormalities and early treatment with vigabatrin in tuberous sclerosis complex. Finally, there is limited evidence for a number of novel treatments, particularly magnesium with pyridoxine, omega-3 fatty acids, the gluten-free casein-free diet and transcranial magnetic simulation. Zinc and L-carnosine are potential novel treatments supported by basic research but not clinical studies. This review demonstrates the wide variety of treatments used to treat seizures in individuals with ASD as well as the striking lack of clinical trials performed to support the use these treatments. Additional studies concerning these treatments for controlling seizures in individuals with ASD
Buttner, Svenja; Pijl, Sip Jan; Bijstra, Jan; van den Bosch, Els
Teaching students with behavioural problems is a challenge for many teachers but other teachers are able to bring out the best in these students. Much research has been done to find out what differentiates expert teachers from their less skilled colleagues. Recent evidence points to personality as an underlying core factor influencing teacher…
... candidates themselves, and background information independently gathered by the SAB Staff Office. Selection... ENVIRONMENTAL PROTECTION AGENCY [FRL-9230-7] Science Advisory Board Staff Office; Request for... Science Advisory Board (SAB) Staff Office is requesting public nominations for technical experts to form...
Franke, K.Y.; Guyon, I.; Schomaker, L.R.B.; Vuurpijl, L.G.
WANDAML is an XML-based markup language for the annotation and filter journaling of digital documents. It addresses in particular the needs of forensic handwriting data examination, by allowing experts to enter information about writer, material (pen, paper), script and content, and to record chains
Franke, K.; Guyon, I.; Schomaker, L.; Vuurpijl, L.
WANDAML is an XML-based markup language for the annotation and filter journaling of digital documents. It addresses in particular the needs of forensic handwriting data examination, by allowing experts to enter information about writer, material (pen, paper), script and content, and to record chains
Reidsma, Dennis; Heylen, Dirk K.J.; Ordelman, Roeland J.F.
We present the results of two trials testing procedures for the annotation of emotion and mental state of the AMI corpus. The first procedure is an adaptation of the FeelTrace method, focusing on a continuous labelling of emotion dimensions. The second method is centered around more discrete
Martinez Alonso, Hector
Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...
Su, Addison Y. S.; Huang, Chester S. J.; Yang, Stephen J. H.; Ding, T. J.; Hsieh, Y. Z.
In Taiwan elementary schools, Scratch programming has been taught for more than four years. Previous studies have shown that personal annotations is a useful learning method that improve learning performance. An annotation-based Scratch programming (ASP) system provides for the creation, share, and review of annotations and homework solutions in…
Dunand, R.; Gondran, M.; Thomas, J.B.
The concepts and the steps to be taken into account for applying expert systems are reviewed. The role of expert systems as a new computer programming concept and the gain in productivity, flexibility and reliability by applying a programming methodology are underlined. The main components of the methodology applied are explained and illustrated. The application of expert systems in the design and operation of the nuclear power plants is presented. The experience acquired and the perspectives in the use of expert systems are discussed [fr
STRING 2008 hold at CERN -- the largest and most important conference on String Theory with the mostly active researchers in the field. The main purpose of the conference is to review the latest developments for experts.
STRING 2008 hold at CERN -- the largest and most important conference on String Theory with the mostly active researchers in the field. The main purpose of the conference is to review the latest developments for experts.
Roberts, Randy S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pope, Paul A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jiang, Ming [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Trucano, Timothy G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aragon, Cecilia R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ni, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wei, Thomas [Argonne National Lab. (ANL), Argonne, IL (United States); Chilton, Lawrence K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bakel, Alan [Argonne National Lab. (ANL), Argonne, IL (United States)
The following annotated bibliography was developed as part of the Geospatial Algorithm Veri cation and Validation (GSV) project for the Simulation, Algorithms and Modeling program of NA-22. Veri cation and Validation of geospatial image analysis algorithms covers a wide range of technologies. Papers in the bibliography are thus organized into the following ve topic areas: Image processing and analysis, usability and validation of geospatial image analysis algorithms, image distance measures, scene modeling and image rendering, and transportation simulation models.
In this work we study the task of image annotation, of which the goal is to describe an image using a few tags. Instead of predicting the full list of tags, here we target for providing a short list of tags under a limited number (e.g., 3), to cover as much information as possible of the image. The tags in such a short list should be representative and diverse. It means they are required to be not only corresponding to the contents of the image, but also be different to each other. To this end, we treat the image annotation as a subset selection problem based on the conditional determinantal point process (DPP) model, which formulates the representation and diversity jointly. We further explore the semantic hierarchy and synonyms among the candidate tags, and require that two tags in a semantic hierarchy or in a pair of synonyms should not be selected simultaneously. This requirement is then embedded into the sampling algorithm according to the learned conditional DPP model. Besides, we find that traditional metrics for image annotation (e.g., precision, recall and F1 score) only consider the representation, but ignore the diversity. Thus we propose new metrics to evaluate the quality of the selected subset (i.e., the tag list), based on the semantic hierarchy and synonyms. Human study through Amazon Mechanical Turk verifies that the proposed metrics are more close to the humans judgment than traditional metrics. Experiments on two benchmark datasets show that the proposed method can produce more representative and diverse tags, compared with existing image annotation methods.
Chakrabarti, Chayan; Jones, Thomas B; Luger, George F; Xu, Jiawei F; Turner, Matthew D; Laird, Angela R; Turner, Jessica A
Ontologies encode relationships within a domain in robust data structures that can be used to annotate data objects, including scientific papers, in ways that ease tasks such as search and meta-analysis. However, the annotation process requires significant time and effort when performed by humans. Text mining algorithms can facilitate this process, but they render an analysis mainly based upon keyword, synonym and semantic matching. They do not leverage information embedded in an ontology's structure. We present a probabilistic framework that facilitates the automatic annotation of literature by indirectly modeling the restrictions among the different classes in the ontology. Our research focuses on annotating human functional neuroimaging literature within the Cognitive Paradigm Ontology (CogPO). We use an approach that combines the stochastic simplicity of naïve Bayes with the formal transparency of decision trees. Our data structure is easily modifiable to reflect changing domain knowledge. We compare our results across naïve Bayes, Bayesian Decision Trees, and Constrained Decision Tree classifiers that keep a human expert in the loop, in terms of the quality measure of the F1-mirco score. Unlike traditional text mining algorithms, our framework can model the knowledge encoded by the dependencies in an ontology, albeit indirectly. We successfully exploit the fact that CogPO has explicitly stated restrictions, and implicit dependencies in the form of patterns in the expert curated annotations.
Neves, Mariana; Leser, Ulf
New approaches to biomedical text mining crucially depend on the existence of comprehensive annotated corpora. Such corpora, commonly called gold standards, are important for learning patterns or models during the training phase, for evaluating and comparing the performance of algorithms and also for better understanding the information sought for by means of examples. Gold standards depend on human understanding and manual annotation of natural language text. This process is very time-consuming and expensive because it requires high intellectual effort from domain experts. Accordingly, the lack of gold standards is considered as one of the main bottlenecks for developing novel text mining methods. This situation led the development of tools that support humans in annotating texts. Such tools should be intuitive to use, should support a range of different input formats, should include visualization of annotated texts and should generate an easy-to-parse output format. Today, a range of tools which implement some of these functionalities are available. In this survey, we present a comprehensive survey of tools for supporting annotation of biomedical texts. Altogether, we considered almost 30 tools, 13 of which were selected for an in-depth comparison. The comparison was performed using predefined criteria and was accompanied by hands-on experiences whenever possible. Our survey shows that current tools can support many of the tasks in biomedical text annotation in a satisfying manner, but also that no tool can be considered as a true comprehensive solution.
Winstanley, Trevor; Courvalin, Patrice
This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the "big three": Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically.
Andrade, M A; Brown, N P; Leroy, C; Hoersch, S; de Daruvar, A; Reich, C; Franchini, A; Tamames, J; Valencia, A; Ouzounis, C; Sander, C
Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming. We present here an automatic system for preliminary functional annotation of protein sequences that has been applied to the analysis of sets of sequences from complete genomes, both to refine overall performance and to make new discoveries comparable to those made by human experts. The GeneQuiz system includes a Web-based browser that allows examination of the evidence leading to an automatic annotation and offers additional information, views of the results, and links to biological databases that complement the automatic analysis. System structure and operating principles concerning the use of multiple sequence databases, underlying sequence analysis tools, lexical analyses of database annotations and decision criteria for functional assignments are detailed. The system makes automatic quality assessments of results based on prior experience with the underlying sequence analysis tools; overall error rates in functional assignment are estimated at 2.5-5% for cases annotated with highest reliability ('clear' cases). Sources of over-interpretation of results are discussed with proposals for improvement. A conservative definition for reporting 'new findings' that takes account of database maturity is presented along with examples of possible kinds of discoveries (new function, family and superfamily) made by the system. System performance in relation to sequence database coverage, database dynamics and database search methods is analysed, demonstrating the inherent advantages of an integrated automatic approach using multiple databases and search methods applied in an objective and repeatable manner. The GeneQuiz system
Hartung, Thomas; Blaauboer, Bas J; Bosgra, Sieto; Carney, Edward; Coenen, Joachim; Conolly, Rory B; Corsini, Emanuela; Green, Sidney; Faustman, Elaine M; Gaspari, Anthony; Hayashi, Makoto; Wallace Hayes, A; Hengstler, Jan G; Knudsen, Lisbeth E; Knudsen, Thomas B; McKim, James M; Pfaller, Walter; Roggen, Erwin L
The European cosmetics legislation foresees a review in 2011 and possible postponement of the 2013 marketing ban to enforce the testing ban for systemic and repeated-dose animal tests. For this purpose, a 119-page report commissioned by the European Commission was published recently. Here, a group of 17 independent experts from the US, Europe, and Japan was brought together to evaluate the report. The expert panel strongly endorsed the report and its conclusions. A number of important options not considered were identified; these do not, however, affect the overall conclusions regarding the current lack of availability of a full replacement, especially for the areas of repeated dose toxicity, carcinogenicity testing, and reproductive toxicity, though a roadmap for change is emerging. However, some of these options may provide adequate data for replacement of some animal studies in the near future pending validation. Various recommendations expand the original report. The reviewers agree with the report that there is greater promise in the short term for the areas of sensitization and toxicokinetics. Additional opportunities lie in more global collaborations and the inclusion of other industry sectors.
McClellan, Molly A; Karumur, Raghav Pavan; Vogel, Rachel Isaksson; Petzel, Sue V; Cragg, Julie; Chan, Daniel; Jacko, Julie A; Sainfort, François; Geller, Melissa A
A broad-based research team developed a Health Insurance Portability and Accountability Act (HIPAA)-compliant educational website for women with ovarian cancer to improve the quality of supportive oncology care. Prior to a randomized clinical trial of the website, initial usability testing was implemented to evaluate the website. The initial review found that 165/247 checklist items had sufficient information to allow for evaluation with the website achieving an overall score of 63%. By category, lowest scores were for the Home Page, Task Orientation, Page Layout & Visual Design, and Help, Feedback & Error Tolerance. Major issues thought to potentially impede actual usage were prioritized in redevelopment and the second usability review, conducted by the same expert, saw an improvement in scores. Incorporating usability concepts from the start of development, fulfilling the positive expectations of end-users and identifying technical and personal factors that optimize use may greatly enhance usage of health websites.
Stoll, W.; Becker, K.
In an expert opinion written by Professor H. Kuni, Marburg, for the North Rhine-Westphalian state government, plutonium is called by far the most dangerous element in the Periodic Table. The Marburg medical expert holds that even improved legal instruments are unable to warrant effective protection of the workers handling this material, in the light of the present standards of industrial safety, because of radiological conditions and measuring problems with plutonium isotopes. In this article by an internationally renowned expert in the field, the ideas expressed in the expert opinion about the toxicity of plutonium, the cause-and-effect relationship in radiation damage by plutonium, and recent findings about the toxicity are subjected to a critical review. On the basis of results of radiation protection and of case studies, the statements in the expert opinion are contrasted with facts which make them appear in a very different light. (orig./RB) [de
Uziel, M.S.; Hannon, E.H.
This bibliography of 655 annotated references on impingement of aquatic organisms at intake structures of thermal-power-plant cooling systems was compiled from the published and unpublished literature. The bibliography includes references from 1928 to 1978 on impingement monitoring programs; impingement impact assessment; applicable law; location and design of intake structures, screens, louvers, and other barriers; fish behavior and swim speed as related to impingement susceptibility; and the effects of light, sound, bubbles, currents, and temperature on fish behavior. References are arranged alphabetically by author or corporate author. Indexes are provided for author, keywords, subject category, geographic location, taxon, and title
Hochheiser, Harry; Ning, Yifan; Hernandez, Andres; Horn, John R; Jacobson, Rebecca; Boyce, Richard D
Because vital details of potential pharmacokinetic drug-drug interactions are often described in free-text structured product labels, manual curation is a necessary but expensive step in the development of electronic drug-drug interaction information resources. The use of nonexperts to annotate potential drug-drug interaction (PDDI) mentions in drug product label annotation may be a means of lessening the burden of manual curation. Our goal was to explore the practicality of using nonexpert participants to annotate drug-drug interaction descriptions from structured product labels. By presenting annotation tasks to both pharmacy experts and relatively naïve participants, we hoped to demonstrate the feasibility of using nonexpert annotators for drug-drug information annotation. We were also interested in exploring whether and to what extent natural language processing (NLP) preannotation helped improve task completion time, accuracy, and subjective satisfaction. Two experts and 4 nonexperts were asked to annotate 208 structured product label sections under 4 conditions completed sequentially: (1) no NLP assistance, (2) preannotation of drug mentions, (3) preannotation of drug mentions and PDDIs, and (4) a repeat of the no-annotation condition. Results were evaluated within the 2 groups and relative to an existing gold standard. Participants were asked to provide reports on the time required to complete tasks and their perceptions of task difficulty. One of the experts and 3 of the nonexperts completed all tasks. Annotation results from the nonexpert group were relatively strong in every scenario and better than the performance of the NLP pipeline. The expert and 2 of the nonexperts were able to complete most tasks in less than 3 hours. Usability perceptions were generally positive (3.67 for expert, mean of 3.33 for nonexperts). The results suggest that nonexpert annotation might be a feasible option for comprehensive labeling of annotated PDDIs across a broader
Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier
High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty...
Brooks, H. M.
Explores what an intelligent information retrieval system involves and why expert system techniques might interest system designers. Expert systems research is reviewed with emphasis on components, architecture, and computer interaction, and it is concluded that information retrieval is not an ideal problem domain for expert system application at…
Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E
It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.
Full Text Available OBJECTIVE: To systematically review the literature on image-based telemedicine for medical expert consultation in acute care of injuries, considering system, user, and clinical aspects. DESIGN: Systematic review of peer-reviewed journal articles. DATA SOURCES: Searches of five databases and in eligible articles, relevant reviews, and specialized peer-reviewed journals. ELIGIBILITY CRITERIA: Studies were included that covered teleconsultation systems based on image capture and transfer with the objective of seeking medical expertise for the diagnostic and treatment of acute injury care and that presented the evaluation of one or several aspects of the system based on empirical data. Studies of systems not under routine practice or including real-time interactive video conferencing were excluded. METHOD: The procedures used in this review followed the PRISMA Statement. Predefined criteria were used for the assessment of the risk of bias. The DeLone and McLean Information System Success Model was used as a framework to synthesise the results according to system quality, user satisfaction, information quality and net benefits. All data extractions were done by at least two reviewers independently. RESULTS: Out of 331 articles, 24 were found eligible. Diagnostic validity and management outcomes were often studied; fewer studies focused on system quality and user satisfaction. Most systems were evaluated at a feasibility stage or during small-scale pilot testing. Although the results of the evaluations were generally positive, biases in the methodology of evaluation were concerning selection, performance and exclusion. Gold standards and statistical tests were not always used when assessing diagnostic validity and patient management. CONCLUSIONS: Image-based telemedicine systems for injury emergency care tend to support valid diagnosis and influence patient management. The evidence relates to a few clinical fields, and has substantial methodological
Hasselberg, Marie; Beer, Netta; Blom, Lisa; Wallis, Lee A; Laflamme, Lucie
To systematically review the literature on image-based telemedicine for medical expert consultation in acute care of injuries, considering system, user, and clinical aspects. Systematic review of peer-reviewed journal articles. Searches of five databases and in eligible articles, relevant reviews, and specialized peer-reviewed journals. Studies were included that covered teleconsultation systems based on image capture and transfer with the objective of seeking medical expertise for the diagnostic and treatment of acute injury care and that presented the evaluation of one or several aspects of the system based on empirical data. Studies of systems not under routine practice or including real-time interactive video conferencing were excluded. The procedures used in this review followed the PRISMA Statement. Predefined criteria were used for the assessment of the risk of bias. The DeLone and McLean Information System Success Model was used as a framework to synthesise the results according to system quality, user satisfaction, information quality and net benefits. All data extractions were done by at least two reviewers independently. Out of 331 articles, 24 were found eligible. Diagnostic validity and management outcomes were often studied; fewer studies focused on system quality and user satisfaction. Most systems were evaluated at a feasibility stage or during small-scale pilot testing. Although the results of the evaluations were generally positive, biases in the methodology of evaluation were concerning selection, performance and exclusion. Gold standards and statistical tests were not always used when assessing diagnostic validity and patient management. Image-based telemedicine systems for injury emergency care tend to support valid diagnosis and influence patient management. The evidence relates to a few clinical fields, and has substantial methodological shortcomings. As in the case of telemedicine in general, user and system quality aspects are poorly
Rifkin, William D.
Presented is a course that applies concepts from sociology, anthropology, linguistics, and social studies of science to the question of expert status. Included are major concepts to be covered, suggested readings and annotated bibliography, and possible class exercises. (KR)
Lorincz, Attila; Raison, Claire
Interview with Attila Lorincz by Claire Raison (Commissioning Editor) To mark the beginning of the 15th year of Expert Review of Molecular Diagnostics, the journal's Editor-in-Chief shares his expert knowledge on translational diagnostics, his opinion on recent controversies and his predictions for molecular diagnostics in 2015 and beyond. Attila Lorincz received his doctorate from Trinity College, Dublin, Republic of Ireland, and went on to become a research fellow at the University of California, Santa Barbara, CA, USA. During Professor Lorincz's research on human papillomavirus (HPV), he found several important and novel carcinogenic HPV types and pioneered the use of HPV DNA testing for clinical diagnostics. In 1988, Professor Lorincz's team produced the first HPV test to be FDA-approved for patients and in 2003, for general population cervical precancer screening. Now Professor of Molecular Epidemiology at the Centre for Cancer Prevention, Queen Mary University of London, UK, he and his team are furthering translational research into DNA methylation assays for cancer risk prediction.
Discusses: (1) the architecture of expert systems; (2) features that distinguish expert systems from conventional programs; (3) conditions necessary to select a particular application for the development of successful expert systems; (4) issues to be resolved when building expert systems; and (5) limitations. Examples of selected expert systems…
Boot, P.; Haentjens Dekker, R.
Annotation in digital scholarly editions (of historical documents, literary works, letters, etc.) has long been recognized as an important desideratum, but has also proven to be an elusive ideal. In so far as annotation functionality is available, it is usually developed for a single edition and
Boot, P.; Boot, P.; Stronks, E.
From the introduction: Annotation is an important item on the wish list for digital scholarly tools. It is one of John Unsworth’s primitives of scholarship (Unsworth 2000). Especially in linguistics,a number of tools have been developed that facilitate the creation of annotations to source material
Final report of the Cosmetic Ingredient Review Expert Panel safety assessment of polymethyl methacrylate (PMMA), methyl methacrylate crosspolymer, and methyl methacrylate/glycol dimethacrylate crosspolymer.
Becker, Lillian C; Bergfeld, Wilma F; Belsito, Donald V; Hill, Ronald A; Klaassen, Curtis D; Liebler, Daniel C; Marks, James G; Shank, Ronald C; Slaga, Thomas J; Snyder, Paul W; Andersen, F Alan
Polymethyl methacrylate (PMMA) and related cosmetic ingredients methyl methacrylate crosspolymer and methyl methacrylate/glycol dimethacrylate crosspolymer are polymers that function as film formers and viscosity-increasing agents in cosmetics. The Food and Drug Administration (FDA) determination of safety of PMMA use in several medical devices, which included human and animal safety data, was used as the basis of safety of PMMA and related polymers in cosmetics by the Cosmetic Ingredient Review (CIR) Expert Panel. The PMMA used in cosmetics is substantially the same as in medical devices. The Panel concluded that these ingredients are safe as cosmetic ingredients in the practices of use and concentrations as described in this safety assessment.
Pesut, Barbara; Greig, Madeleine
Nurses and nursing care providers provide the most direct care to patients at end of life. Yet, evidence indicates that many feel ill-prepared for the complexity of palliative care. To review the resources required to ensure adequate education, training, and mentorship for nurses and nursing care providers who care for Canadians experiencing life-limiting illness and their families. This is a systematic search and narrative review in the Canadian context. Six previous reviews and 26 primary studies were identified. Studies focusing on regulated nurses indicated that even amid variability in content, delivery methods, and duration, palliative education improves nurses' knowledge, confidence, attitudes, and communication abilities, and decreases nurses' stress. Results from palliative education in undergraduate curriculum were less definitive. However, studies on palliative simulation in undergraduate education suggest that it improves knowledge and confidence. Studies focusing on educating nursing care providers, either alone or in collaboration with regulated nurses, indicated positive outcomes in knowledge, confidence, communication, identification of clients who are dying, abilities to interact with patients and families, and a better understanding of their own contributions to care. Curricular resources in Canada have been developed. However, there is no dedicated and funded capacity-building strategy. Resources exist to support palliative education for nurses and nursing care providers. Furthermore, the evidence suggests good outcomes from this education. However, there is no dedicated strategy for implementing those resources. Furthermore, there is little evidence of the critical role of knowledge translation in preparing nurses and nursing care providers for evidence-informed palliative practice.
Petit, A; Rozenberg, S; Fassier, J B; Rousseau, S; Mairiaux, P; Roquelaure, Y
The pre-return-to-work medical consultation during sick leave for low back pain (LBP) aims at assessing the worker's ability to resume working without risk for his/her health, and anticipating any difficulties inherent to returning to work and job retention. This article summarizes the good practices guidelines proposed by the French Society of Occupational Medicine (SFMT) and the French National Health Authority (HAS), and published in October 2013. Good practices guidelines developed by a multidisciplinary and independent task force (24 experts) and peer review committee (50 experts) based on a literature review from 1990 to 2012, according to the HAS methodology. According to the labour regulations, workers can request a medical consultation with their occupational physician at any time. The pre-return-to-work consultation precedes the effective return-to-work and can be requested by the employee regardless of their sick leave duration. It must be scheduled early enough to: (i) deliver reassuring information regarding risks to the lower back and managing LBP; (ii) evaluate prognostic factors of chronicity and prolonged disability in relations to LBP and its physical, social and occupational consequences in order to implement the necessary conditions for returning to work; (iii) support and promote staying at work by taking into account all medical, social and occupational aspects of the situation and ensure proper coordination between the different actors. A better understanding of the pre-return-to-work consultation would improve collaboration and coordination of actions to facilitate resuming work and job retention for patients with LBP. Copyright © 2015 Elsevier Masson SAS. All rights reserved.
Full Text Available The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation.
Pesch, Robert; Lysenko, Artem; Hindle, Matthew; Hassani-Pak, Keywan; Thiele, Ralf; Rawlings, Christopher; Köhler, Jacob; Taubert, Jan
The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara-Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.
Sagar, Budhi; Devillers, C.; Smith, Paul; Laliuex, P.; Pescatore, C.
The recently completed SITE-94 project is an SKI effort directed at building competence and capacity in the assessment of safety of a spent-fuel geologic repository. Emphasis is given to the assimilation of site-specific data, with its associated uncertainties, into the performance assessment. Specific attention is also given to improving the understanding of mechanisms that might compromise canister integrity. This report represents the common views of an International Review Team (IRT) established by the NEA Secretariat, at the request of SKI, to perform a peer review of SITE-94. The basis for the report is the understanding of SITE-94 and its background obtained by IRT in the course of several months of study of SITE-94 documentation, internal discussions and a meeting with SKI in Stockholm. The report is limited to the main findings of IRT. The intended audience of the report is the staff of SKI and, accordingly, the style of the report is suited to a technical audience familiar with the contents of the SITE-94 project
This article briefly discusses the role of the expert physician witness at trial and describes what is emerging as the physician professional witness (AKA hired gun). The trial court's powers to evaluate the professionalism and objectivity of an expert witness are examined in light of a recent Western District Missouri Court of Appeals case. This case, while limited to its peculiar set of facts, permitted both a hearing and production of documents of a physician who had been hired to testify. This article reviews the role of the expert physician witness in Missouri litigation in light of recent caselaw outlining discovery procedures to monitor use of professional witnesses. The term "professional witness" does not refer to witnesses who are professionals, but rather to persons who make their entire living witnessing. The Missouri Court of Appeals ruling in State ex rel. Lichtor v. Clark, 845 S.W.2d (Mo.App. W.D. 1992) elucidates the Missouri Courts' authority in sorting out unprofessional physicians who would offer unobjective expert testimony. While this particular article is intended for medical readership and discusses expert physician witnesses, expert witnesses can come from any profession including engineering, accounting, nursing, etc. It might thus be assumed that the Lichtor Court's procedure may be applied to any expert whose objectivity has been put into question.
The terms of reference of the committee were to review the published scientific literature and other relevant scientific data on the short and long-term effects of fallout arising from British nuclear tests in Australia; to comment on the adequacy of the data available and the collection methodology; to assess the fallout levels arising from each of the tests, the immediate and subsequent hazards from the fallout to the Australian population and individual Australians, including Australian personnel involved and aborigines in South Australia, and the adequacy of the criteria for safe firing of each of the tests. A comparison is made of radiation protection standards adopted during the nuclear test period with current standards. The recommendations include the setting up of a public inquiry to determine how the conduct and consequences of the British nuclear tests affected the health and well-being of Australians
Eriksson, Leif G.
On the 18th of May 1998, based on the information provided by the United Sates Department of Energy (DOE) in support of the 1996 Waste Isolation Pilot Plant (WIPP) Compliance Certification Application, the U.S. Environmental Protection Agency certified the proposed deep geological repository for disposal of long-lived, defense-generated, transuranic radioactive waste at the WIPP site in New Mexico, United States of America, was compliant with all applicable radioactive waste disposal regulations. Seven domestic and one joint international peer reviews commissioned by the DOE were instrumental in making complex scientific and engineering information, as well as the related WIPP decision-making process, both credible and transparent to the majority of affected and interested parties and, ultimately, to the regulator
Zingg, Walter; Holmes, Alison; Dettenkofer, Markus; Goetting, Tim; Secci, Federica; Clack, Lauren; Allegranzi, Benedetta; Magiorakos, Anna-Pelagia; Pittet, Didier
Despite control efforts, the burden of health-care-associated infections in Europe is high and leads to around 37,000 deaths each year. We did a systematic review to identify crucial elements for the organisation of effective infection-prevention programmes in hospitals and key components for implementation of monitoring. 92 studies published from 1996 to 2012 were assessed and ten key components identified: organisation of infection control at the hospital level; bed occupancy, staffing, workload, and employment of pool or agency nurses; availability of and ease of access to materials and equipment and optimum ergonomics; appropriate use of guidelines; education and training; auditing; surveillance and feedback; multimodal and multidisciplinary prevention programmes that include behavioural change; engagement of champions; and positive organisational culture. These components comprise manageable and widely applicable ways to reduce health-care-associated infections and improve patients' safety. Copyright © 2015 Elsevier Ltd. All rights reserved.
Guignon, Valentin; Droc, Gaëtan; Alaux, Michael; Baurens, Franc-Christophe; Garsmeur, Olivier; Poiron, Claire; Carver, Tim; Rouard, Mathieu; Bocs, Stéphanie
We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl. The Chado Controller package is available for download at http://www.gnpannot.org/content/chado-controller and runs on any Unix-like operating system, and documentation is available at http://www.gnpannot.org/content/chado-controller-doc The system can be tested using the GNPAnnot Sandbox at http://www.gnpannot.org/content/gnpannot-sandbox-form email@example.com; firstname.lastname@example.org Supplementary data are available at Bioinformatics online.
Keugoung, Basile; Fouelifack, Florent Ymele; Fotsing, Richard; Macq, Jean; Meli, Jean; Criel, Bart
In sub-Saharan Africa, HIV/AIDS and tuberculosis are major public health problems. In 2010, 64% of the 34 million of people infected with HIV were reported to be living in sub-Saharan Africa. Only 41% of eligible HIV-positive people had access to antiretroviral therapy (ART). Regarding tuberculosis, in 2010, the region had 12% of the world's population but reported 26% of the 8.8 million incident cases and 254000 tuberculosis-related deaths. This paper aims to review missed opportunities for improving HIV/AIDS and tuberculosis prevention and care. We conducted a systematic review in PubMed using the terms 'missed'(Title) AND 'opportunities'(Title). We included systematic review and original research articles done in sub-Saharan Africa on missed opportunities in HIV/AIDS and/or tuberculosis care. Missed opportunities for improving HIV/AIDS and/or tuberculosis care can be classified into five categories: i) patient and community; ii) health professional; iii) health facility; iv) local health system; and v) vertical programme (HIV/AIDS and/or tuberculosis control programmes). None of the reviewed studies identified any missed opportunities related to health system strengthening. Opportunities that are missed hamper tuberculosis and/or HIV/AIDS care in sub-Saharan Africa where health systems remain weak. What is still missing in the analysis of health experts is the acknowledgement that opportunities that are missed to strengthen health systems also undermine tuberculosis and HIV/AIDS prevention and care. Studying why these opportunities are missed will help to understand the rationales behind the missed opportunities, and customize adequate strategies to seize them and for effective diseases control.
Voorink-Moret, M; Goorden, S M I; van Kuilenburg, A B P; Wijburg, F A; Ghauharali-van der Vlugt, J M M; Beers-Stet, F S; Zoetekouw, A; Kulik, W; Hollak, C E M; Vaz, F M
In patients suspected of a lipid storage disorder (sphingolipidoses, lipidoses), confirmation of the diagnosis relies predominantly on the measurement of specific enzymatic activities and genetic studies. New UPLC-MS/MS methods have been developed to measure lysosphingolipids and oxysterols, which, combined with chitotriosidase activity may represent a rapid first tier screening for lipid storage disorders. A lysosphingolipid panel consisting of lysoglobotriaosylceramide (LysoGb3), lysohexosylceramide (LysoHexCer: both lysoglucosylceramide and lysogalactosylceramide), lysosphingomyelin (LysoSM) and its carboxylated analogue lysosphingomyelin-509 (LysoSM-509) was measured in control subjects and plasma samples of predominantly untreated patients affected with lipid storage disorders (n=74). In addition, the oxysterols cholestane-3β,5α,6β-triol and 7-ketocholesterol were measured in a subset of these patients (n=36) as well as chitotriosidase activity (n=43). A systematic review of the literature was performed to assess the usefulness of these biochemical markers. Specific elevations of metabolites, i.e. without overlap between controls and other lipid storage disorders, were found for several lysosomal storage diseases: increased LysoSM levels in acid sphingomyelinase deficiency (Niemann-Pick disease type A/B), LysoGb3 levels in males with classical phenotype Fabry disease and LysoHexCer (i.e. lysoglucosylceramide/lysogalactosylceramide) in Gaucher and Krabbe diseases. While elevated levels of LysoSM-509 and cholestane-3β,5α,6β-triol did not discriminate between Niemann Pick disease type C and acid sphingomyelinase deficiency, LysoSM-509/LysoSM ratio was specifically elevated in Niemann-Pick disease type C. In Gaucher disease type I, mild increases in several lysosphingolipids were found including LysoGb3 with levels in the range of non-classical Fabry males and females. Chitotriosidase showed specific elevations in symptomatic Gaucher disease, and was mildly
Kahrilas, Peter J; Katzka, David; Richter, Joel E
The purpose of this review is to describe a place for per-oral endoscopic myotomy (POEM) among the currently available robust treatments for achalasia. The recommendations outlined in this review are based on expert opinion and on relevant publications from PubMed and EMbase. The Clinical Practice Updates Committee of the American Gastroenterological Association proposes the following recommendations: 1) in determining the need for achalasia therapy, patient-specific parameters (Chicago Classification subtype, comorbidities, early vs late disease, primary or secondary causes) should be considered along with published efficacy data; 2) given the complexity of this procedure, POEM should be performed by experienced physicians in high-volume centers because an estimated 20-40 procedures are needed to achieve competence; 3) if the expertise is available, POEM should be considered as primary therapy for type III achalasia; 4) if the expertise is available, POEM should be considered as treatment option comparable with laparoscopic Heller myotomy for any of the achalasia syndromes; and 5) post-POEM patients should be considered high risk to develop reflux esophagitis and advised of the management considerations (potential indefinite proton pump inhibitor therapy and/or surveillance endoscopy) of this before undergoing the procedure. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.
Ketelaar, P. E.; Willemsen, L. M.; Sleven, L.; Kerkhof, P.
This study aims to shed more light on the question whether, and under what circumstances, valence affects consumers' intention to buy a product after reading an online review. We hypothesize that receiver expertise could possibly moderate (a) the impact of review valence on consumers' purchase
Ketelaar, P.E.; Willemsen, L.M.; Sleven, L.; Kerkhof, P.
This study aims to shed more light on the question whether, and under what circumstances, valence affects consumers' intention to buy a product after reading an online review. We hypothesize that receiver expertise could possibly moderate (a) the impact of review valence on consumers' purchase
Situmeang, F.B.I.; Leenders, M.A.A.M.; Wijnberg, N.M.
Product reviews are assumed to be based on the observable characteristics of the underlying product. However, in the case of new editions in a product series, the determinants may include signals that originate from the reviews and the sales of editions that precede the focal product edition. Our
Johannsen, J.; Macallister, J.; Michalek, T.; Ross, S.
Various authors have pointed out that humans can become quite adept at deriving phonetic transcriptions from speech spectrograms (as good as 90percent accuracy at the phoneme level). The authors describe an expert system which attempts to simulate this performance. The speech spectrogram expert (spex) is actually a society made up of three experts: a 2-dimensional vision expert, an acoustic-phonetic expert, and a phonetics expert. The visual reasoning expert finds important visual features of the spectrogram. The acoustic-phonetic expert reasons about how visual features relates to phonemes, and about how phonemes change visually in different contexts. The phonetics expert reasons about allowable phoneme sequences and transformations, and deduces an english spelling for phoneme strings. The speech spectrogram expert is highly interactive, allowing users to investigate hypotheses and edit rules. 10 references.
Mantry, Parvez S; Pathak, Lakshmikant
Hepatitis C virus (HCV) affects nearly 1.3% of US population and around 2% of people worldwide. It is associated with serious complication of Cirrhosis and Hepatocellular carcinoma leading to significant morbidity and mortality. Until now the only treatment option for this serious disease was interferon based therapy which had poor tolerance and at best SVR (Sustained virological response) in only 50% of cases. With the introduction of other direct - acting antiviral agents the treatment of HCV has been revolutionized with significantly high rates of cure. Among novel Direct acting antivirals are non-nucleoside inhibitor NS5B which is highly effective in treatment of HCV genotype 1 a and 1b including those with compensated cirrhosis achieving high cure rates with SVR more than 97 % in pooled analysis from six different phase 3 trials. This review will discuss the DAA - Dasabuvir, a non - nucleoside NS5B inhibitor, its mechanism of action, efficacy, safety & tolerance, and drug resistance. Dasabuvir is approved by FDA in combination with other DAA agents called as the 3D(Viekira Pak) in various interferon free regimens achieving high cure rates (SVR >95%) with low adverse effects. In Europe, it is approved by European medicines agency for use in combination with Ombitasvir, Paritaprevir, and ritonavir with or without ribavirin. The drug is used in treatment naive as well as previously treated patient with high success rates. It is also approved in patients with compensated cirrhosis, patients with HIV co-infection and liver transplant recipients which were in the past were excluded from treatment with interferon based therapy. Dasabuvir is extensively evaluated in large clinical trials and shown excellent SVR among HCV genotype1 patient population in combination with other oral DAAs, with good safety profile and tolerance. Its drawback is its genotype restriction, need for ribavirin (RBV) for 1a genotype, low resistance barrier and high cost. It is well tolerated
Rissanen, Mikko J; Kume, Naoto; Kuroda, Yoshihiro; Kuroda, Tomohiro; Yoshimura, Koji; Yoshihara, Hiroyuki
Many VR technology based training systems use expert's motion data as the training aid, but would not provide any short-cut to teaching medical skills that do not depend on exact motions. Earlier we presented Annotated Simulation Records (ASRs), which can be used to encapsulate experts' insight on psychomotor skills. Annotations made to behavioural parameters in training simulators enable asynchronous teaching instead of just motion training in a proactive way to the learner. We evaluated ASRs for asynchronous teaching of Digital Rectal Examination (DRE) with 3 urologists and 8 medical students. The ASRs were found more effective than motion-based training with verbal feedback.
O'Brien, Nicola; Heaven, Ben; Teal, Gemma; Evans, Elizabeth H; Cleland, Claire; Moffatt, Suzanne; Sniehotta, Falko F; White, Martin; Mathers, John C
Background Integrating stakeholder involvement in complex health intervention design maximizes acceptability and potential effectiveness. However, there is little methodological guidance about how to integrate evidence systematically from various sources in this process. Scientific evidence derived from different approaches can be difficult to integrate and the problem is compounded when attempting to include diverse, subjective input from stakeholders. Objective The intent of the study was to describe and appraise a systematic, sequential approach to integrate scientific evidence, expert knowledge and experience, and stakeholder involvement in the co-design and development of a complex health intervention. The development of a Web-based lifestyle intervention for people in retirement is used as an example. Methods Evidence from three systematic reviews, qualitative research findings, and expert knowledge was compiled to produce evidence statements (stage 1). Face validity of these statements was assessed by key stakeholders in a co-design workshop resulting in a set of intervention principles (stage 2). These principles were assessed for face validity in a second workshop, resulting in core intervention concepts and hand-drawn prototypes (stage 3). The outputs from stages 1-3 were translated into a design brief and specification (stage 4), which guided the building of a functioning prototype, Web-based intervention (stage 5). This prototype was de-risked resulting in an optimized functioning prototype (stage 6), which was subject to iterative testing and optimization (stage 7), prior to formal pilot evaluation. Results The evidence statements (stage 1) highlighted the effectiveness of physical activity, dietary and social role interventions in retirement; the idiosyncratic nature of retirement and well-being; the value of using specific behavior change techniques including those derived from the Health Action Process Approach; and the need for signposting to local
O'Brien, Nicola; Heaven, Ben; Teal, Gemma; Evans, Elizabeth H; Cleland, Claire; Moffatt, Suzanne; Sniehotta, Falko F; White, Martin; Mathers, John C; Moynihan, Paula
Integrating stakeholder involvement in complex health intervention design maximizes acceptability and potential effectiveness. However, there is little methodological guidance about how to integrate evidence systematically from various sources in this process. Scientific evidence derived from different approaches can be difficult to integrate and the problem is compounded when attempting to include diverse, subjective input from stakeholders. The intent of the study was to describe and appraise a systematic, sequential approach to integrate scientific evidence, expert knowledge and experience, and stakeholder involvement in the co-design and development of a complex health intervention. The development of a Web-based lifestyle intervention for people in retirement is used as an example. Evidence from three systematic reviews, qualitative research findings, and expert knowledge was compiled to produce evidence statements (stage 1). Face validity of these statements was assessed by key stakeholders in a co-design workshop resulting in a set of intervention principles (stage 2). These principles were assessed for face validity in a second workshop, resulting in core intervention concepts and hand-drawn prototypes (stage 3). The outputs from stages 1-3 were translated into a design brief and specification (stage 4), which guided the building of a functioning prototype, Web-based intervention (stage 5). This prototype was de-risked resulting in an optimized functioning prototype (stage 6), which was subject to iterative testing and optimization (stage 7), prior to formal pilot evaluation. The evidence statements (stage 1) highlighted the effectiveness of physical activity, dietary and social role interventions in retirement; the idiosyncratic nature of retirement and well-being; the value of using specific behavior change techniques including those derived from the Health Action Process Approach; and the need for signposting to local resources. The intervention
Michaelis, J.; Zednik, S.; West, P.; Fox, P. A.; McGuinness, D. L.
eScience based systems generate provenance of their data products, related to such things as: data processing, data collection conditions, expert evaluation, and data product quality. Recent advances in web-based technology offer users the possibility of making annotations to both data products and steps in accompanying provenance traces, thereby expanding the utility of such provenance for others. These contributing users may have varying backgrounds, ranging from system experts to outside domain experts to citizen scientists. Furthermore, such users may wish to make varying types of annotations - ranging from documenting the purpose of a provenance step to raising concerns about the quality of data dependencies. Semantic Web technologies allow for such kinds of rich annotations to be made to provenance through the use of ontology vocabularies for (i) organizing provenance, and (ii) organizing user/annotation classifications. Furthermore, through Linked Data practices, Semantic linkages may be made from provenance steps to external data of interest. A desire for Semantically-annotated provenance has been motivated by data management issues in the Mauna Loa Solar Observatory’s (MLSO) Advanced Coronal Observing System (ACOS). In ACOS, photomoeter-based readings are taken of solar activity and subsequently processed into final data products consumable by end users. At intermediate stages of ACOS processing, factors such as evaluations by human experts and weather conditions are logged, which could impact data product quality. If such factors are linked via user-submitted annotations to provenance, it could be significantly beneficial for other users. Likewise, the background of a user could impact the credibility of their annotations. For example, an annotation made by a citizen scientist describing the purpose of a provenance step may not be as reliable as a similar annotation made by an ACOS project member. For this work, we have developed a software package that
Pereira, José L.; Davis, Daniel H.J.; Currow, David C.; Meagher, David; Rabheru, Kiran; Wright, David; Bruera, Eduardo; Hartwick, Michael; Gagnon, Pierre R.; Gagnon, Bruno; Breitbart, William; Regnier, Laura; Lawlor, Peter G.
Context Delirium is a highly prevalent complication in patients in palliative care settings, especially in the end-of-life context. Objectives To review the current evidence base for treating episodes of delirium in palliative care settings and propose a framework for future development. Methods We combined multidisciplinary input from delirium researchers and other purposely selected stakeholders at an international delirium study planning meeting. This was supplemented by a literature search of multiple databases and relevant reference lists to identify studies regarding therapeutic interventions for delirium. Results The context of delirium management in palliative care is highly variable. The standard management of a delirium episode includes the investigation of precipitating and aggravating factors followed by symptomatic treatment with drug therapy. However, the intensity of this management depends on illness trajectory and goals of care in addition to the local availability of both investigative modalities and therapeutic interventions. Pharmacologically, haloperidol remains the practice standard by consensus for symptomatic control. Dosing schedules are derived from expert opinion and various clinical practice guidelines as evidence-based data from palliative care settings are limited. The commonly used pharmacologic interventions for delirium in this population warrant evaluation in clinical trials to examine dosing and titration regimens, different routes of administration, and safety and efficacy compared with placebo. Conclusion Delirium treatment is multidimensional and includes the identification of precipitating and aggravating factors. For symptomatic management, haloperidol remains the practice standard. Further high-quality collaborative research investigating the appropriate treatment of this complex syndrome is needed. PMID:24480529
... Environment Programme (UNEP) and the World Meteorological Organization (WMO) established the IPCC in 1988. In... the following Web sites: http://www.ipcc.ch/organization/organization_review.shtml#.UEY0LqSe7x8 http://ipcc.ch/organization/organization_procedures.shtml . Following an invitation from the UNFCCC to...
Becker, G.K.; Determan, J.C.
Nondestructive assay waste characterization data generated for use in the National TRU Program must be of known and demonstrable quality. Each measurement is required to receive an independent technical review by a qualified expert. An expert system prototype has been developed to automate waste NDA data review of a passive/active neutron drum counter system. The expert system is designed to yield a confidence rating regarding measurement validity. Expert system rules are derived from data in a process involving data clustering, fuzzy logic, and genetic algorithms. Expert system performance is assessed against confidence assignments elicited from waste NDA domain experts. Performance levels varied for the active, passive shielded, and passive system assay modes of the drum counter system, ranging from 78% to 94% correct classifications
Becker, G.K.; Determan, J.C.
Nondestructive assay waste characterization data generated for use in the National TRU Program must be of known and demonstrable quality. Each measurement is required to receive an independent technical review by a qualified expert. An expert system prototype has been developed to automate waste NDA data review of a passive/active neutron drum counter system. The expert system is designed to yield a confidence rating regarding measurement validity. Expert system rules are derived from data in a process involving data clustering, fuzzy logic, and genetic algorithms. Expert system performance is assessed against confidence assignments elicited from waste NDA domain experts. Performance levels varied for the active, passive shielded, and passive system assay modes of the drum counter system, ranging from 78% to 94% correct classifications.
Mao, Qi; Tsang, Ivor Wai-Hung; Gao, Shenghua
Automatic image annotation, which is usually formulated as a multi-label classification problem, is one of the major tools used to enhance the semantic understanding of web images. Many multimedia applications (e.g., tag-based image retrieval) can greatly benefit from image annotation. However, the insufficient performance of image annotation methods prevents these applications from being practical. On the other hand, specific measures are usually designed to evaluate how well one annotation method performs for a specific objective or application, but most image annotation methods do not consider optimization of these measures, so that they are inevitably trapped into suboptimal performance of these objective-specific measures. To address this issue, we first summarize a variety of objective-guided performance measures under a unified representation. Our analysis reveals that macro-averaging measures are very sensitive to infrequent keywords, and hamming measure is easily affected by skewed distributions. We then propose a unified multi-label learning framework, which directly optimizes a variety of objective-specific measures of multi-label learning tasks. Specifically, we first present a multilayer hierarchical structure of learning hypotheses for multi-label problems based on which a variety of loss functions with respect to objective-guided measures are defined. And then, we formulate these loss functions as relaxed surrogate functions and optimize them by structural SVMs. According to the analysis of various measures and the high time complexity of optimizing micro-averaging measures, in this paper, we focus on example-based measures that are tailor-made for image annotation tasks but are seldom explored in the literature. Experiments show consistency with the formal analysis on two widely used multi-label datasets, and demonstrate the superior performance of our proposed method over state-of-the-art baseline methods in terms of example-based measures on four
Higginson, Irene J; Evans, Catherine J; Grande, Gunn; Preston, Nancy; Morgan, Myfanwy; McCrone, Paul; Lewis, Penney; Fayers, Peter; Harding, Richard; Hotopf, Matthew; Murray, Scott A; Benalia, Hamid; Gysels, Marjolein; Farquhar, Morag; Todd, Chris
Despite being a core business of medicine, end of life care (EoLC) is neglected. It is hampered by research that is difficult to conduct with no common standards. We aimed to develop evidence-based guidance on the best methods for the design and conduct of research on EoLC to further knowledge in the field. The Methods Of Researching End of life Care (MORECare) project built on the Medical Research Council guidance on the development and evaluation of complex circumstances. We conducted systematic literature reviews, transparent expert consultations (TEC) involving consensus methods of nominal group and online voting, and stakeholder workshops to identify challenges and best practice in EoLC research, including: participation recruitment, ethics, attrition, integration of mixed methods, complex outcomes and economic evaluation. We synthesised all findings to develop a guidance statement on the best methods to research EoLC. We integrated data from three systematic reviews and five TECs with 133 online responses. We recommend research designs extending beyond randomised trials and encompassing mixed methods. Patients and families value participation in research, and consumer or patient collaboration in developing studies can resolve some ethical concerns. It is ethically desirable to offer patients and families the opportunity to participate in research. Outcome measures should be short, responsive to change and ideally used for both clinical practice and research. Attrition should be anticipated in studies and may affirm inclusion of the relevant population, but careful reporting is necessitated using a new classification. Eventual implementation requires consideration at all stages of the project. The MORECare statement provides 36 best practice solutions for research evaluating services and treatments in EoLC to improve study quality and set the standard for future research. The statement may be used alongside existing statements and provides a first step in
Angelis, Aris; Lange, Ansgar; Kanavos, Panos
Although health technology assessment (HTA) systems base their decision making process either on economic evaluations or comparative clinical benefit assessment, a central aim of recent approaches to value measurement, including value based assessment and pricing, points towards the incorporation of supplementary evidence and criteria that capture additional dimensions of value. To study the practices, processes and policies of value-assessment for new medicines across eight European countries and the role of HTA beyond economic evaluation and clinical benefit assessment. A systematic (peer review and grey) literature review was conducted using an analytical framework examining: (1) 'Responsibilities and structure of HTA agencies'; (2) 'Evidence and evaluation criteria considered in HTAs'; (3) 'Methods and techniques applied in HTAs'; and (4) 'Outcomes and implementation of HTAs'. Study countries were France, Germany, England, Sweden, Italy, Netherlands, Poland and Spain. Evidence from the literature was validated and updated through two rounds of feedback involving primary data collection from national experts. All countries assess similar types of evidence; however, the specific criteria/endpoints used, their level of provision and requirement, and the way they are incorporated (e.g. explicitly vs. implicitly) varies across countries, with their relative importance remaining generally unknown. Incorporation of additional 'social value judgements' (beyond clinical benefit assessment) and economic evaluation could help explain heterogeneity in coverage recommendations and decision-making. More comprehensive and systematic assessment procedures characterised by increased transparency, in terms of selection of evaluation criteria, their importance and intensity of use, could lead to more rational evidence-based decision-making, possibly improving efficiency in resource allocation, while also raising public confidence and fairness.
A general description of expert systems is given. The operation of a fast reactor is reviewed. The expert system to the diagnosis of breakdowns limited to the reactor core. The structure of the system is described: specification of the diagnostics; structure of the data bank and evaluation of the rules; specification of the prediagnostics and evaluation; explanation of the diagnostics; time evolution of the system; comparison with other expert systems. Applications to some cases of faults are finally presented [fr
A mechanism for attaching graphic and overlay annotation to multiple bits/pixel imagery while providing levels of performance approaching that of native mode graphics systems is presented. This mechanism isolates programming complexity from the application programmer through software encapsulation under the X Window System. It ensures display accuracy throughout operations on the imagery and annotation including zooms, pans, and modifications of the annotation. Trade-offs that affect speed of display, consumption of memory, and system functionality are explored. The use of resource files to tune the display system is discussed. The mechanism makes use of an abstraction consisting of four parts; a graphics overlay, a dithered overlay, an image overly, and a physical display window. Data structures are maintained that retain the distinction between the four parts so that they can be modified independently, providing system flexibility. A unique technique for associating user color preferences with annotation is introduced. An interface that allows interactive modification of the mapping between image value and color is discussed. A procedure that provides for the colorization of imagery on 8-bit display systems using pixel dithering is explained. Finally, the application of annotation mechanisms to various applications is discussed.
The profession of an expert auditor is a public trust occupation with a distinctive feature of taking responsibility for actions in the public interest. The main responsibility of expert auditors is performing financial auditing; however, expert auditors are prepared to carry out different tasks which encompass a wide plethora of financial and auditing services for different kinds of institutions and companies. The aim of the article is first of all the description of expert auditors’ service...
controls. Neither Polyisobutene nor Hydrogenated Polyisobutene were ocular irritants, nor were they dermal irritants or sensitizers. Polyisobutene was not comedogenic in a rabbit ear study. Polyisobutene did not induce transformation in the Syrian hamster embryo (SHE) cell transformation assay, but did enhance 3-methylcholanthrene-induced transformation of C3H/10T1/2 cells. In a carcinogenicity study in mice, Polyisobutene was not carcinogenic, nor did it promote the carcinogenicity of 7,12-dimethylbenz(alpha)anthracene. Clinical patch tests uncovered no evidence of dermal irritation and repeat-insult patch tests with a product containing 4% Hydrogenated Polyisobutene or 1.44% Hydrogenated Polyisobutene found no reactions greater than slight erythema. These products also were not phototoxic or photoallergenic. The product containing 4% Hydrogenated Polyisobutene was not an ocular irritant in a clinical test. The Cosmetic Ingredient Review (CIR) Expert Panel recognized that there are data gaps regarding use and concentration of these ingredients. However, the overall information available on the types of products in which these ingredients are used and at what concentrations indicate a pattern of use, which was considered by the Expert Panel in assessing safety. Although there is an absence of dermal absorption data for Polyisobutene and Hydrogenated Polyisobutene, the available octanol water partition coefficient data and the low solubility in water suggest very slow absorption, so additional data are not needed. Gastrointestinal absorption is also not a major concern due to the low solubility of these chemicals. Although one in vitro study did report that Polyisobutene did promote cellular transformation, a mouse study did not find evidence of tumor promotion. Because lifetime exposure studies using rats and dogs exposed to Polybutene failed to demonstrate any carcinogenic or tumor promotion effect, and a three-generation reproductive/developmental toxicity study produced
Dijkstra, JJ; Liebrand, WBG; Timminga, E; Liebrand, Wim B.G.
Expert system advice is not always evaluated by examining its contents. Users can be persuaded by expert system advice because they have certain beliefs about advice given by a computer. The experiment in this paper shows that subjects (n = 84) thought that, given the same argumentation, expert
Pfaff, Claas-Thido; Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian
Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
Eichenberg, David; Liebergesell, Mario; König-Ries, Birgitta; Wirth, Christian
Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines. PMID:29023519
Full Text Available Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.
Sagar, Budhi (Center for Nuclear Waste Regulatory Analyses, Southwest Research Inst., San Antonio, TX (US)); Egan, Michael (Quintessa Limited, Henley-on-Thames (GB)); Roehlig, Klaus-Juergen (Gesellschaft fuer Anlagen- und Reaktorsicherheit mbH (DE)); Chapman, Neil (Independent Consultant (XX)); Wilmot, Roger (Galson Sciences Limited, Oakham (GB))
In 2006, SKB published a safety assessment (SR-Can) as part of its work to support a licence application for the construction of a final repository for spent nuclear fuel. The purposes of the SR-Can project were stated in the main project report to be: 1. To make a first assessment of the safety of potential KBS-3 repositories at Forsmark and Laxemar to dispose of canisters as specified in the application for the encapsulation plant. 2. To provide feedback to design development, to SKB's research and development (R and D) programme, to further site investigations and to future safety assessments. 3. To foster a dialogue with the authorities that oversee SKB's activities, i.e. the Swedish Nuclear Power Inspectorate, SKI, and the Swedish Radiation Protection Authority, SSI, regarding interpretation of applicable regulations, as a preparation for the SR-Site project. To help inform their review of SKB's proposed approach to development of the longterm safety case, the authorities appointed three international expert review teams to carry out a review of SKB's SR-Can safety assessment report. Comments from one of these teams - the Safety Assessment Methodology (SAM) review team - are presented in this document. The SAM review team's scope of work included an examination of SKB's documentation of the assessment ('Long-term safety for KBS-3 Repositories at Forsmark and Laxemar - a first evaluation' and several supporting reports) and hearings with SKB staff and contractors, held in March 2007. As directed by SKI and SSI, the SAM review team focused on methodological aspects and sought to determine whether SKB's proposed safety assessment methodology is likely to be suitable for use in the future SR-Site and to assess its consistency with the Swedish regulatory framework. No specific evaluation of long-term safety or site acceptability was undertaken by any of the review teams. SKI and SSI's Terms of Reference for the SAM
The feasibility of using expert systems as an aid in regulatory compliance functions has been investigated. A literature review was carried out to identify applications of expert systems to regulatory affairs. A bibliography of the small literature on such applications was prepared. A prototype system, ARIES, was developed to demonstrate the use of an expert system as an aid to a Project Officer in assuring compliance with licence requirements. The system runs on a personal computer with a graphical interface. Extensive use is made of hypertext to link interrelated rules and requirements as well as to provide an explanation facility. Based on the performance of ARIES the development of a field version is recommended
Cooke, Roger M.; Goossens, Louis L.H.J.
We review the applications of structured expert judgment uncertainty quantification using the 'classical model' developed at the Delft University of Technology over the last 17 years [Cooke RM. Experts in uncertainty. Oxford: Oxford University Press; 1991; Expert judgment study on atmospheric dispersion and deposition. Report Faculty of Technical Mathematics and Informatics No.01-81, Delft University of Technology; 1991]. These involve 45 expert panels, performed under contract with problem owners who reviewed and approved the results. With a few exceptions, all these applications involved the use of seed variables; that is, variables from the experts' area of expertise for which the true values are available post hoc. Seed variables are used to (1) measure expert performance, (2) enable performance-based weighted combination of experts' distributions, and (3) evaluate and hopefully validate the resulting combination or 'decision maker'. This article reviews the classical model for structured expert judgment and the performance measures, reviews applications, comparing performance-based decision makers with 'equal weight' decision makers, and collects some lessons learned
Bomelburg, H.J.; Counts, C.A.; Cowan, C.E.; Davis, W.E.; DeSteese, J.G.; Pelto, P.J.
This document updates the bibliography published in Liquefied Gaseous Fuels Safety and Environmental Control Assessment Program: third status report (PNL-4172) and is a complete listing of literature reviewed and reported under the LNG Technical Surveillance Task. The bibliography is organized alphabetically by author.
Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas
Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Quade, Mandy; Kirch, Wilhelm
Background A multitude of mhealth (mobile health) apps have been developed in recent years to support effective self-management of patients with diabetes mellitus type 1 or 2. Objective We carried out a systematic review of all currently available diabetes apps for the operating systems iOS and Android. We considered the number of newly released diabetes apps, range of functions, target user groups, languages, acquisition costs, user ratings, available interfaces, and the connection between acquisition costs and user ratings. Additionally, we examined whether the available applications serve the special needs of diabetes patients aged 50 or older by performing an expert-based usability evaluation. Methods We identified relevant keywords, comparative categories, and their specifications. Subsequently, we performed the app review based on the information given in the Google Play Store, the Apple App Store, and the apps themselves. In addition, we carried out an expert-based usability evaluation based on a representative 10% sample of diabetes apps. Results In total, we analyzed 656 apps finding that 355 (54.1%) offered just one function and 348 (53.0%) provided a documentation function. The dominating app language was English (85.4%, 560/656), patients represented the main user group (96.0%, 630/656), and the analysis of the costs revealed a trend toward free apps (53.7%, 352/656). The median price of paid apps was €1.90. The average user rating was 3.6 stars (maximum 5). Our analyses indicated no clear differences in the user rating between free and paid apps. Only 30 (4.6%) of the 656 available diabetes apps offered an interface to a measurement device. We evaluated 66 apps within the usability evaluation. On average, apps were rated best regarding the criterion “comprehensibility” (4.0 out of 5.0), while showing a lack of “fault tolerance” (2.8 out of 5.0). Of the 66 apps, 48 (72.7%) offered the ability to read the screen content aloud. The number of
Arnhold, Madlen; Quade, Mandy; Kirch, Wilhelm
A multitude of mhealth (mobile health) apps have been developed in recent years to support effective self-management of patients with diabetes mellitus type 1 or 2. We carried out a systematic review of all currently available diabetes apps for the operating systems iOS and Android. We considered the number of newly released diabetes apps, range of functions, target user groups, languages, acquisition costs, user ratings, available interfaces, and the connection between acquisition costs and user ratings. Additionally, we examined whether the available applications serve the special needs of diabetes patients aged 50 or older by performing an expert-based usability evaluation. We identified relevant keywords, comparative categories, and their specifications. Subsequently, we performed the app review based on the information given in the Google Play Store, the Apple App Store, and the apps themselves. In addition, we carried out an expert-based usability evaluation based on a representative 10% sample of diabetes apps. In total, we analyzed 656 apps finding that 355 (54.1%) offered just one function and 348 (53.0%) provided a documentation function. The dominating app language was English (85.4%, 560/656), patients represented the main user group (96.0%, 630/656), and the analysis of the costs revealed a trend toward free apps (53.7%, 352/656). The median price of paid apps was €1.90. The average user rating was 3.6 stars (maximum 5). Our analyses indicated no clear differences in the user rating between free and paid apps. Only 30 (4.6%) of the 656 available diabetes apps offered an interface to a measurement device. We evaluated 66 apps within the usability evaluation. On average, apps were rated best regarding the criterion "comprehensibility" (4.0 out of 5.0), while showing a lack of "fault tolerance" (2.8 out of 5.0). Of the 66 apps, 48 (72.7%) offered the ability to read the screen content aloud. The number of functions was significantly negative correlated
Mark A Burgman
Full Text Available Expert judgements are essential when time and resources are stretched or we face novel dilemmas requiring fast solutions. Good advice can save lives and large sums of money. Typically, experts are defined by their qualifications, track record and experience. The social expectation hypothesis argues that more highly regarded and more experienced experts will give better advice. We asked experts to predict how they will perform, and how their peers will perform, on sets of questions. The results indicate that the way experts regard each other is consistent, but unfortunately, ranks are a poor guide to actual performance. Expert advice will be more accurate if technical decisions routinely use broadly-defined expert groups, structured question protocols and feedback.
As a bibliography of annotated references addressing interdisciplinary environmental research, the collection reviews a broad spectrum of literature to illustrate the breadth of issues that bear on the role of humankind in environmental context. Categories of culture, environmental law, public policy, environmental valuation strategies, philosophy, interdisciplinary...
Heinrich, Hartmut; Gevensleben, Holger; Strehl, Ute
Background: Neurofeedback (NF) is a form of behavioural training aimed at developing skills for self-regulation of brain activity. Within the past decade, several NF studies have been published that tend to overcome the methodological shortcomings of earlier studies. This annotation describes the methodical basis of NF and reviews the evidence…
Bush, Shirley H; Kanji, Salmaan; Pereira, José L; Davis, Daniel H J; Currow, David C; Meagher, David; Rabheru, Kiran; Wright, David; Bruera, Eduardo; Hartwick, Michael; Gagnon, Pierre R; Gagnon, Bruno; Breitbart, William; Regnier, Laura; Lawlor, Peter G
Delirium is a highly prevalent complication in patients in palliative care settings, especially in the end-of-life context. To review the current evidence base for treating episodes of delirium in palliative care settings and propose a framework for future development. We combined multidisciplinary input from delirium researchers and other purposely selected stakeholders at an international delirium study planning meeting. This was supplemented by a literature search of multiple databases and relevant reference lists to identify studies regarding therapeutic interventions for delirium. The context of delirium management in palliative care is highly variable. The standard management of a delirium episode includes the investigation of precipitating and aggravating factors followed by symptomatic treatment with drug therapy. However, the intensity of this management depends on illness trajectory and goals of care in addition to the local availability of both investigative modalities and therapeutic interventions. Pharmacologically, haloperidol remains the practice standard by consensus for symptomatic control. Dosing schedules are derived from expert opinion and various clinical practice guidelines as evidence-based data from palliative care settings are limited. The commonly used pharmacologic interventions for delirium in this population warrant evaluation in clinical trials to examine dosing and titration regimens, different routes of administration, and safety and efficacy compared with placebo. Delirium treatment is multidimensional and includes the identification of precipitating and aggravating factors. For symptomatic management, haloperidol remains the practice standard. Further high-quality collaborative research investigating the appropriate treatment of this complex syndrome is needed. Copyright © 2014 American Academy of Hospice and Palliative Medicine. All rights reserved.
van Hecke, Oliver; Kamerman, Peter R; Attal, Nadine; Baron, Ralf; Bjornsdottir, Gyda; Bennett, David L H; Bennett, Michael I; Bouhassira, Didier; Diatchenko, Luda; Freeman, Roy; Freynhagen, Rainer; Haanpää, Maija; Jensen, Troels S; Raja, Srinivasa N; Rice, Andrew S C; Seltzer, Zeʼev; Thorgeirsson, Thorgeir E; Yarnitsky, David; Smith, Blair H
For genetic research to contribute more fully to furthering our knowledge of neuropathic pain, we require an agreed, valid, and feasible approach to phenotyping, to allow collaboration and replication in samples of sufficient size. Results from genetic studies on neuropathic pain have been inconsistent and have met with replication difficulties, in part because of differences in phenotypes used for case ascertainment. Because there is no consensus on the nature of these phenotypes, nor on the methods of collecting them, this study aimed to provide guidelines on collecting and reporting phenotypes in cases and controls for genetic studies. Consensus was achieved through a staged approach: (1) systematic literature review to identify all neuropathic pain phenotypes used in previous genetic studies; (2) Delphi survey to identify the most useful neuropathic pain phenotypes and their validity and feasibility; and (3) meeting of experts to reach consensus on the optimal phenotype(s) to be collected from patients with neuropathic pain for genetic studies. A basic "entry level" set of phenotypes was identified for any genetic study of neuropathic pain. This set identifies cases of "possible" neuropathic pain, and controls, and includes: (1) a validated symptom-based questionnaire to determine whether any pain is likely to be neuropathic; (2) body chart or checklist to identify whether the area of pain distribution is neuroanatomically logical; and (3) details of pain history (intensity, duration, any formal diagnosis). This NeuroPPIC "entry level" set of phenotypes can be expanded by more extensive and specific measures, as determined by scientific requirements and resource availability.
Zarri, Gian Piero
Operational Expert System Applications in Europe describes the representative case studies of the operational expert systems (ESs) that are used in Europe.This compilation provides examples of operational ES that are realized in 10 different European countries, including countries not usually examined in the standard reviews of the field.This book discusses the decision support system using several artificial intelligence tools; expert systems for fault diagnosis on computerized numerical control (CNC) machines; and expert consultation system for personal portfolio management. The failure prob
This article reviews the utility of expert opinion in legal proceedings and the deployment of expert witnesses in adversarial litigation. The use of expert witnesses to assist courts in making just and fair conclusions may be contrasted with the partisan interests of those who call them. An adversarial system is a bad method of scientific enquiry and undermines the court's capacity to reach the 'right' answer. As a consequence, courts may reach the wrong conclusion based on bad science. The role of the expert as a witness places strain on an expert to provide certainty, where in fact there may be none. Recent reforms in the civil courts have changed little and the problem is even more acute in criminal trials. The expert can rely solely on the integrity of his or her own opinion, tempered with a little humility. However, when filtered through the rhetoric and advocacy of a court arena, even this may be compromised.
Poli, Rosario, Comp.
An annotated bibliography lists 74 articles and reports on instructional materials centers (IMC) which appeared from 1967-70. The articles deal with such topics as the purposes of an IMC, guidelines for setting up an IMC, and the relationship of an IMC to technology. Most articles deal with use of an IMC on an elementary or secondary level, but…
F.-M. Nack (Frank); W. Putz
textabstractThis paper considers the automated and semi-automated annotation of audiovisual media in a new type of production framework, A4SM (Authoring System for Syntactic, Semantic and Semiotic Modelling). We present the architecture of the framework and outline the underlying XML-Schema based
T. Tsikrika (Theodora); C. Diou; A.P. de Vries (Arjen); A. Delopoulos
htmlabstractAutomatic image annotation using supervised learning is performed by concept classifiers trained on labelled example images. This work proposes the use of clickthrough data collected from search logs as a source for the automatic generation of concept training data, thus avoiding the
Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.
Konyushkova, Ksenia; Uijlings, Jasper; Lampert, Christoph; Ferrari, Vittorio
We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification , where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other bas...
Wang, X.J.; Zhang, L.; Li, X.; Ma, W.Y.
Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search
Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.
Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.
Brechet, Y.; Musseau, O.; Bruna, G.; Sperandio, M.; Roulleaux-Dugage, M.; Andrieux, S.; Metteau, L.
This series of short articles are dedicated to the role of the expert in the enterprise. There is an important difference between a scientific counsellor and an expert, the expert, recognized by his peers, can speak publicly in his field of expertise but has a duty of transparency while the job of a scientific counsellor requires confidentiality. The making and the use of an expert in an enterprise requires a dedicated organization. The organization of the expertise in 5 enterprises in nuclear industry are considered: CEA (French Alternative Energies and Atomic Energy Commission), IRSN (Institute of Radioprotection and Nuclear Safety), AREVA, ANDRA (National Radioactive Waste Management Agency) and EDF (Electricity of France)
Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel
Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were
McFee, Brian; Nieto, Oriol; Farbood, Morwaread M; Bello, Juan Pablo
Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for "flat" descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement.
Asami, Tohru; Hashimoto, Kazuo; Yamamoto, Seiichi
Recently, aiming at the application to the plant control for nuclear reactors and traffic and communication control, the research and the practical use of the expert system suitable to real time processing have become conspicuous. In this report, the condition for the required function to control the object that dynamically changes within a limited time is presented, and the technical difference between the real time expert system developed so as to satisfy it and the expert system of conventional type is explained with the actual examples and from theoretical aspect. The expert system of conventional type has the technical base in the problem-solving equipment originating in STRIPS. The real time expert system is applied to the fields accompanied by surveillance and control, to which conventional expert system is hard to be applied. The requirement for the real time expert system, the example of the real time expert system, and as the techniques of realizing real time processing, the realization of interruption processing, dispersion processing, and the mechanism of maintaining the consistency of knowledge are explained. (K.I.)
Hendrix, E.M.T.; Kornelis, M.; Pegge, S.M.; Galen, van M.A.
In this study, focus is on a systematic way to detect future changes in trends that may effect the dynamics in the agro-food sector, and on the combination of opinions of experts. For the combination of expert opinions, the usefulness of multilevel models is investigated. Bayesian data analysis is
The purpose of this article is to introduce readers to the basic principles of rule-based expert systems. Four topics are discussed in subsequent sections: (1) Definition; (2) Structure of an expert system; (3) State of the art and (4) Impact and future research. (orig.)
This paper argues that the concepts and techniques used in the development of expert systems should be expanded and applied to the field of education, particularly in the area of intelligent tutoring systems. It is noted that expert systems are a well known area of artificial intelligence and have been proven effective in well-defined topic areas.…
W.M. Koolen-Wijkstra (Wouter); S. de Rooij (Steven)
htmlabstractWe show how models for prediction with expert advice can be defined concisely and clearly using hidden Markov models (HMMs); standard HMM algorithms can then be used to efficiently calculate, among other things, how the expert predictions should be weighted according to the model. We
Wilmot, R.D.; Galson, D.A.
This report is a pilot study that systematically describes the various types of expert judgement that are made throughout the development of a PA, and summarizes existing tools and practices for dealing with expert judgements. The report also includes recommendations for further work in the area of expert judgement. Expert judgements can be classified in a number of ways, including classification according to why the judgements are made and according to how the judgements are made. In terms of why judgements are made, there is a broad distinction between: Judgements concerning data that are made because alternatives are not feasible; and Judgements about the conduct of a PA that are made because there are no alternative approaches for making the decision. In the case of how judgements are made, the report distinguishes between non-elicited judgements made by individuals, non-elicited judgements made by groups, and elicited judgements made by individuals or groups. These types of judgement can generally be distinguished by the extent of the associated documentation, and hence their traceability. Tools for assessing judgements vary depending on the type of judgements being examined. Key tools are peer review, an appropriate QA regime, documentation, and elicitation. Dialogue with stake holders is also identified as important in establishing whether judgements are justified in the context in which they are used. The PA process comprises a number of stages, from establishing the assessment context, through site selection and repository design, to scenario and model development and parametrisation. The report discusses how judgements are used in each of these stages, and identifies which of the tools and procedures for assessing judgements are most appropriate at each stage. Recommendations for further work include the conduct of a trial expert elicitation to gain experience in the advantages and disadvantages of this technique, the development of guidance for peer
Burghardt, Manuel; Wolff, Christian
Wir diskutieren zunächst die Problematik der (syntaktischen) Annotation diachroner Korpora und stellen anschließend eine Evaluationsstudie vor, bei der mehr als 50 Annotationswerkzeuge und -frameworks vor dem Hintergrund eines funktionalen und software-ergonomischen Anforderungsprofils nach dem Qualitätsmodell von ISO/IEC 9126-1:2001 (Software engineering – Product quality – Part 1: Quality model) und ISO/IEC 25000:2005 (Software Engineering – Software product Quality Requirements and Evaluat...
Holt, Carson; Yandell, Mark
Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.
Singh, Harpreet; Singh, Reema; Malhotra, Arjun; Kaur, Manjit
Efficient identification of subject experts or expert communities is vital for the growth of any organization. Most of the available expert finding systems are based on self-nomination, which can be biased, and are unable to rank experts. Thus, the objective of this work was to develop a robust and unbiased expert finding system which can quantitatively measure expertise. Medical Subject Headings (MeSH) is a controlled vocabulary developed by the National Library of Medicine (NLM) for indexing research publications, articles and books. Using the MeSH terms associated with peer-reviewed articles published from India and indexed in PubMed, we developed a Web-based program which can be used to identify subject experts and subjects associated with an expert. We have extensively tested our system to identify experts from India in various subjects. The system provides a ranked list of experts where known experts rank at the top of the list. The system is general; since it uses information available with the PubMed, it can be implemented for any country. The expert finding system is able to successfully identify subject experts in India. Our system is unique because it allows the quantification of subject expertise, thus enabling the ranking of experts. Our system is based on peer-reviewed information. Use of MeSH terms as subjects has standardized the subject terminology. The system matches requirements of an ideal expert finding system.
Based upon a request of the Government of Bulgaria and in order to assist its Regulatory Body, an experts' mission was carried out to Sofia and Kozloduy, 21-25 November 1994 within the framework of the IAEA TC Project BUL/9/013-05 and of the IAEA Extrabudgetary Programme on the Safety of the WWER NPPs. The mission also specified the technical content of further assistance by the IAEA. With respect to the findings and recommendations made in November 1994, WWER-SC-109, a follow-up expert's mission was carried out to Sofia, Bulgaria, April 3-7, 1995. The objective of the mission was to review the selection of transients, thermal hydraulic, stress and fracture mechanics analyses for reactor pressure vessel integrity assessment of Kozloduy unit 1-4. In addition, an update on the activities completed, underway and planned related to unit 1 reactor pressure vessel embrittlement was presented and discussed. The review was carried out by 4 international experts from Finland, France, Russia and IAEA in co-operation with the Bulgarian regulatory body, plant, Energoproject Sofia and Institute of Metals staff. The mission was conducted out within the frame of the IAEA TC Project BUL/9/013-05 and of the IAEA Extrabudgetary Programme on the Safety of the WWER NPPs. 18 refs
Abreha Mesele Zinabu
The Reception of Incriminating Expert Evidence (i.e., Forensic Science) in Four. Adversarial Jurisdictions. University of Denver Criminal Law Review, Vol. 3, pp 31-109. 9 This is all about competence where it incorporates both the relevance of the qualification and the capability of the expert to provide the expert testimony.
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a case study of the May 2003 Danish consensus conference on environmental economics as a policy tool, the article reflects on the politics of expert authority permeating practices of public participation. Adopting concepts from the sociology of scientific knowledge (SSK), the conference is seen......-than-successful defense in the citizen perspective. Further, consensus conferences are viewed alternatively as "expert dissent conferences," serving to disclose a multiplicity of expert commitments. From this perspective, some challenges for democratizing expertise through future exercises in public participation...
Lingutla, Nikhil Tej; Preece, Justin; Todorovic, Sinisa; Cooper, Laurel; Moore, Laura; Jaiswal, Pankaj
Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors under which the organisms were sampled. At present, most of these annotations are described in free text, may involve limited use of non-standard vocabularies, and rarely specify precise coordinates of features on the image plane such that a computer vision algorithm could identify, extract and annotate them. Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms. Such a tool would generate data useful for inter and intra-specific comparison and encourage the integration of curation standards. In the future, quality annotated image segments may provide training data sets for developing machine learning applications for automated image annotation. We developed a novel image segmentation and annotation software application, "Annotation of Image Segments with Ontologies" (AISO). The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary. AISO is a freely available Java-based desktop application and runs on multiple platforms. It can be downloaded at http://www.plantontology.org/software/AISO. AISO enables curators and researchers to annotate digital images with ontology terms in a manner which ensures the future computational value of the annotated images. We foresee uses for such data-encoded image annotations in biological data mining, machine learning, predictive annotation, semantic inference, and comparative analyses.
Pinoli, Pietro; Chicco, Davide; Masseroli, Marco
Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biological experiments and interpret their results. Despite their importance, these sources of information have some known issues. They are incomplete, since biological knowledge is far from being definitive and it rapidly evolves, and some erroneous annotations may be present. Since the curation process of novel annotations is a costly procedure, both in economical and time terms, computational tools that can reliably predict likely annotations, and thus quicken the discovery of new gene annotations, are very useful. We used a set of computational algorithms and weighting schemes to infer novel gene annotations from a set of known ones. We used the latent semantic analysis approach, implementing two popular algorithms (Latent Semantic Indexing and Probabilistic Latent Semantic Analysis) and propose a novel method, the Semantic IMproved Latent Semantic Analysis, which adds a clustering step on the set of considered genes. Furthermore, we propose the improvement of these algorithms by weighting the annotations in the input set. We tested our methods and their weighted variants on the Gene Ontology annotation sets of three model organism genes (Bos taurus, Danio rerio and Drosophila melanogaster ). The methods showed their ability in predicting novel gene annotations and the weighting procedures demonstrated to lead to a valuable improvement, although the obtained results vary according to the dimension of the input annotation set and the considered algorithm. Out of the three considered methods, the Semantic IMproved Latent Semantic Analysis is the one that provides better results. In particular, when coupled with a proper weighting policy, it is able to predict a
Full Text Available Annotating remote sensing images is a challenging task for its labor demanding annotation process and requirement of expert knowledge, especially when images can be annotated with multiple semantic concepts (or labels. To automatically annotate these multi-label images, we introduce an approach called Multi-Label Classification based on Low Rank Representation (MLC-LRR. MLC-LRR firstly utilizes low rank representation in the feature space of images to compute the low rank constrained coefficient matrix, then it adapts the coefficient matrix to define a feature-based graph and to capture the global relationships between images. Next, it utilizes low rank representation in the label space of labeled images to construct a semantic graph. Finally, these two graphs are exploited to train a graph-based multi-label classifier. To validate the performance of MLC-LRR against other related graph-based multi-label methods in annotating images, we conduct experiments on a public available multi-label remote sensing images (Land Cover. We perform additional experiments on five real-world multi-label image datasets to further investigate the performance of MLC-LRR. Empirical study demonstrates that MLC-LRR achieves better performance on annotating images than these comparing methods across various evaluation criteria; it also can effectively exploit global structure and label correlations of multi-label images.
Lin, Andrew H; Welstead, Bethany L; Morey, Brittany L; Mahnke, C Becket; Cole, Jacob H; Johnston, Michael G
Health Experts onLine at Portsmouth (HELP) is a web-based teleconsultation system launched in June 2014 to facilitate communication between specialists at Naval Medical Center Portsmouth and providers assigned to both the fleet forces and primary care clinics across the eastern United States, Europe, and the Middle East. Specialist consultations through the HELP system purport to improve access to care for patients who otherwise might be referred to the civilian network or medically evacuated (MEDEVACed) to Naval Medical Center Portsmouth for specialized care. If HELP-facilitated communications help avoid civilian referrals or MEDEVACs, the associated costs of that care should be reduced. We evaluated cost savings associated with prevented MEDEVACs by analyzing both tangible savings (prevented costs of flights, per diems, and consults) and intangible savings (reduced lost productivity time). We compared these savings to the costs of maintaining and utilizing the HELP system: startup costs, administrative costs, and provider time costs. We used patient and provider data from the HELP database to evaluate clinical consult cases. Before this analysis, a panel of 3 physicians associated with HELP reviewed each consult to determine whether a case qualified as a prevented MEDEVAC. Data from the Military Health System (MHS) Management and Analysis Reporting Tool and the MHS Data Repository were used to estimate costs associated with provider time, patient time, and direct care medical encounters. The HELP program delivered measurable, positive returns on investment (ROIs) between June 2014 and December 2015. In that time frame, 559 consult cases occurred in the HELP system. Of the 559 total consult cases, 50 consults prevented MEDEVACs. Incorporating only tangible savings, HELP produced an 80% ROI on the basis of prevented medical evacuations; the addition of intangible savings such as reduced lost productivity increased the ROI to 250%. The dollar values of these savings
Oliva, Peter F.; Henson, Kenneth T.
The curriculum and instruction specialist should not fall prey to the "expert syndrome," in which the specialist decides on the "best" curriculum or instructional method without considering the teacher's discipline or personality. (CJ)
The brochure presents, in full wording, 20 papers read at the experts' meeting ''Maintenance '83'' in Wiesbaden. Most of the papers discuss reliability data (acquisition, evaluation, processing) of nearly all fields of industry. (RW) [de
Full Text Available Abstract Background Large volumes of morphological descriptions of whole organisms have been created as print or electronic text in a human-readable format. Converting the descriptions into computer- readable formats gives a new life to the valuable knowledge on biodiversity. Research in this area started 20 years ago, yet not sufficient progress has been made to produce an automated system that requires only minimal human intervention but works on descriptions of various plant and animal groups. This paper attempts to examine the hindering factors by identifying the mismatches between existing research and the characteristics of morphological descriptions. Results This paper reviews the techniques that have been used for automated annotation, reports exploratory results on characteristics of morphological descriptions as a genre, and identifies challenges facing automated annotation systems. Based on these criteria, the paper proposes an overall strategy for converting descriptions of various taxon groups with the least human effort. Conclusions A combined unsupervised and supervised machine learning strategy is needed to construct domain ontologies and lexicons and to ultimately achieve automated semantic annotation of morphological descriptions. Further, we suggest that each effort in creating a new description or annotating an individual description collection should be shared and contribute to the "biodiversity information commons" for the Semantic Web. This cannot be done without a sound strategy and a close partnership between and among information scientists and biologists.
Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I
Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.
Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria
We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods......: majority voting with a theory-compliant backoff strategy, and MACE, an unsuper- vised system to choose the most likely sense from all the annotations....
López-Fernández, H; Reboiro-Jato, M; Glez-Peña, D; Aparicio, F; Gachet, D; Buenaga, M; Fdez-Riverola, F
Automatic term annotation from biomedical documents and external information linking are becoming a necessary prerequisite in modern computer-aided medical learning systems. In this context, this paper presents BioAnnote, a flexible and extensible open-source platform for automatically annotating biomedical resources. Apart from other valuable features, the software platform includes (i) a rich client enabling users to annotate multiple documents in a user friendly environment, (ii) an extensible and embeddable annotation meta-server allowing for the annotation of documents with local or remote vocabularies and (iii) a simple client/server protocol which facilitates the use of our meta-server from any other third-party application. In addition, BioAnnote implements a powerful scripting engine able to perform advanced batch annotations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.
Pundhir, Sachin; Poirazi, Panayiota; Gorodkin, Jan
Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS dat...... of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation....
Sun, Weiyi; Rumshisky, Anna; Uzuner, Ozlem
Temporal information in clinical narratives plays an important role in patients' diagnosis, treatment and prognosis. In order to represent narrative information accurately, medical natural language processing (MLP) systems need to correctly identify and interpret temporal information. To promote research in this area, the Informatics for Integrating Biology and the Bedside (i2b2) project developed a temporally annotated corpus of clinical narratives. This corpus contains 310 de-identified discharge summaries, with annotations of clinical events, temporal expressions and temporal relations. This paper describes the process followed for the development of this corpus and discusses annotation guideline development, annotation methodology, and corpus quality. Copyright © 2013 Elsevier Inc. All rights reserved.
Jeffrey J. Brooks; Alexander N. Bujak; Joseph G. Champ; Daniel R. Williams
We reviewed, annotated, and organized recent social science research and developed a framework for addressing the wildland fire social problem. We annotated articles related to three topic areas or factors, which are critical for understanding collective action, particularly in the wildland-urban interface. These factors are collaborative capacity, problem framing, and...
Full Text Available Tracking occluded objects at different depths has become as extremely important component of study for any video sequence having wide applications in object tracking, scene recognition, coding, editing the videos and mosaicking. The paper studies the ability of annotation to track the occluded object based on pyramids with variation in depth further establishing a threshold at which the ability of the system to track the occluded object fails. Image annotation is applied on 3 similar video sequences varying in depth. In the experiment, one bike occludes the other at a depth of 60cm, 80cm and 100cm respectively. Another experiment is performed on tracking humans with similar depth to authenticate the results. The paper also computes the frame by frame error incurred by the system, supported by detailed simulations. This system can be effectively used to analyze the error in motion tracking and further correcting the error leading to flawless tracking. This can be of great interest to computer scientists while designing surveillance systems etc.
Thorndahl, Kathrine Liedtke; Ravn, Susanne
and autoethnographic material from one former elite skipper, we take some initial steps toward the development of a more nuanced understanding of the concept of incorporation; one that is able to accommodate the experiences of expert tool users. In sum, our analyses indicate that the possibility for experiencing...... a tool as incorporated depends on the existence of an extraordinary kind of relationship between the tool and the expert tool user. This relation, that can persist even when successful manipulation of the tool fails, is not only cultivated through deliberate practice of physical skills, but also through...... the collective sense-making process going on within a particular community of practice. Therefore, expert tool users may experience a more profound kind of incorporation that can persist even when normal motor incorporation fails....
Citizen deliberation on technoscientific developments is regularly regarded as a hallmark of Danish democracy, embodied in particular by the Danish Board of Technology. Few empirically guided questions have been raised, however, as to how the Board's democratic projects actually work. Through...... a case study of the May 2003 Danish consensus conference on environmental economics as a policy tool, the article reflects on the politics of expert authority permeating practices of public participation. Adopting concepts from the sociology of scientific knowledge (SSK), the conference is seen......-than-successful defense in the citizen perspective. Further, consensus conferences are viewed alternatively as "expert dissent conferences," serving to disclose a multiplicity of expert commitments. From this perspective, some challenges for democratizing expertise through future exercises in public participation...
Full Text Available In 1999, Molodtsov introduced the concept of soft set theory as a general mathematical tool for dealing with uncertainty. Many researchers have studied this theory, and they created some models to solve problems in decision making and medical diagnosis, but most of these models deal only with one expert. This causes a problem with the user, especially with those who use questionnaires in their work and studies. In our model, the user can know the opinion of all experts in one model. So, in this paper, we introduce the concept of a soft expert set, which will more effective and useful. We also define its basic operations, namely, complement, union intersection AND, and OR. Finally, we show an application of this concept in decision-making problem.
Schmid, Ralf; Blaxter, Mark L
The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.
Park, Jungkap; Rosania, Gus R; Saitou, Kazuhiro
We present a tunable, machine vision-based strategy for automated annotation of virtual small molecule databases. The proposed strategy is based on the use of a machine vision-based tool for extracting structure diagrams in research articles and converting them into connection tables, a virtual "Chemical Expert" system for screening the converted structures based on the adjustable levels of estimated conversion accuracy, and a fragment-based measure for calculating intermolecular similarity. For annotation, calculated chemical similarity between the converted structures and entries in a virtual small molecule database is used to establish the links. The overall annotation performances can be tuned by adjusting the cutoff threshold of the estimated conversion accuracy. We perform an annotation test which attempts to link 121 journal articles registered in PubMed to entries in PubChem which is the largest, publicly accessible chemical database. Two cases of tests are performed, and their results are compared to see how the overall annotation performances are affected by the different threshold levels of the estimated accuracy of the converted structure. Our work demonstrates that over 45% of the articles could have true positive links to entries in the PubChem database with promising recall and precision rates in both tests. Furthermore, we illustrate that the Chemical Expert system which can screen converted structures based on the adjustable levels of estimated conversion accuracy is a key factor impacting the overall annotation performance. We propose that this machine vision-based strategy can be incorporated with the text-mining approach to facilitate extraction of contextual scientific knowledge about a chemical structure, from the scientific literature.
Newman, Constance; Ng, Crystal; Pacqu?-Margolis, Sara; Frymus, Diana
Background Gender discrimination and inequality in health professional education (HPE) affect students and faculty and hinder production of the robust health workforces needed to meet health and development goals, yet HPE reformers pay scant attention to these gender barriers. Gender equality must be a core value and professional practice competency for all actors in HPE and health employment systems. Methods Peer-review and non-peer-review literature previously identified in a review of the ...
Review of K. Barclay, 'Love, Intimacy and Power' as part of a feature in which experts on Scottish History were asked to choose their book of the year.......Review of K. Barclay, 'Love, Intimacy and Power' as part of a feature in which experts on Scottish History were asked to choose their book of the year....
This report describes a program that uses annotations in the teacher's editions of existing reading programs to indicate the characteristics of black English that may interfere with the reading process of black children. The first part of the report provides a rationale for the annotation approach, explaining that the discrepancy between written…
This video shows how to annotate the ground truth tracks in the thermal videos. The ground truth tracks are produced to be able to compare them to tracks obtained from a Computer Vision tracking approach. The program used for annotation is T-Analyst, which is developed by Aliaksei Laureshyn, Ph...
Leopold, H.; Meilicke, C.; Fellmann, M.; Pittke, F.; Stuckenschmidt, H.; Mendling, J.
Many techniques for the advanced analysis of process models build on the annotation of process models with elements from predefined vocabularies such as taxonomies. However, the manual annotation of process models is cumbersome and sometimes even hardly manageable taking the size of taxonomies into
Balhoff, James P; Dahdul, Wasila M; Dececchi, T Alexander; Lapp, Hilmar; Mabee, Paula M; Vision, Todd J
Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.
In May 2012, a HESI-sponsored expert workshop yielded a proposed research strategy for systematically discovering, characterizing, and annotating fish early life-stage (FELS) adverse outcome pathways (AOPs) as well as prioritizing AOP development in light of current restrictions ...
Mardanbeigi, Diako; Qvarfordt, Pernilla
To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion......, the user simply captures an image using the HMD’s camera, looks at an object of interest in the image, and speaks out the information to be associated with the object. The gaze location is recorded and visualized with a marker. The voice is transcribed using speech recognition. Gaze annotations can...... be shared. Our study showed that users found that gaze annotations add precision and expressive- ness compared to annotations of the image as a whole...
Ting, R.N.; Subramanyam, K.
Ion implantation is a technique for introducing controlled amounts of dopants into target substrates, and has been successfully used for the manufacture of silicon semiconductor devices. Ion implantation is superior to other methods of doping such as thermal diffusion and epitaxy, in view of its advantages such as high degree of control, flexibility, and amenability to automation. This annotated bibliography of 416 references consists of journal articles, books, and conference papers in English and foreign languages published during 1973-74, on all aspects of ion implantation including range distribution and concentration profile, channeling, radiation damage and annealing, compound semiconductors, structural and electrical characterization, applications, equipment and ion sources. Earlier bibliographies on ion implantation, and national and international conferences in which papers on ion implantation were presented have also been listed separately
Helton, William S
The motor control of novice participants is often cognitively demanding and susceptible to interference by other tasks. As people develop expertise, their motor control becomes less susceptible to interference from other tasks. Researchers propose a transition in human motor skill from active control to automaticity. This progression may also be the case with nonhuman animals. Differences in performance characteristics between expert, advanced, intermediate, and novice dogs competing in the sport of agility were investigated. There were statistically significant differences between dogs of varying competitive levels in speed, motor control, and signal detections suggestive of increasing motor control automaticity in highly skilled, or expert, dogs. The largest sequential motor control difference was between novice and intermediate dogs, d = .96, whereas the largest sequential signal detection difference was between advanced and expert dogs, d = .90. These findings have two significant implications for expertise researchers: first, the observed similarities between dogs and humans may enable dogs to be used as expert models; and second, expertise science and methods may be profitably employed in the future to create more proficient canine workers.
Dowell, Laurie; Gary, Jack; Illingworth, Bill; Sargent, Tom
Gathering information, necessary forms, and financial calculations needed to generate a "capital investment proposal" is an extremely complex and difficult process. The intent of the capital investment proposal is to ensure management that the proposed investment has been thoroughly investigated and will have a positive impact on corporate goals. Meeting this requirement typically takes four or five experts a total of 12 hours to generate a "Capital Package." A Capital Expert System was therefore developed using "Personal Consultant." The completed system is hybrid and as such does not depend solely on rules but incorporates several different software packages that communicate through variables and functions passed from one to another. This paper describes the use of expert system techniques, methodology in building the knowledge base, contexts, LISP functions, data base, and special challenges that had to be overcome to create this system. The Capital Expert System is the successful result of a unique integration of artificial intelligence with business accounting, financial forms generation, and investment proposal expertise.
Roč. 8, č. 2 (1995), s. 261-271 ISSN 0893-6080 R&D Projects: GA ČR GA201/95/0976 Keywords : expert system * knowledge representation * multilayered neural network * back propagation * interval neuron function * incomplete information * explanation Impact factor: 1.262, year: 1995
Atkins, T.; Demuysere, P.
The EXPERT Program is funded by ESA. The objective of the EXPERT mission is to perform a sub-orbital flight during which measurements of critical aero- thermodynamic phenomena will be obtained by using state-of-the-art instrumentation. As part of the EXPERT Flight Segment, the responsibility of the Cold Structure Development Design, Manufacturing and Validation was committed to the Belgian industrial team SONACA/SABCA. The EXPERT Cold Structure includes the Launcher Adapter, the Bottom Panel, the Upper Panel, two Cross Panels and the Parachute Bay. An additional Launcher Adapter was manufactured for the separation tests. The selected assembly definition and manufacturing technologies ( machined parts and sandwich panels) were dictated classically by the mass and stiffness, but also by the CoG location and the sensitive separation interface. Used as support for the various on-board equipment, the Cold Structure is fixed to but thermally uncoupled from the PM 1000 thermal shield. It is protect on its bottom panel by a thermal blanket. As it is a protoflight, analysis was the main tool for the verification. Low level stiffness and modal analysis tests have also been performed on the Cold Structure equipped with its ballast. It allowed to complete its qualification and to prepare SONACA/SABCA support for the system dynamic tests foreseen in 2011. The structure was finally coated with a thermal control black painting and delivered on time to Thales Alenia Space-Italy end of March 201.
Gresham Cathy R
Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and
Bada, Michael; Eckert, Miriam; Evans, Donald; Garcia, Kristin; Shipley, Krista; Sitnikov, Dmitry; Baumgartner, William A; Cohen, K Bretonnel; Verspoor, Karin; Blake, Judith A; Hunter, Lawrence E
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
van der Pluijm, B.
What do colleagues do with your assigned textbook? What they say or think about the material? Want students to be more engaged in their learning experience? If so, online materials that complement standard lecture format provide new opportunity through managed, online group annotation that leverages the ubiquity of internet access, while personalizing learning. The concept is illustrated with the new online textbook "Processes in Structural Geology and Tectonics", by Ben van der Pluijm and Stephen Marshak, which offers a platform for sharing of experiences, supplementary materials and approaches, including readings, mathematical applications, exercises, challenge questions, quizzes, alternative explanations, and more. The annotation framework used is Hypothes.is, which offers a free, open platform markup environment for annotation of websites and PDF postings. The annotations can be public, grouped or individualized, as desired, including export access and download of annotations. A teacher group, hosted by a moderator/owner, limits access to members of a user group of teachers, so that its members can use, copy or transcribe annotations for their own lesson material. Likewise, an instructor can host a student group that encourages sharing of observations, questions and answers among students and instructor. Also, the instructor can create one or more closed groups that offers study help and hints to students. Options galore, all of which aim to engage students and to promote greater responsibility for their learning experience. Beyond new capacity, the ability to analyze student annotation supports individual learners and their needs. For example, student notes can be analyzed for key phrases and concepts, and identify misunderstandings, omissions and problems. Also, example annotations can be shared to enhance notetaking skills and to help with studying. Lastly, online annotation allows active application to lecture posted slides, supporting real-time notetaking
Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http
We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements....... The annotations are a useful supplement to manual annotations and may help human annotators to quickly and reliably determine onset of head movements and to suggest which kind of head movement is taking place....
Kilicoglu, Halil; Ben Abacha, Asma; Mrabet, Yassine; Shooshan, Sonya E; Rodriguez, Laritza; Masterton, Kate; Demner-Fushman, Dina
Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding). To develop effective question understanding tools, question corpora semantically annotated for relevant question elements are needed. In this paper, we present a two-part consumer health question corpus annotated with several semantic categories: named entities, question triggers/types, question frames, and question topic. The first part (CHQA-email) consists of relatively long email requests received by the U.S. National Library of Medicine (NLM) customer service, while the second part (CHQA-web) consists of shorter questions posed to MedlinePlus search engine as queries. Each question has been annotated by two annotators. The annotation methodology is largely the same between the two parts of the corpus; however, we also explain and justify the differences between them. Additionally, we provide information about corpus characteristics, inter-annotator agreement, and our attempts to measure annotation confidence in the absence of adjudication of annotations. The resulting corpus consists of 2614 questions (CHQA-email: 1740, CHQA-web: 874). Problems are the most frequent named entities, while treatment and general information questions are the most common question types. Inter-annotator agreement was generally modest: question types and topics yielded highest agreement, while the agreement for more complex frame annotations was lower. Agreement in CHQA-web was consistently higher than that in CHQA-email. Pairwise inter-annotator agreement proved most
Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory
As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.
Along with rapidly expanding applications of life science and technology, technical experts have been implicated more and more often with ethical, social, and legal problems than before. It should be noted that in this background there are scientific and social uncertainty elements which are inevitable during the progress of life science in addition to the historically-established social unreliability to scientists and engineers. In order to solve these problems, therefore, we should establish the social governance with ‘relief’ and ‘reliance’ which enables for both citizens and engineers to share the awareness of the issues, to design social orders and criterions based on hypothetical sense of values for bioethics, to carry out practical use management of each subject carefully, and to improve the sense of values from hypothetical to universal. Concerning these measures, the technical experts can learn many things from the present performance in the medical field.
Expert PL/SQL Practices is a book of collected wisdom on PL/SQL programming from some of the best and the brightest in the field. Each chapter is a deep-dive into a specific problem, technology, or feature set that you'll face as a PL/SQL programmer. Each author has chosen their topic out of the strong belief that what they share can make a positive difference in the quality and scalability of code that you write. The path to mastery begins with syntax and the mechanics of writing statements to make things happen. If you've reached that point with PL/SQL, then let the authors of Expert PL/SQL
was able to prove such a machine could exist. 3 Lady Ada Lovelace was a contemporary of George Babbage. She studied with Babbage and wrote a popular...essay explaining the analytical engine. She is sometimes credited with inventing computer languages. The Ada computer language is named in her honor. -8...documentation and logic flow charting of the whole system. If your expert system is written in a highly structured language such as Ada , logic flow
Ionita, C; Carena, F
The ALICE experiment at CERN employs a number of human operators (shifters), who have to make sure that the experiment is always in a state compatible with taking Physics data. Given the complexity of the system and the myriad of errors that can arise, this is not always a trivial task. The aim of this paper is to describe an expert system that is capable of assisting human shifters in the ALICE control room. The system diagnoses potential issues and attempts to make smart recommendations for troubleshooting. At its core, a Prolog engine infers whether a Physics or a technical run can be started based on the current state of the underlying sub-systems. A separate C++ component queries certain SMI objects and stores their state as facts in a Prolog knowledge base. By mining the data stored in different system logs, the expert system can also diagnose errors arising during a run. Currently the system is used by the on-call experts for faster response times, but we expect it to be adopted as a standard tool by regular shifters during the next data taking period
Neely, Elaine M.
Entries in this annotated bibliography are divided into three sections: (1) an overview of information about the effect of divorce on the parent and child; (2) a review of studies and literature pertaining to the impact of divorce on elementary school students; and (3) a review of literature suggesting guidelines, activities, and techniques for…
Comprehensive review of the evidence regarding the effectiveness of community-based primary health care in improving maternal, neonatal and child health: 8. summary and recommendations of the Expert Panel.
Black, Robert E; Taylor, Carl E; Arole, Shobha; Bang, Abhay; Bhutta, Zulfiqar A; Chowdhury, A Mushtaque R; Kirkwood, Betty R; Kureshy, Nazo; Lanata, Claudio F; Phillips, James F; Taylor, Mary; Victora, Cesar G; Zhu, Zonghan; Perry, Henry B
The contributions that community-based primary health care (CBPHC) and engaging with communities as valued partners can make to the improvement of maternal, neonatal and child health (MNCH) is not widely appreciated. This unfortunate reality is one of the reasons why so few priority countries failed to achieve the health-related Millennium Development Goals by 2015. This article provides a summary of a series of articles about the effectiveness of CBPHC in improving MNCH and offers recommendations from an Expert Panel for strengthening CBPHC that were formulated in 2008 and have been updated on the basis of more recent evidence. An Expert Panel convened to guide the review of the effectiveness of community-based primary health care (CBPHC). The Expert Panel met in 2008 in New York City with senior UNICEF staff. In 2016, following the completion of the review, the Panel considered the review's findings and made recommendations. The review consisted of an analysis of 661 unique reports, including 583 peer-reviewed journal articles, 12 books/monographs, 4 book chapters, and 72 reports from the gray literature. The analysis consisted of 700 assessments since 39 were analyzed twice (once for an assessment of improvements in neonatal and/or child health and once for an assessment in maternal health). The Expert Panel recommends that CBPHC should be a priority for strengthening health systems, accelerating progress in achieving universal health coverage, and ending preventable child and maternal deaths. The Panel also recommends that expenditures for CBPHC be monitored against expenditures for primary health care facilities and hospitals and reflect the importance of CBPHC for averting mortality. Governments, government health programs, and NGOs should develop health systems that respect and value communities as full partners and work collaboratively with them in building and strengthening CBPHC programs - through engagement with planning, implementation (including the
Full Text Available Nous décrivons une méthode semi-automatique pour la création d’un corpus annoté en français. Ce corpus vise à permettre l’apprentissage d’un système d’analyse d’opinions dans des textes portant sur l’évaluation d’établissements de recherche et d’enseignement supérieur. La création de ce corpus s’effectue de manière itérative. Au cours de ces itérations une ontologie, une terminologie ainsi qu’un ensemble de patrons syntaxico sémantiques sont créés automatiquement à partir d’annotations antérieures effectuées par des experts du domaine. Ces ressources permettent par la suite de guider l’annotation automatique de nouveaux corpus. Chaque corpus annoté automatiquement est alors soumis à une nouvelle annotation manuelle des experts. Des résultats empiriques montrent que notre méthode permet d’accélérer et de faciliter le processus d’annotation. Le corpus résultat est annoté à la fois sémantiquement et syntaxiquement. Il est disponible gratuitement.
Schiltenwolf, Marcus; Beckmann, Nickolas; Gaidzik, Peter
Experts in criminal, civil and, increasingly, in social court cases have to present their expert opinions in court. This should be regarded not only as a burden, even if this may at times appear superfluous to the expert, perhaps because the discussion is mere repetition of the opinion he has already written, or because the questions appear to be biased against the expert. Nonetheless, the expert is always advised to appear calm and objective during the interrogation by judges and parties or participants and their legal representatives, and should not allow himself or herself to be provoked by questioning. Furthermore, it may be necessary to correct the written expert statement in the course of the interrogation, but this can be a sign of a truly competent medical expert. The expert consulted can be held liable for adverse health effects resulting from the interrogation and investigation, as well as for deliberate or grossly faulty reports. Georg Thieme Verlag KG Stuttgart · New York.
This report is structured into 3 main chapters. Chapter 1 is an introduction. Chapter 2 describes the results of the review of the Rovno 4 modernization programme area by area according to the Issue Book. Chapter 3 summarizes the important general conclusions and recommendations
Hartung, T.; Blaauboer, B.J.; Bosgra, S.; Carney, E.; Coenen, J.; Conolly, R.B.; Corsini, E.; Green, S.; Faustman, E.M.; Gaspari, A.; Hayashi, M.; Hayes, A.W.; Hengstler, J.G.; Knudsen, L.E.; Knudsen, T.B.; McKim, J.M.; Pfaller, W.; Roggen, E.L.
The European cosmetics legislation foresees a review in 2011 and possible postponement of the 2013 marketing ban to enforce the testing ban for systemic and repeated-dose animal tests. For this purpose, a 119-page report commissioned by the European Commission was published recently. Here, a group
Tavella, Elena; Papadopoulos, Thanos
the behaviour of one expert and two novice facilitators during a Viable System Model workshop. The findings suggest common facilitation patterns in the behaviour of experts and novices. This contrasts literature claiming that experts and novices behave and use their available knowledge differently......This paper provides an empirical study based on action research in which expert and novice facilitators in facilitated modelling workshops are compared. There is limited empirical research analysing the differences between expert and novice facilitators. Aiming to address this gap we study...... and facilitation strategies in contexts in which external, expert facilitation is not always possible are also discussed, and limitations of this study are provided....
Kronk, Gary W
Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...
Newman, Constance; Ng, Crystal; Pacqué-Margolis, Sara; Frymus, Diana
Gender discrimination and inequality in health professional education (HPE) affect students and faculty and hinder production of the robust health workforces needed to meet health and development goals, yet HPE reformers pay scant attention to these gender barriers. Gender equality must be a core value and professional practice competency for all actors in HPE and health employment systems. Peer-review and non-peer-review literature previously identified in a review of the literature identified interventions to counter gender discrimination and inequality in HPE and tertiary education systems in North America and the Caribbean; West, East, and Southern Africa; Asia; the Middle East and North Africa; Europe; Australia; and South America. An assessment considered 51 interventions addressing sexual harassment (18), caregiver discrimination (27), and gender equality (6). Reviewers with expertise in gender and health system strengthening rated and ranked interventions according to six gender-transformative criteria. Thirteen interventions were considered to have transformational potential to address gender-related obstacles to entry, retention, career progression, and graduation in HPE, when implemented in core sets of interventions. The review identified one set with potential to counter sexual harassment in HPE and two sets to counter caregiver discrimination. Gender centers and equal employment opportunity units are structural interventions that can address multiple forms of gender discrimination and inequality. The paper's broad aim is to encourage HPE leaders to make gender-transformative reforms in the current way of doing business and commit to themselves to countering gender discrimination and inequality. Interventions to counter gender discrimination should be seen as integral parts of institutional and instructional reforms and essential investments to scale up quality HPE and recruit and retain health workers in the systems that educate and employ them
This annotated bibliography of sociolinguistics is divided into the following sections: speech events, ethnography of speaking and anthropological approaches to analysis of conversation; discourse analysis (including analysis of conversation and narrative), ethnomethodology and nonverbal communication; sociolinguistics; pragmatics (including…
Cannataro, Mario; Hiram Guzzi, Pietro; Veltri, Pierangelo
Biological databases have been developed with a special focus on the efficient retrieval of single records or the efficient computation of specialized bioinformatics algorithms against the overall database, such as in sequence alignment. The continuos production of biological knowledge spread on several biological databases and ontologies, such as Gene Ontology, and the availability of efficient techniques to handle such knowledge, such as annotation and semantic similarity measures, enable the development on novel bioinformatics applications that explicitly use and integrate such knowledge. After introducing the annotation process and the main semantic similarity measures, this paper shows how annotations and semantic similarity can be exploited to improve the extraction and analysis of biologically relevant data from protein interaction databases. As case studies, the paper presents two novel software tools, OntoPIN and CytoSeVis, both based on the use of Gene Ontology annotations, for the advanced querying of protein interaction databases and for the enhanced visualization of protein interaction networks.
Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai
Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.
Styler, William F.; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet C; Erickson, Brad; Miller, Timothy; Lin, Chen; Savova, Guergana; Pustejovsky, James
This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task. PMID:29082229
Pararas-Carayannis, G.; Dong, B.; Farmer, R.
This compilation contains annotated citations to nearly 3000 tsunami-related publications from 1962 to 1976 in English and several other languages. The foreign-language citations have English titles and abstracts
Viborg Andersen, Kim; Debenham, John; Wagner, Roland
submissions. The papers are organized in topical sections on workflow automation, database queries, data classification and recommendation systems, information retrieval in multimedia databases, Web applications, implementational aspects of databases, multimedia databases, XML processing, security, XML......This book constitutes the refereed proceedings of the 16th International Conference on Database and Expert Systems Applications, DEXA 2005, held in Copenhagen, Denmark, in August 2005.The 92 revised full papers presented together with 2 invited papers were carefully reviewed and selected from 390...... schemata, query evaluation, semantic processing, information retrieval, temporal and spatial databases, querying XML, organisational aspects of databases, natural language processing, ontologies, Web data extraction, semantic Web, data stream management, data extraction, distributed database systems...
Kalkatawi, Manal M.
Genome annotation is an important topic since it provides information for the foundation of downstream genomic and biological research. It is considered as a way of summarizing part of existing knowledge about the genomic characteristics of an organism. Annotating different regions of a genome sequence is known as structural annotation, while identifying functions of these regions is considered as a functional annotation. In silico approaches can facilitate both tasks that otherwise would be difficult and timeconsuming. This study contributes to genome annotation by introducing several novel bioinformatics methods, some based on machine learning (ML) approaches. First, we present Dragon PolyA Spotter (DPS), a method for accurate identification of the polyadenylation signals (PAS) within human genomic DNA sequences. For this, we derived a novel feature-set able to characterize properties of the genomic region surrounding the PAS, enabling development of high accuracy optimized ML predictive models. DPS considerably outperformed the state-of-the-art results. The second contribution concerns developing generic models for structural annotation, i.e., the recognition of different genomic signals and regions (GSR) within eukaryotic DNA. We developed DeepGSR, a systematic framework that facilitates generating ML models to predict GSR with high accuracy. To the best of our knowledge, no available generic and automated method exists for such task that could facilitate the studies of newly sequenced organisms. The prediction module of DeepGSR uses deep learning algorithms to derive highly abstract features that depend mainly on proper data representation and hyperparameters calibration. DeepGSR, which was evaluated on recognition of PAS and translation initiation sites (TIS) in different organisms, yields a simpler and more precise representation of the problem under study, compared to some other hand-tailored models, while producing high accuracy prediction results. Finally
Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning
Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment...... to layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....
Wang, Qinghua; Arighi, Cecilia N; King, Benjamin L; Polson, Shawn W; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F; Page, Shallee T; Rendino, Marc Farnum; Thomas, William Kelley; Udwary, Daniel W; Wu, Cathy H
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome.
Wang, Qinghua; Arighi, Cecilia N.; King, Benjamin L.; Polson, Shawn W.; Vincent, James; Chen, Chuming; Huang, Hongzhan; Kingham, Brewster F.; Page, Shallee T.; Farnum Rendino, Marc; Thomas, William Kelley; Udwary, Daniel W.; Wu, Cathy H.
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (Leucoraja erinacea) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (http://skatebase.org) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the L. erinacea genome. PMID:22434832
As a first evaluation of long-term safety for KBS-3 repositories at Forsmark and Laxemar, the SIG (Site Investigation Group) found SR-Can to be a well-produced and generally well-argued safety assessment. Overall, SKB is to be complimented on this project. Members of of the two groups INSITE and OVERSITE within the SIG had somewhat differing views on how well SKB had made use of the site data available at the end of the SDM 1.2 stage of investigations. This difference is less to do with the extent of site characterisation than of its use and application, reflecting the different levels of maturity of SKB's geosphere and biosphere assessment programmes. The more recent and current work on the sites means that our concerns expressed in this review should, to a large extent, be addressable in or prior to SR-Site, provided SKB is so minded. However, we acknowledge that some of the issues we raise will not be fully resolved until underground rock characterisation from excavations or longer records of surface conditions are available. There are also some key aspects of SKB's methodology still under development that would benefit from review prior to their use in SR-Site. More space in the currently pressing schedule would allow for this review and a consequent increase in confidence. In any case, the authorities should be aware that SKB may face residual programmatic risks, associated principally with the underground design and layout (and their knockon effects into performance), even after SR-Site. An early understanding of some of these relationships would be helped by a plan (at least on an outline level) of the underground characterisation programme. We also note that many engineering matters are still to be confronted, not least the EBS design and its implementation, along with the treatment of high stresses, if Forsmark is selected. However, our views on the nature of the SR-Can analysis and the way in which site data have been utilised in it (our
Full Text Available SE41_AM1 PowerGet annotation In annotation process, KEGG, KNApSAcK and LipidMAPS ar..., predicted molecular formulas are used for the annotation. MS/MS patterns was used to suggest functional gr...-MS Fragment Viewer (http://webs2.kazusa.or.jp/msmsfragmentviewer/) are used for annotation and identification of the compounds. ...
Recent developments in expert system technology have led to the question whether such systems could be used for the enhancement of nuclear safety, particularly as advisory system during abnormal plant conditions. This document was produced during the Technical Committee Meeting (TCM) to Demonstrate and Review Expert System Prototypes, which was organized jointly by the International Atomic Energy Agency and British Nuclear Fuels Ltd (BNFL) and held at the BNFL site in Springfields, United Kingdom, from 30 September to 4 October 1991. A separate abstract was prepared for each of the 14 papers in this document. Refs, figs and tabs
Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese
Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.
Peyretaillade, Eric; Parisot, Nicolas; Polonais, Valérie; Terrat, Sébastien; Denonfoux, Jérémie; Dugat-Bony, Eric; Wawrzyniak, Ivan; Biderre-Petit, Corinne; Mahul, Antoine; Rimour, Sébastien; Gonçalves, Olivier; Bornes, Stéphanie; Delbac, Frédéric; Chebance, Brigitte; Duprat, Simone; Samson, Gaëlle; Katinka, Michael; Weissenbach, Jean; Wincker, Patrick; Peyret, Pierre
High-quality annotation of microsporidian genomes is essential for understanding the biological processes that govern the development of these parasites. Here we present an improved structural annotation method using transcriptional DNA signals. We apply this method to re-annotate four previously annotated genomes, which allow us to detect annotation errors and identify a significant number of unpredicted genes. We then annotate the newly sequenced genome of Anncaliia algerae. A comparative genomic analysis of A. algerae permits the identification of not only microsporidian core genes, but also potentially highly expressed genes encoding membrane-associated proteins, which represent good candidates involved in the spore architecture, the invasion process and the microsporidian-host relationships. Furthermore, we find that the ten-fold variation in microsporidian genome sizes is not due to gene number, size or complexity, but instead stems from the presence of transposable elements. Such elements, along with kinase regulatory pathways and specific transporters, appear to be key factors in microsporidian adaptive processes.
Osborne, John D; Flatow, Jared; Holko, Michelle; Lin, Simon M; Kibbe, Warren A; Zhu, Lihua (Julie); Danila, Maria I; Feng, Gang; Chisholm, Rex L
Background The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. Results We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations. Conclusion The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome. PMID:19594883
CHAIRMAN Ousmane Sy, Minister of territorial administration and local institutions (Republic of Mali) SCIENTIFIC COORDINATORS Jérôme Marie (Paris 10 University) Pierre Morand (IRD) Hamady N’Djim (Consulting engineer) MEMBERS Jean-François Bélières (Cirad) Cheik Cissé (Consulting legal expert) Lassine Diarra (IER-CRRA) Almoustapha Fofana (DNH) Pierrick Givone (Cemagref) Housseini Maïga (DNH) Mamadou Kabirou N’Diaye (IER) Didier Orange (IRD) Pierre Sibiri Traoré (Icrisat/IER)
In an article critical of experts, the cases argued for and against nuclear power are discussed under the headings: environmental hazards arising from the nuclear fuel cycle; proliferation of nuclear weapons capabilities via expansion of the nuclear power industry; political and social threats and restraints of a nuclear society (terrorism, reduction in civil liberties, centralised political and economic power); economic and employment disadvantages of nuclear power; impact of uranium mining on (Australian) aboriginal culture; inadequacy of nuclear power as a solution to energy problems; advantages of a 'soft energy path' based around conservation and renewable energy technologies. (U.K.)
Limitations of Expert Evidence Edited by Stephen Leadbeatter MB ChB MCRPath ISBN 1 86016 029 8 Printed in Great Britain by Cathedral Print Services Ltd, Salisbury, 1996 Kitap 25 Ekim 1994 te The Royal College of Physicians ve The Royal College of Pathologists tarafından düzenlenen konferanstan sonra hekimlere ve avukatlara konuyu tartışmaya açmak için basılmış. Bilirkişi görüşünün temel filozofisinin, bu görevi yapanlar ve bu hizmeti alanların yapabileceklerin...
Throughout history, advances in technology have come in spurts. A single great idea can often spur rapid change as the idea takes hold and is propagated, often in totally unexpected directions. Exadata embodies such a change in how we think about and manage relational databases. The key change lies in the concept of offloading SQL processing to the storage layer. That concept is a huge win, and its implementation in the form of Exadata is truly a game changer. Expert Oracle Exadata will give you a look under the covers at how the combination of hardware and software that comprise Exadata actua
Montoya Romero, Jose de Jesús; Castelazo Morales, Ernesto; Valerio Castro, Emilio; Velázquez Cornejo, Gerardo; Nava Muñoz, David Antonio; Escárcega Preciado, Jaime Arturo; Montoya Cossío, Javier; Pichardo Villalón, Guadalupe Mireya; Maldonado Aragón, Aristeo; Santana García, Héctor Rogelio; Fajardo Dueñas, Sergio; Mondragón Galindo, César Germán; García Lee, Teresa; García, Angel; Hernández de Morán, Marcela; Chávez Güitrón, Luis Eduardo; Jiménez Gutiérrez, Carlos
According to data from the World Health Organization and UNICEF from year 2009, iron deficiency is the most widespread nutritional deficiency worldwide. This deficiency causes an imbalance between needs and iron supply, which consequently results in anemia. Around the world, two million people suffer from anemia, half of which is due to iron deficiency. The most impacted groups are children and teenagers, due to their highest requirements derived from the growing process, and women in their reproductive age, due to their loss of iron derived from menstruating or to their highest iron needs during pregnancy. This increase in needs is not satisfied by the regular diet, since it includes an insufficient amount and/or low bioavailability of iron. To share with the medical community treating pregnant women the experience of an expert group so that they always bear in mind the repercussions caused by anemia during pregnancy, know more about the diagnostic possibilities and have a reference point for prescribing iron supplements. The consensus method was used through the expert panel group technique. Two rounds were taken for structuring the clinical questions. The first one was to facilitate working groups their focusing in the clinical topics and the population of interest; the second one was to aid in posing specific questions observing the Patient, Intervention, Compare and Outcome (PICO) structure. The primary and clinical secondary study variables were defined by the working groups from the previously developed questions and during the face-to-face working period, according to the natural history of the disease: risk factors, diagnostic classification, (either pharmacological or non pharmacological) treatment and prognosis. The level of evidence and clinical recommendation was classified based on the Evidence Classification Level and Clinical Recommendation of the Medicine Group based on Evidence from Oxford University. In Mexico, 20.6% of pregnant women suffer from
Li, Mulin Jun; Wang, Junwen
As high throughput methods, such as whole genome genotyping arrays, whole exome sequencing (WES) and whole genome sequencing (WGS), have detected huge amounts of genetic variants associated with human diseases, function annotation of these variants is an indispensable step in understanding disease etiology. Large-scale functional genomics projects, such as The ENCODE Project and Roadmap Epigenomics Project, provide genome-wide profiling of functional elements across different human cell types and tissues. With the urgent demands for identification of disease-causal variants, comprehensive and easy-to-use annotation tool is highly in demand. Here we review and discuss current progress and trend of the variant annotation field. Furthermore, we introduce a comprehensive web portal for annotating human genetic variants. We use gene-based features and the latest functional genomics datasets to annotate single nucleotide variation (SNVs) in human, at whole genome scale. We further apply several function prediction algorithms to annotate SNVs that might affect different biological processes, including transcriptional gene regulation, alternative splicing, post-transcriptional regulation, translation and post-translational modifications. The SNVrap web portal is freely available at http://jjwanglab.org/snvrap. Copyright © 2014 Elsevier Inc. All rights reserved.
In summary, there is a close analogical relationship between Expert Systems fundamental processes and Darwinian evolution processes: Just as evolution reaches a stabilization phase only after a successful mutation survives the natural selection, so does the new knowledge of the expert become a habit and noticeable only after it has been successfully transmitted as rules in the Expert System26.
Asari, S A L; Cho, M S; Kim, N K
Anastomotic leak and stricture formation are recognised complications of colorectal anastomoses. Surgical technique has been implicated in its aetiology. The use of innovative anastomotic techniques and technical standardisation may facilitate risk modification. Early detection of complications using novel diagnostic tests can lead to reduction in delay of diagnosis as long as a standard system is used. We review our practice for creation a safe anastomosis for minimal invasive rectal cancer resection. Several technical points discussed and evaluated based on the evidence. We propose several recommendations aiming to standardize the technique and to minimize anastomotic complications. Copyright © 2014 Elsevier Ltd. All rights reserved.
Tsoukalas, L.; Ikonomopoulos, A.; Uhrig, R.E.
This paper presents a methodology that couples rule-based expert systems using fuzzy logic, to pre-trained artificial neutral networks (ANN) for the purpose of transient identification in Nuclear Power Plants (NPP). In order to provide timely concise, and task-specific information about the may aspects of the transient and to determine the state of the system based on the interpretation of potentially noisy data a model-referenced approach is utilized. In it, the expert system performs the basic interpretation and processing of the model data, and pre-trained ANNs provide the model. having access to a set of neural networks that typify general categories of transients, the rule based system is able to perform identification functions. Membership functions - condensing information about a transient in a form convenient for a rule-based identification system characterizing a transient - are the output of neural computations. This allows the identification function to be performed with a speed comparable to or faster than that of the temporal evolution of the system. Simulator data form major secondary system pipe rupture is used to demonstrate the methodology. The results indicate excellent noise-tolerance for ANN's and suggest a new method for transient identification within the framework of Fuzzy Logic
Constantin, Anca; Feitosa, Klebert
We present here a program that aims at significantly diminishing the increasingly pervasive fear of approaching scientific concepts, particularly for people without math related backgrounds or interests. We built a series of grassroots yet unique science shows delivered in an up-beat, visually, and socially appealing environment, that bring forward the crucially needed bridge between the realm of scientific research and that of ordinary people through... comedy. While staged by two physics professors as hosts, the hilarious interactions between a science expert and a student-led improvisational comedy troupe constitute the main tool to unlock, decipher, and enjoy the mystery of the scientific research. Our program gets everyone in with lots of laughs, at no expense to academic quality, community involvement, diversity, excellence, integrity, and student focus. Our independent dedicated website for this project (sites.jmu.edu/demystifying), archives the podcasts (soundcloud.com/demystifying), short segment videos, blog posts, experts' bios, photo albums, testimonials, press releases, along with quantitative results of our assessment efforts. The overarching goal of this program is to pioneer a low cost yet efficient method of science education that can be replicated world wide.
Weiss, Kenneth J
In this clinical paper, the author discusses criminal confessions from the point of view of the expert witness who may be asked to comment on the reliability of the statement and waiver of rights. From the time a suspect is in police custody, constitutional protections against self-incrimination and for due process are in place. The Supreme Court set the standard for these situations in the 1966 Miranda v. Arizona decision. Although it has long been criticized by law enforcement, the decision was upheld in the 2000 decision in Dickerson v. U.S. For a waiver of rights to be valid, it must be a knowing, intelligent, and voluntary decision. Voluntariness is an equation of objective and subjective variables. Treatment by police, physical conditions of interrogation, the suspect's experience and mental state can alter the reliability of a confession. Accordingly, the author has devised a mnemonic for the recognition of conditions that may give rise to expert testimony. The conditions are: Mental illness, Intoxication, Retardation, Acquiescence, Narcotic withdrawal, Deception, and Abuse. These are discussed, supported by examples from the author's practice.
Full Text Available Abstract Background The expressed sequence tag (EST methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways. Results annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO, Enzyme Commission (EC and Kyoto Encyclopaedia of Genes and Genomes (KEGG annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools. Conclusion annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non
Duvick, Jon; Standage, Daniel S; Merchant, Nirav; Brendel, Volker P
Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today's pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant's Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. © 2016 American Society of Plant Biologists. All rights reserved.
The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/ PMID:25810773
The face is the most exposed part of our body, and deterioration of facial appearance, through disease or ageing, causes psychological distress. Acne lesions and subsequent pigmentation changes contribute to the unevenness of skin colour that is detrimental to facial attractiveness and leads to rejection and stigmatization in our society. The purpose of this review is to look at the root causes of premenstrual acne and, for the first time ever, propose that the specific timing of treatment can, at least in part, resolve the acne lesions. We postulate that it is the timing of the manual extraction that matters in resolving premenstrual acne and that the effectiveness of this therapy could be improved. Based on the reviewed evidence, we propose that it is important to remove the comedones at the time of ovulation, prior to the reduction of the size of the sebaceous orifice and epidermal barrier function, to counteract the onset of increased sebum production, prevent blockage of the pores and subsequent bacterial colonization and inflammation. If performed successfully, the extraction may contribute to a reduction in inflamed acne lesions and thus benefit women by increasing their facial attractiveness, well-being, social function and thereby decrease psychological stress. © 2010 The Author. ICS © 2010 Society of Cosmetic Scientists and the Société Française de Cosmétologie.
Howard, Dale C.
The paper examines implications of the application of computer expert systems in the field of education, particularly special education. The development of expert systems in general is reviewed as are its applications in education as intelligent tutoring systems and in special education in the areas of student classification, teacher education,…
Napier, Bruce A.
This article is a book review of a report from the International Atomic Energy Agency that was prepared by a team of scientists from Belarus, the Russian Federation, and Ukraine as an assessment of radiological contamination of the Dnieper River, which flows through these three countries. The topics covered begin with radioactive sources (actual and potential) including areas affected by the Chernobyl nuclear accident, nuclear power plants along the river and its tributaries, uranium mining and ore processing, radioactive waste storage and disposal sites, and non-power sources, such as medicine, industry, and research. The report continues with an assessment of human exposures to radiation from these sources. An additional area of consideration is radiological 'hot spots' in the region. The report finishes with conclusions and recommendations to the regional governments for a strategic action plan and individual government national plans.
Napier, Bruce A.
This article is a book review of a report from the International Atomic Energy Agency that was prepared by a team of scientists from Belarus, the Russian Federation, and Ukraine as an assessment of radiological contamination of the Dnieper River, which flows through these three countries. The topics covered begin with radioactive sources (actual and potential) including areas affected by the Chernobyl nuclear accident, nuclear power plants along the river and its tributaries, uranium mining and ore processing, radioactive waste storage and disposal sites, and non-power sources, such as medicine, industry, and research. The report continues with an assessment of human exposures to radiation from these sources. An additional area of consideration is radiological “hot spots” in the region. The report finishes with conclusions and recommendations to the regional governments for a strategic action plan and individual government national plans.
Watson, Clarence; Weiss, Kenneth J; Pouncey, Claire
The confession of a criminal defendant serves as a prosecutor's most compelling piece of evidence during trial. Courts must preserve a defendant's constitutional right to a fair trial while upholding the judicial interests of presenting competent and reliable evidence to the jury. When a defendant seeks to challenge the validity of that confession through expert testimony, the prosecution often contests the admissibility of the expert's opinion. Depending on the content and methodology of the expert's opinion, testimony addressing the phenomenon of false confessions may or may not be admissible. This article outlines the scientific and epistemological bases of expert testimony on false confession, notes the obstacles facing its admissibility, and provides guidance to the expert in formulating opinions that will reach the judge or jury. We review the 2006 New Jersey Superior Court decision in State of New Jersey v. George King to illustrate what is involved in the admissibility of false-confession testimony and use the case as a starting point in developing a best-practice approach to working in this area.
Gille, Christoph; Hübner, Katrin; Hoppe, Andreas; Holzhütter, Hermann-Georg
Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse and merging of existing models which concern present-day systems biology research more often. Two types of tools for the reconstruction of biological networks currently exist: (i) several sophisticated programs support graphical network editing and visualization. (ii) Data management systems permit reconstruction and curation of huge networks in a team of scientists including data integration, annotation and cross-referencing. We seeked ways to combine the advantages of both approaches. Metannogen, which was previously developed for network reconstruction, has been considerably improved. From now on, Metannogen provides sbml import and annotation of networks created elsewhere. This permits users of other network reconstruction platforms or modeling software to annotate their networks using Metannogen's advanced information management. We implemented word-autocompletion, multipattern highlighting, spell check, brace-expansion and publication management, and improved annotation, cross-referencing and team work requirements. Unspecific enzymes and transporters acting on a spectrum of different substrates are efficiently handled. The network can be exported in sbml format where the annotations are embedded in line with the miriam standard. For more comfort, Metannogen may be tightly coupled with the network editor such that Metannogen becomes an additional view for the focused reaction in the network editor. Finally, Metannogen provides local single user, shared password protected multiuser or public access to the annotation data. Metannogen is available free of charge at: http://www.bioinformatics.org/strap/metannogen/ or http://3d-alignment.eu/metannogen/. email@example.com Supplementary data are available at Bioinformatics online.
Full Text Available This work elaborates the semi-semantic part of speech annotation guidelines for the URDU.KON-TB treebank: an annotated corpus. A hierarchical annotation scheme was designed to label the part of speech and then applied on the corpus. This raw corpus was collected from the Urdu Wikipedia and the Jang newspaper and then annotated with the proposed semi-semantic part of speech labels. The corpus contains text of local & international news, social stories, sports, culture, finance, religion, traveling, etc. This exercise finally contributed a part of speech annotation to the URDU.KON-TB treebank. Twenty-two main part of speech categories are divided into subcategories, which conclude the morphological, and semantical information encoded in it. This article reports the annotation guidelines in major; however, it also briefs the development of the URDU.KON-TB treebank, which includes the raw corpus collection, designing & employment of annotation scheme and finally, its statistical evaluation and results. The guidelines presented as follows, will be useful for linguistic community to annotate the sentences not only for the national language Urdu but for the other indigenous languages like Punjab, Sindhi, Pashto, etc., as well.
Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.
Pack, R.W.; Lazar, P.M.; Schmidt, R.V.; Gaddy, C.D.
The project described in this paper explored the use of expert systems for plant operations training and assistance. Three computer technologies were reviewed: computer-aided instruction, expert systems, and expert training systems (ETS). The technology of CAI has been developed since the early 1960s, and a wide range of applications are available commercially today. Expert systems have been developed primarily as job performance aids, and the number of commercial applications is increasing. A fully developed ETS has models of the trainer and trainee, in addition to a knowledge base
Fishman, Julianna L.; Mudgett, Paul D.; Packham, Nigel J.; Schultz, John R.; Straub, John E., II
On August 9, 2003, NASA, with the cooperative support of the Vehicle Office of the International Space Station Program, the Advanced Human Support Technology Program, and the Johnson Space Center Habitability and Environmental Factors Office released a Request for Information, or RFI, to identify next-generation environmental monitoring systems that have demonstrated ability or the potential to meet defined requirements for monitoring air and water quality onboard the International Space Station. This report summarizes the review and analysis of the proposed solutions submitted to meet the water quality monitoring requirements. Proposals were to improve upon the functionality of the existing Space Station Total Organic Carbon Analyzer (TOCA) and monitor additional contaminants in water samples. The TOCA is responsible for in-flight measurement of total organic carbon, total inorganic carbon, total carbon, pH, and conductivity in the Space Station potable water supplies. The current TOCA requires hazardous reagents to accomplish the carbon analyses. NASA is using the request for information process to investigate new technologies that may improve upon existing capabilities, as well as reduce or eliminate the need for hazardous reagents. Ideally, a replacement for the TOCA would be deployed in conjunction with the delivery of the Node 3 water recovery system currently scheduled for November 2007.
Pai, Madhukar; Raison, Claire
Interview with Professor Madhukar Pai, MD, PhD by Claire Raison (Commissioning Editor). Professor Madhukar Pai did his medical training and community medicine residency in Vellore, India. He completed his PhD in epidemiology at the University of California, Berkeley (CA, USA) and a postdoctoral fellowship at the University of California, San Francisco (CA, USA). He is currently an associate professor of epidemiology at McGill University in Montreal (Canada). He serves as the Director of Global Health Programs, and as an Associate Director of the McGill International Tuberculosis Centre. In addition, he serves as a Consultant for the Bill & Melinda Gates Foundation. He also serves on the Scientific Advisory Committee of the Foundation for Innovative New Diagnostics, Geneva, Switzerland. His research is focused on improving the diagnosis and treatment of tuberculosis, especially in high-burden countries such as India and South Africa. His research is supported by grant funding from the Gates Foundation, Grand Challenges Canada and Canadian Institutes of Health Research. He has more than 200 peer-reviewed publications. He is recipient of the Union Scientific Prize, Chanchlani Global Health Research Award and Stars in Global Health award from Grand Challenges Canada, and is a member of the Royal Society of Canada.
Ramsey, J. E., Jr.
Three expert systems (ATEOPS, ATEFEXPERS, and ATEFATLAS), which were created to direct automatic test equipment (ATE), are reviewed. The purpose of the project was to develop an expert system to troubleshoot the converter-programmer power supply card for the F-15 aircraft and have that expert system direct the automatic test equipment. Each expert system uses a different knowledge base or inference engine, basing the testing on the circuit schematic, test requirements document, or ATLAS code. Implementing generalized modules allows the expert systems to be used for any different unit under test. Using converted ATLAS to LISP code allows the expert system to direct any ATE using ATLAS. The constraint propagated frame system allows for the expansion of control by creating the ATLAS code, checking the code for good software engineering techniques, directing the ATE, and changing the test sequence as needed (planning).
Full Text Available Since the past half century, expert testimony has played an increasingly important role in Chinese litigation. As the amount of expert testimony has grown, the issues about its admissibility and scientific foundation related to evidence are becoming to be questioned commonly. Since eighteenth central committee (China adopted the decision of the Central Committee of China on several important issues in promoting the legal system, the evidence was redefined to become the predominance in the whole proceeding. This article reviews the expert knowledge implicit in the opinions. It argues that the expert opinions ask judges to be aware of the role of communicationg between participants. Expert opinion is not only gained from laboratory, but also socially constructed in the rational expression and communication, which requir us think logically in terms of legal perceptions of science and expert knowledge in the empirical world.
Roberts, Kirk; Demner-Fushman, Dina
This paper discusses the creation of a semantically annotated corpus of questions about patient data in electronic health records (EHRs). The goal is to provide the training data necessary for semantic parsers to automatically convert EHR questions into a structured query. A layered annotation strategy is used which mirrors a typical natural language processing (NLP) pipeline. First, questions are syntactically analyzed to identify multi-part questions. Second, medical concepts are recognized and normalized to a clinical ontology. Finally, logical forms are created using a lambda calculus representation. We use a corpus of 446 questions asking for patient-specific information. From these, 468 specific questions are found containing 259 unique medical concepts and requiring 53 unique predicates to represent the logical forms. We further present detailed characteristics of the corpus, including inter-annotator agreement results, and describe the challenges automatic NLP systems will face on this task.
McCauley, Stephen; de Groot, Saskia; Mailund, Thomas
- and intergenomic regions. The presence of multiple coding regions complicates the concept of Ka/Ks ratio, and thus begs for an alternative approach when investigating selection strengths. Building on the paper by McCauley & Hein (2006), we develop a method for annotating a viral genome coding in overlapping...... may thus achieve an annotation both of coding regions as well as selection strengths, allowing us to investigate different selection patterns and hypotheses. Results: We illustrate our method by applying it to a multiple alignment of four HIV2 sequences, as well as four Hepatitis B sequences. We...... obtain an annotation of the coding regions, as well as a posterior probability for each site of the strength of selection acting on it. From this we may deduce the average posterior selection acting on the different genes. Whilst we are encouraged to see in HIV2, that the known to be conserved genes gag...
Cooper, E. G.
The Automation Technology Branch of NASA's Langley Research Center is employing increasingly complex degrees of operator/robot cooperation (telerobotics). A good relationship between the operator and computer is essential for smooth performance by a telerobotic system. ESG (Expert Script Generator) is a software package that automatically generates high-level task objective commands from the NASA Intelligent Systems Research Lab's (ISRL's) complex menu-driven language. ESG reduces errors and makes the telerobotics lab accessible to researchers who are not familiar with the comprehensive language developed by ISRL for interacting with the various systems of the ISRL testbed. ESG incorporates expert system technology to capture the typical rules of operation that a skilled operator would use. The result is an operator interface which optimizes the system's capability to perform a task remotely in a hazardous environment, in a timely manner, and without undue stress to the operator, while minimizing the chance for operator errors that may damage equipment. The intricate menu-driven command interface which provides for various control modes of both manipulators and their associated sensors in the TeleRobotic System Simulation (TRSS) has a syntax which is both irregular and verbose. ESG eliminates the following two problems with this command "language": 1) knowing the correct command sequence to accomplish a task, and 2) inputting a known command sequence without typos and other errors. ESG serves as an additional layer of interface, working in conjunction with the menu command processor, not supplanting it. By specifying task-level commands, such as GRASP, CONNECT, etc., ESG will generate the appropriate menu elements to accomplish the task. These elements will be collected in a script file which can then be executed by the ISRL menu command processor. In addition, the operator can extend the list of task-level commands to include customized tasks composed of sub
Kobayashi, Daisuke; Sakamoto, Ryota; Nomura, Yoshihiko
This paper describes a learning assistant system using motion capture data and annotation to teach "Naginata-jutsu" (a skill to practice Japanese halberd) performance. There are some video annotation tools such as YouTube. However these video based tools have only single angle of view. Our approach that uses motion-captured data allows us to view any angle. A lecturer can write annotations related to parts of body. We have made a comparison of effectiveness between the annotation tool of YouTube and the proposed system. The experimental result showed that our system triggered more annotations than the annotation tool of YouTube.
Tobita, Yoshimasa; Yamaguchi, Takashi; Matsumoto, Mitsuo; Ono, Kiyoshi.
The computer code system which can evaluate the mass balance and cycle cost in nuclear fuel cycle has been developing a PNC using an artificial intelligence technique. This system is composed of the expert system, data base and analysis codes. The expert system is the most important one in the system and the content of the expert system is explained in this paper. The expert system has the three functions. The first is the function of understanding the meaning of user's questions by natural language, the second is the function of selecting the best way to solve the problem given by the user using the knowledge which is already installed in the system, and the last is the function of answering the questions. The knowledge of the experts installed in the expert system is represented by the frame-type rules. Therefore, the knowledge will be simply added to the system, and consequently the system will be easily extended. (author)
Stegmann, Mikkel Bille
Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J
We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
Koney, Nii; Roudenko, Alexandra; Ro, Maryann; Bahl, Sumeet; Kagen, Alexander
The evolving health care landscape demands a multidisciplinary approach to care and increased emphasis on patient engagement. Radiologists may play an important role in this respect, by improving patient agency and understanding through direct patient interaction. The purpose of this study is to assess patient preferences and perceptions regarding direct communication with radiologists, focusing on a medically underserved demographic. Our institutional review board approved this HIPAA-compliant study. English- and/or Spanish-speaking adults undergoing imaging studies across two tertiary-care hospitals and a busy outpatient center were surveyed over a consecutive two-month period, to assess knowledge of the role of a radiologist, interest in, and perceived benefits of reviewing examination results with imaging experts. A total of 628 surveys were completed: 20% of total respondents accurately identified the role of radiologists; 28% identified radiologists as doctors. A total of 68% of respondents expressed an interest in receiving imaging results immediately, or whenever results became available, regardless of when referring physicians received results. An interest in reviewing imaging results with an expert was indicated by 81% of respondents; 88% anticipated that reviewing imaging results with an expert would be beneficial. Although 58% of respondents indicated that they might be willing to pay out of pocket for such a service, 50% selected $0 when asked to indicate an amount. Although most patients do not know the role of radiologists, they want immediate results, and perceive value in consulting directly with imaging experts. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.
Goben, Abigail; Raszewski, Rebecca
Librarians navigating research data management self-education have an increasing body of literature to choose from, which may become overwhelming. This annotated bibliography reviews: (1) U.S. federal policies; (2) articles; and (3) books to assist librarians who are self-educating on research data management or are seeking background reading…
Johnson, William B.; And Others
This annotated bibliography developed in connection with an ongoing investigation of the use of computer simulations for fault diagnosis training cites 61 published works taken predominantly from the disciplines of engineering, psychology, and education. A review of the existing literature included computer searches of the past ten years of…
This paper reviews the role of multimedia vocabulary annotation (MVA) in facilitating second language (L2) reading and listening activities. It examines the multimedia learning and multimedia language learning theories that underlie the MVA research, synthesizes the findings on MVA in the last decade, and identifies three underresearched areas on…
An annotated list of 80 species of lady beetles (Coccinellidae: Coleoptera) that occur in the state of Iowa, U.S.A., is presented based on literature searches and a review of over 3500 specimens from institutional and private collections. The list includes new state records for Scymnus tenebrosus M...
Roberts, Dayton Y., Ed.
The selected annotations in this bibliography were compiled from articles in college and university law reviews and journals, other specialized law journals and from educational journals and periodicals. Topics covered include student discipline, academic freedom, faculty tenure, political speakers, collective bargaining, student rights, financial…
Klappholz, Lowell, Ed.
Presented is a research bibliography (covering the years 1888 to 1975) which contains annotations of 439 studies and bibliographical citations of 419 additional projects on physical education, recreation, and psychomotor function of mentally retarded persons. In addition to review and analyses of trends and major findings, unanswered questions…
de Monchy, Allan R.; And Others
Discusses two computer problem solving programs: rule-based expert systems and decision analysis expert systems. Explores the application of expert systems to automated chemical analyses. Presents six factors to consider before using expert systems. (MVL)
Grider, Daryl A.
Discusses expertise, what an expert system is, what an expert system shell is, what expert systems can and cannot do, knowledge engineering and technical communicators, and planning and managing expert system projects. (SR)
Zahir, Sajjad; Chang, Chew Lik
Describes the design and development of a prototype expert system called ONLINE-EXPERT that helps users select online databases and vendors that meet users' needs. Search strategies are discussed; knowledge acquisition and knowledge bases are described; and the Analytic Hierarchy Process (AHP), a decision analysis technique that ranks databases,…
Mieg, Harald A.
Purpose: This paper aims at a better understanding of expert roles in transdisciplinary projects. Thus, the main purpose is the analysis of the roles of experts in transdisciplinary projects. Design/methodology/approach: The analysis of the ETH-UNS case studies from the point of view of the psychology of expertise and the sociology of professions…
Full Text Available Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator’s knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user’s vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large.
Guo, Haihong; Na, Xu; Li, Jiao
Health question-answering (QA) systems have become a typical application scenario of Artificial Intelligent (AI). An annotated question corpus is prerequisite for training machines to understand health information needs of users. Thus, we aimed to develop an annotated classification corpus of Chinese health questions (Qcorp) and make it openly accessible. We developed a two-layered classification schema and corresponding annotation rules on basis of our previous work. Using the schema, we annotated 5000 questions that were randomly selected from 5 Chinese health websites within 6 broad sections. 8 annotators participated in the annotation task, and the inter-annotator agreement was evaluated to ensure the corpus quality. Furthermore, the distribution and relationship of the annotated tags were measured by descriptive statistics and social network map. The questions were annotated using 7101 tags that covers 29 topic categories in the two-layered schema. In our released corpus, the distribution of questions on the top-layered categories was treatment of 64.22%, diagnosis of 37.14%, epidemiology of 14.96%, healthy lifestyle of 10.38%, and health provider choice of 4.54% respectively. Both the annotated health questions and annotation schema were openly accessible on the Qcorp website. Users can download the annotated Chinese questions in CSV, XML, and HTML format. We developed a Chinese health question corpus including 5000 manually annotated questions. It is openly accessible and would contribute to the intelligent health QA system development.
Li, Minghui; Goncearenco, Alexander; Panchenko, Anna R
In this review we describe a protocol to annotate the effects of missense mutations on proteins, their functions, stability, and binding. For this purpose we present a collection of the most comprehensive databases which store different types of sequencing data on missense mutations, we discuss their relationships, possible intersections, and unique features. Next, we suggest an annotation workflow using the state-of-the art methods and highlight their usability, advantages, and limitations for different cases. Finally, we address a particularly difficult problem of deciphering the molecular mechanisms of mutations on proteins and protein complexes to understand the origins and mechanisms of diseases.
Schwartz, David Charles; Severin, Jessica
There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.
Bakke, Peter; Carney, Nick; DeLoache, Will
Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited...... in databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology...... and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species-specific consensus...
Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis
This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups...
L. Rutledge (Lloyd); J.R. van Ossenbruggen (Jacco); L. Hardman (Lynda)
textabstractThe Semantic Web envisions a Web that is both human readable and machine processible. In practice, however, there is still a large conceptual gap between annotated content repositories on the one hand, and coherent, human readable Web pages on the other. To bridge this conceptual gap,
Hardman, L.; Obrenović, Ž.; Nack, F.; Troncy, R.; Huet, B.; Schenk, S.
While many multimedia systems allow the association of semantic annotations with media assets, there is no agreed way of sharing these among systems. This chapter identifies a small number of fundamental processes of media production, which the author terms canonical processes, which can be
L. Hardman (Lynda); Z. Obrenovic; F.-M. Nack (Frank); B. Kerhervé; K. Piersol
htmlabstractWhile many multimedia systems allow the association of semantic annotations with media assets, there is no agreed-upon way of sharing these among systems. As an initial step within the multimedia community, we identify a small number of fundamental processes of media production, which we
Hardman, L.; Obrenović, Ž.; Nack, F.; Kerhervé, B.; Piersol, K.
While many multimedia systems allow the association of semantic annotations with media assets, there is no agreed-upon way of sharing these among systems. As an initial step within the multimedia community, we identify a small number of fundamental processes of media production, which we term
NHSA Dialog, 2008
This article provides an annotated bibliography of various children's books. It includes listings of books that illustrate the dynamic relationships within the natural environment, economic context, racial and cultural identities, cross-group similarities and differences, gender, different abilities and stories of injustice and resistance.
Hoyle, David C.; Brass, Andrew
We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.
Dorothy B. Durband
Full Text Available The following annotated bibliography contains a summary of articles and websites, as well as a list of books related to financial therapy. The resources were compiled through e-mail solicitation from members of the Financial Therapy Forum in November 2008. Members of the forum are marked with an asterisk.
J.C. van de Pol (Jaco)
textabstractA simple kind of strategy annotations is investigated, giving rise to a class of strategies, including leftmost-innermost. It is shown that under certain restrictions, an interpreter can be written which computes the normal form of a term in a bottom-up traversal. The main contribution
Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.
Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.
Stamou, G.; Ossenbruggen, J.R.; Pan, J.; Schreiber, A.T.
Multimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich descriptions of
G. Stamou; J.R. van Ossenbruggen (Jacco); J.Z. Pan (Jeff); G. Schreiber (Guus)
textabstractMultimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich
Chapa, Evey, Ed.; And Others
Intended to provide interested persons, researchers, and educators with information about "la mujer Chicana", this annotated bibliography cites 320 materials published between 1916 and 1975, with the majority being between 1960 and 1975. The 12 sections cover the following subject areas: Chicana publications; Chicana feminism and…
Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.
Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.
Strachan, J.D.; Corrigan, G.
This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables
This annotated bibliography contains over 500 sources on the historical and contemporary development and expression of male and female sexuality. There are 68 topic headings which provide easy access for subject areas. A major portion of the bibliography is devoted to contemporary male-female sexuality. These materials consist of research findings…
McDowell, Jillian Marie; Johnson, Gillian Margaret; Hetherington, Barbara Helen
Quality technique documentation is integral to the practice of manual therapy, ensuring uniform application and reproducibility of treatment. Manual therapy techniques are described by annotations utilizing a range of acronyms, abbreviations and universal terminology based on biomechanical and anatomical concepts. The various combinations of therapist and patient generated forces utilized in a variety of weight-bearing positions, which are synonymous with Mulligan Concept, challenge practitioners existing annotational skills. An annotation framework with recording rules adapted to the Mulligan Concept is proposed in which the abbreviations incorporate established manual therapy tenets and are detailed in the following sequence of; starting position, side, joint/s, method of application, glide/s, Mulligan technique, movement (or function), whether an assistant is used, overpressure (and by whom) and numbers of repetitions or time and sets. Therapist or patient application of overpressure and utilization of treatment belts or manual techniques must be recorded to capture the complete description. The adoption of the Mulligan Concept annotation framework in this way for documentation purposes will provide uniformity and clarity of information transfer for the future purposes of teaching, clinical practice and audit for its practitioners. Copyright © 2014 Elsevier Ltd. All rights reserved.
Tutunjian, Beth Ann
This annotated publications list on homelessness contains citations for 19 publications, most of which deal with problems of alcohol or drug abuse among homeless persons. Citations are listed alphabetically by author and cover the topics of homelessness and alcoholism, drug abuse, public policy, research methodologies, mental illness, alcohol- and…
Lamy, Philippe; Andersen, Claus Lindbjerg; Wikman, Friedrik
allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose-response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree...
Li, Shengting; Ma, Lijia; Li, Heng
Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...
Heylen, Dirk K.J.; Reidsma, Dennis; Ordelman, Roeland J.F.; Devillers, L.; Martin, J-C.; Cowie, R.; Batliner, A.
We discuss the annotation procedure for mental state and emotion that is under development for the AMI (Augmented Multiparty Interaction) corpus. The categories that were found to be most appropriate relate not only to emotions but also to (meta-)cognitive states and interpersonal variables. The
newapplicationsfor the ePNK and, in particular, visualizing the result of an application in the graphical editor of the ePNK by singannotations, and interacting with the end user using these annotations. In this paper, we give an overview of the concepts of ePNK applications by discussing the implementation...
Bloem, J.; Bański, P.; Kupietz, M.; Lüngen, H.; Witt, A.; Barbaresi, A.; Biber, H.; Breiteneder, E.; Clematide, S.
This study discusses evaluation methods for linguists to use when employing an automatically annotated treebank as a source of linguistic evidence. While treebanks are usually evaluated with a general measure over all the data, linguistic studies often focus on a particular construction or a group
Popovich, Mark, Comp.; And Others
The purposes of this bibliography are to bring together materials that relate to the history of newspapers in Indiana and to assess, in a general way, the value of the material. The bibliography contains 415 entries, with descriptive annotations, arranged in seven sections: books; special materials; general newspaper histories and lists of…
Liu, Weifeng; Tao, Dacheng
The rapid development of computer hardware and Internet technology makes large scale data dependent models computationally tractable, and opens a bright avenue for annotating images through innovative machine learning algorithms. Semisupervised learning (SSL) therefore received intensive attention in recent years and was successfully deployed in image annotation. One representative work in SSL is Laplacian regularization (LR), which smoothes the conditional distribution for classification along the manifold encoded in the graph Laplacian, however, it is observed that LR biases the classification function toward a constant function that possibly results in poor generalization. In addition, LR is developed to handle uniformly distributed data (or single-view data), although instances or objects, such as images and videos, are usually represented by multiview features, such as color, shape, and texture. In this paper, we present multiview Hessian regularization (mHR) to address the above two problems in LR-based image annotation. In particular, mHR optimally combines multiple HR, each of which is obtained from a particular view of instances, and steers the classification function that varies linearly along the data manifold. We apply mHR to kernel least squares and support vector machines as two examples for image annotation. Extensive experiments on the PASCAL VOC'07 dataset validate the effectiveness of mHR by comparing it with baseline algorithms, including LR and HR.
Allix, Beverley, Comp.
This annotated bibliography covers the following types of materials of use to teachers of English for Special Purposes: (1) books, monographs, reports, and conference papers; (2) periodical articles and essays in collections; (3) theses and dissertations; (4) bibliographies; (5) dictionaries; and (6) textbooks in series by publisher. Section (1)…
E. Durant McArthur; Bryce A. Richardson; Stanley G. Kitchen
This annotated bibliography documents the research that has been conducted on the Great Basin Experimental Range (GBER, also known as the Utah Experiment Station, Great Basin Station, the Great Basin Branch Experiment Station, Great Basin Experimental Center, and other similar name variants) over the 102 years of its existence. Entries were drawn from the original...
Tykodi, R. J.
Urges chemistry teachers to have students annotate the chemical reactions in aqueous-solutions that they see in their textbooks and witness in the laboratory. Suggests this will help students recognize the reaction type more readily. Examples are given for gas formation, precipitate formation, redox interaction, acid-base interaction, and…
Fore, C.S.; Carrier, R.F.; Brewster, R.H.; Hyder, L.K.; Barnes, K.A.
This annotated bibliography of 416 references represents the third in a series to be published by the Hazardous Materials Information Center containing scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on disposal site, environmental transport, and waste treatment studies as well as general reviews on the subject. The publication covers both domestic and foreign literature for the period 1951 to 1981. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology, and Site Resources; Regulatory and Economic Aspects; Social Aspects; Transportation Technology; Waste Production; and Waste Treatment. Entries in each of the chapters are further classified as a field study, laboratory study, theoretical study, or general overview involving one or more of these research areas
Coruh, Ceyda; Shahid, Saima; Axtell, Michael J
A key goal in genomics is the complete annotation of the expressed regions of the genome. In plants, substantial portions of the genome make regulatory small RNAs produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins. These include miRNAs and various types of endogenous siRNAs. Small RNA-seq, enabled by cheap and fast DNA sequencing, has produced an enormous volume of data on plant miRNA and siRNA expression in recent years. In this review, we discuss recent progress in using small RNA-seq data to produce stable and reliable annotations of miRNA and siRNA genes in plants. In addition, we highlight key goals for the future of small RNA gene annotation in plants. Copyright © 2014 Elsevier Ltd. All rights reserved.
Full Text Available We describe an "Annotated Lectures" system, which will be used in a global virtual teaching and student collaboration event on embodied intelligence presented by the University of Zurich. The lectures will be broadcasted via video-conference to lecture halls of different universities around the globe. Among other collaboration features, an "Annotated Lectures" system will be implemented in a 3D collaborative virtual environment and used by the participating students to make annotations to the video-recorded lectures, which will be sent to and answered by their supervisors, and forwarded to the lecturers in an aggregated way. The "Annotated Lectures" system aims to overcome the issues of limited studentinstructor interaction in large-scale education, and to foster an intercultural and multidisciplinary discourse among students who review the lectures in a group. After presenting the concept of the "Annotated Lectures" system, we discuss a prototype version including a description of the technical components and its expected benefit for large-scale global education.
Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L
The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Grossman, Arthur R
Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual
Roysdon, Christine, Ed.; White, Howard D., Ed.
Eleven articles introduce expert systems applications in library and information science, and present design and implementation issues of system development for reference services. Topics covered include knowledge based systems, prototype development, the use of artificial intelligence to remedy current system inadequacies, and an expert system to…
Hofmeister, Alan M.; Ferrara, Joseph M.
The application of artificial intelligence to the problems of education is examined. One of the most promising areas in artificial intelligence is expert systems technology which engages the user in a problem-solving diaglogue. Some of the characteristics that make expert systems "intelligent" are identified and exemplified. The rise of…
-printer specialist solve their printer problems, and give time-based assistance to those who are in need of instant help when the maintenance experts are not handy. 2.0. Architecture of the LAPTEX Expert System. Working memory. (Fact base).
This paper presents an annotation model for harmonic structure of a piece of music, and a rule system that supports the automatic generation of harmonic annotations. Musical structure has so far received relatively little attention in the context of musical metadata and annotation, although it is highly relevant for musicians, musicologists and indirectly for music listeners. Activities in semantic annotation of music have so far mostly concentrated on features derived from audio data and fil...
Kalkatawi, Manal M.
Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/
Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B
Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .
As part of SCK-CEN's social sciences and humanities programme, a reflection group on 'Expert Culture' was established. The objectives of the reflection group are: (1) to clarify the role of SCK-CEN experts; (2) to clarify the new role of expertise in the evolving context of risk society; (3) to confront external views and internal SCK-CEN experiences on expert culture; (4) to improve trust building of experts and credibility of SCK-CEN as a nuclear actor in society; (5) to develop a draft for a deontological code; (6) to integrate the approach in training on assertivity and communication; (7) to create an output for a topical day on the subject of expert culture. The programme, achievements and perspectives of the refection group are summarised
Jones, Darrick C.
One important goal of physics education is to help students develop reasoning patterns similar to those of expert physicists. To achieve this goal, physics educators must know what makes physics experts so successful at solving challenging physics problems. However, this dimension of physics expertise has not been fully explored by the physics education research (PER) community. In this dissertation, I describe several studies I have conducted that further the PER community's understanding of physics expertise. In these studies, I investigate how expert physicists reason as they solve unfamiliar, challenging physics problems by using a resource-based model of cognition to analyze videotaped recordings of problem solving sessions. By developing a way to determine when experts are making conceptual breakthroughs I analyze what resources experts use during conceptual breakthroughs. In the first study, I show that physics conceptual breakthroughs are characterized by reasoning which combines resources related to intuitive knowledge, higher level physics based conceptual knowledge, and epistemological knowledge. In the second study, I develop a way to reliably code for epistemological resources and determine what epistemological resources experts rely on most during conceptual breakthroughs. My findings show that experts rely on contrasting cases more often than any other epistemological resource. In the third study, I use variation theory to investigate how experts use contrasting cases. I look for patterns across all instances when experts use contrasting cases to make a conceptual breakthrough and show how scientific epistemology can be used to better understand experts' use of contrasting cases. I discuss how the findings of each study can be used to inform physics education.
Boot, P.; Braungart, Georg; Jannidis, Fotis; Gendolla, Peter
Robinson and others have recently called for dynamic and collaborative digital scholarly editions. Annotation is a key component for editions that are not merely passive, read-only repositories of knowledge. Annotation facilities (both annotation creation and display), however, require complex
van Son, C.M.; Caselli, T.; Fokkens, A.S.; Maks, E.; Morante Vallejo, R.; Aroyo, L.M.; Vossen, P.T.J.M.
This paper presents a framework and methodology for the annotation of perspectives in text. In the last decade, different aspects of linguistic encoding of perspectives have been targeted as separated phenomena through different annotation initiatives. We propose an annotation scheme that integrates
Full Text Available SE22_AM1 Annotation based on a grading system Collected mass spectral features, tog...ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Co...mparison with public databases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...
Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...
Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.
Brettin, Thomas; Davis, James J; Disz, Terry; Edwards, Robert A; Gerdes, Svetlana; Olsen, Gary J; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D; Shukla, Maulik; Thomason, James A; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R; Xia, Fangfang
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.
Chen, Geng; Shi, Tieliu; Shi, Leming
Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts (especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome- guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.
Maier-Hein, Lena; Mersmann, Sven; Kondermann, Daniel; Bodenstedt, Sebastian; Sanchez, Alexandro; Stock, Christian; Kenngott, Hannes Gotz; Eisenmann, Mathias; Speidel, Stefanie
Machine learning algorithms are gaining increasing interest in the context of computer-assisted interventions. One of the bottlenecks so far, however, has been the availability of training data, typically generated by medical experts with very limited resources. Crowdsourcing is a new trend that is based on outsourcing cognitive tasks to many anonymous untrained individuals from an online community. In this work, we investigate the potential of crowdsourcing for segmenting medical instruments in endoscopic image data. Our study suggests that (1) segmentations computed from annotations of multiple anonymous non-experts are comparable to those made by medical experts and (2) training data generated by the crowd is of the same quality as that annotated by medical experts. Given the speed of annotation, scalability and low costs, this implies that the scientific community might no longer need to rely on experts to generate reference or training data for certain applications. To trigger further research in endoscopic image processing, the data used in this study will be made publicly available.
Dobnikar, M.; Nemec, T.; Muehleisen, A.
Each type of an accident in a Nuclear Power Plant (NPP) causes immediately after the start of the accident variations of physical parameters that are typical for that type of the accident thus enabling its identification. Examples of these parameter are: decrease of reactor coolant system pressure, increase of radiation level in the containment, increase of pressure in the containment. An expert software enabling a fast preliminary identification of the type of the accident in Krsko NPP has been developed. As input data selected typical parameters from Emergency Response Data System (ERDS) of the Krsko NPP are used. Based on these parameters the expert software identifies the type of the accident and also provides the user with appropriate references (past analyses and other documentation of such an accident). The expert software is to be used as a support tool by an expert team that forms in case of an emergency at Slovenian Nuclear Safety Administration (SNSA) with the task to determine the cause of the accident, its most probable scenario and the source term. The expert software should provide initial identification of the event, while the final one is still to be made after appropriate assessment of the event by the expert group considering possibility of non-typical events, multiple causes, initial conditions, influences of operators' actions etc. The expert software can be also used as an educational/training tool and even as a simple database of available accident analyses. (author)
Grigorenko, Elena L; Klin, Ami; Volkmar, Fred
Hyperlexia is the phenomenon of spontaneous and precocious mastery of single-word reading that has been of interest to clinicians and researchers since the beginning of the last century. An extensive search of publications on the subject of hyperlexia was undertaken and all available publications were reviewed. The literature can be subdivided into discussions of the following issues: (1) whether hyperlexia is a phenomenon that is characteristic only of specific clinical populations (e.g., children with developmental delays) or whether it can also be observed in the general population; (2) whether hyperlexia is a distinct syndrome comorbid with a number of different disorders or whether it is a part of the spectrum of some other clinical condition(s); (3) whether hyperlexia should be defined through single-word reading superiority with regard to reading comprehension, vocabulary, general intelligence, any combination of the three, or all three characteristics; (4) whether there is a specific neuropsychological profile associated with hyperlexia; (5) whether hyperlexia is characterized by a particular developmental profile; and (6) whether hyperlexia should be viewed as a disability (deficit) or superability (talent). We interpret the literature as supporting the view that hyperlexia is a superability demonstrated by a very specific group of individuals with developmental disorders (defined through unexpected single-word reading in the context of otherwise suppressed intellectual functioning) rather than as a disability exhibited by a portion of the general population (defined through a discrepancy between levels of single-word reading and comprehension). We simultaneously argue, however, that multifaceted and multi-methodological approaches to studying the phenomenon of hyperlexia, defined within the research framework of understanding single-word reading, are warranted and encouraged.
Das, Kamalika; Avrekh, Ilya; Matthews, Bryan; Sharma, Manali; Oza, Nikunj
Often the manual review of large data sets, either for purposes of labeling unlabeled instances or for classifying meaningful results from uninteresting (but statistically significant) ones is extremely resource intensive, especially in terms of subject matter expert (SME) time. Use of active learning has been shown to diminish this review time significantly. However, since active learning is an iterative process of learning a classifier based on a small number of SME-provided labels at each iteration, the lack of an enabling tool can hinder the process of adoption of these technologies in real-life, in spite of their labor-saving potential. In this demo we present ASK-the-Expert, an interactive tool that allows SMEs to review instances from a data set and provide labels within a single framework. ASK-the-Expert is powered by an active learning algorithm for training a classifier in the backend. We demonstrate this system in the context of an aviation safety application, but the tool can be adopted to work as a simple review and labeling tool as well, without the use of active learning.
Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos
Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/.
Kveladze, Irma; Kraak, Menno-Jan
Movement data is collected by nearly everyone at any time. This data is not limited the trajectories of people, today’s technology also allows the simultaneous collection of trip related annotations like photos, video’s, voice, and texts. The combination of trajectories and annotations is a rich...... source to monitor movement in a context and discover known and unknown patterns. Often the annotations are implicitly geotagged by the gps-enabled devices like phones and cameras which are used to collect the annotations. This allows a match between the track and annotation based on coordinates....... Otherwise the trajectories and annotations can be matched based on their respective time stamps. The geotagged material is often used on social media sites to exchange the whereabouts of people. The annotations are place on dedicated site such as Flickr and Panoramio. Via mash-ups it is also possible...
and dhurrin, which have not previously been characterized in blueberries. There are more than 44,500 spider species with distinct habitats and unique characteristics. Spiders are masters of producing silk webs to catch prey and using venom to neutralize. The exploration of the genetics behind these properties...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... has just started. We have assembled and annotated the first two spider genomes to facilitate our understanding of spiders at the molecular level. The need for analyzing the large and increasing amount of sequencing data has increased the demand for efficient, user friendly, and broadly applicable...
japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... biology and genetics studies. We present an improved Lotus genome assembly and annotation, a catalog of natural variation based on re-sequencing of 29 accessions, and describe the involvement of small RNAs in the plant-bacteria symbiosis. Blueberries contain anthocyanins, other pigments and various...... polyphenolic compounds, which have been linked to protection against diabetes, cardiovascular disease and age-related cognitive decline. We present the first genome- guided approach in blueberry to identify genes involved in the synthesis of health-protective compounds. Using RNA-Seq data from five stages...
Nawrocki, Eric P
Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome's initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.
Janssen, José; Stoyanov, Slavi
Janssen, J., & Stoyanov, S. (2012, 20 November). Online Consultation for a Digital Competence Framework: Experts' views on Digital Competence. Workshop presentation at the Institute for Prospective Technological Studies, Seville, Spain.
Byrd, J.S.; Fisher, J.J.; DeVries, K.R.; Martin, T.P.
Expert robots will enhance safety and operations in nuclear plants. E. I. du Pont de Nemours and Company, Savannah River Laboratory, is developing expert mobile robots for deployment in nuclear applications at the Savannah River Plant. Knowledge-based expert systems are being evaluated to simplify operator control, to assist in navigation and manipulation functions, and to analyze sensory information. Development work using two research vehicles is underway to demonstrate semiautonomous, intelligent, expert robot system operation in process areas. A description of the mechanical equipment, control systems, and operating modes is presented, including the integration of onboard sensors. A control hierarchy that uses modest computational methods is being used to allow mobile robots to autonomously navigate and perform tasks in known environments without the need for large computer systems
This page provides an overview Cornell Mixing Zone Expert System water quality modeling and decision support system designed for environmental impact assessment of mixing zones resulting from wastewater discharge from point sources
Herman, Rod A; Raybould, Alan
Expert opinion is often sought by government regulatory agencies when there is insufficient empirical evidence to judge the safety implications of a course of action. However, it can be reckless to continue following expert opinion when a preponderance of evidence is amassed that conflicts with this opinion. Factual evidence should always trump opinion in prioritizing the information that is used to guide regulatory policy. Evidence-based medicine has seen a dramatic upturn in recent years spurred by examples where evidence indicated that certain treatments recommended by expert opinions increased death rates. We suggest that scientific evidence should also take priority over expert opinion in the regulation of genetically modified crops (GM). Examples of regulatory data requirements that are not justified based on the mass of evidence are described, and it is suggested that expertise in risk assessment should guide evidence-based regulation of GM crops. PMID:24637724
Byrd, J.S.; Fisher, J.J.; DeVries, K.R.; Martin, T.P.
Expert robots enhance a safety and operations in nuclear plants. E.I. du Pont de Nemours and Company, Savannah River Laboratory, is developing expert mobile robots for deployment in nuclear applications at the Savannah River Plant. Knowledge-based expert systems are being evaluated to simplify operator control, to assist in navigation and manipulation functions, and to analyze sensory information. Development work using two research vehicles is underway to demonstrate semiautonomous, intelligence, expert robot system operation in process areas. A description of the mechanical equipment, control systems, and operating modes is presented, including the integration of onboard sensors. A control hierarchy that uses modest computational methods is being used to allow mobile robots to autonomously navigate and perform tasks in known environments without the need for large computer systems
Wilson, Harold O.; Burford, Anna Marie
Delineates artificial intelligence/expert systems (AI/ES) concepts; provides an exposition of some business application areas; relates progress; and creates an awareness of the benefits, limitations, and reservations of AI/ES. (Author)
Brown, Rachel M; Zatorre, Robert J; Penhune, Virginia B
In this chapter, we explore what happens in the brain of an expert musician during performance. Understanding expert music performance is interesting to cognitive neuroscientists not only because it tests the limits of human memory and movement, but also because studying expert musicianship can help us understand skilled human behavior in general. In this chapter, we outline important facets of our current understanding of the cognitive and neural basis for music performance, and developmental factors that may underlie musical ability. We address three main questions. (1) What is expert performance? (2) How do musicians achieve expert-level performance? (3) How does expert performance come about? We address the first question by describing musicians' ability to remember, plan, execute, and monitor their performances in order to perform music accurately and expressively. We address the second question by reviewing evidence for possible cognitive and neural mechanisms that may underlie or contribute to expert music performance, including the integration of sound and movement, feedforward and feedback motor control processes, expectancy, and imagery. We further discuss how neural circuits in auditory, motor, parietal, subcortical, and frontal cortex all contribute to different facets of musical expertise. Finally, we address the third question by reviewing evidence for the heritability of musical expertise and for how expertise develops through training and practice. We end by discussing outlooks for future work. © 2015 Elsevier B.V. All rights reserved.
An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.
An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred
Rehfeld, Jens F
Gastrointestinal hormones are peptides released from neuroendocrine cells in the digestive tract. More than 30 hormone genes are currently known to be expressed in the gut, which makes it the largest hormone-producing organ in the body. Modern biology makes it feasible to conceive the hormones un......, but also constitute regulatory systems operating in the whole organism. This overview of gut hormone biology is supplemented with an annotation on some Scandinavian contributions to gastrointestinal hormone research....
An expert system plays an important role on alleviating primarily shortage of experts in a specific area of interest. With the help of an expert system, personnel with little expertise can solve problems that require expert knowledge. In this paper all major aspects of an expert system development have been presented.
Full Text Available Development of image analysis and machine learning methods for segmentation of clinically significant pathology in retinal spectral-domain optical coherence tomography (SD-OCT, used in disease detection and prediction, is limited due to the availability of expertly annotated reference data. Retinal segmentation methods use datasets that either are not publicly available, come from only one device, or use different evaluation methodologies making them difficult to compare. Thus we present and evaluate a multiple expert annotated reference dataset for the problem of intraretinal cystoid fluid (IRF segmentation, a key indicator in exudative macular disease. In addition, a standardized framework for segmentation accuracy evaluation, applicable to other pathological structures, is presented. Integral to this work is the dataset used which must be fit for purpose for IRF segmentation algorithm training and testing. We describe here a multivendor dataset comprised of 30 scans. Each OCT scan for system training has been annotated by multiple graders using a proprietary system. Evaluation of the intergrader annotations shows a good correlation, thus making the reproducibly annotated scans suitable for the training and validation of image processing and machine learning based segmentation methods. The dataset will be made publicly available in the form of a segmentation Grand Challenge.
In today's complex world, we have come to rely increasingly on those who have expertise in specific areas and can bring their knowledge to bear on crucial social, political and scientific questions. Taking the viewpoint that experts are consulted when there is something important at stake for an individual, a group, or society at large, Experts in Science and Society explores expertise as a relational concept. How do experts balance their commitment to science with that to society? How does a society actually determine that a person has expertise? What personal traits are valued in an expert? From where does the expert derive authority? What makes new forms of expertise emerge? These and related questions are addressed from a wide range of areas in order to be inclusive, as well as to demonstrate similarities across areas. Likewise, in order to be culturally comparative, this volume includes examples and discussions of experts in different countries and even in different time periods. The topics include the r...
Jiu, Mingyuan; Sahbi, Hichem
Multiple kernel learning (MKL) is a widely used technique for kernel design. Its principle consists in learning, for a given support vector classifier, the most suitable convex (or sparse) linear combination of standard elementary kernels. However, these combinations are shallow and often powerless to capture the actual similarity between highly semantic data, especially for challenging classification tasks such as image annotation. In this paper, we redefine multiple kernels using deep multi-layer networks. In this new contribution, a deep multiple kernel is recursively defined as a multi-layered combination of nonlinear activation functions, each one involves a combination of several elementary or intermediate kernels, and results into a positive semi-definite deep kernel. We propose four different frameworks in order to learn the weights of these networks: supervised, unsupervised, kernel-based semisupervised and Laplacian-based semi-supervised. When plugged into support vector machines (SVMs), the resulting deep kernel networks show clear gain, compared to several shallow kernels for the task of image annotation. Extensive experiments and analysis on the challenging ImageCLEF photo annotation benchmark, the COREL5k database and the Banana dataset validate the effectiveness of the proposed method.
Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert
As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108
Gregorio Sergio E
Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.
Farriol-Mathis, Nathalie; Garavelli, John S; Boeckmann, Brigitte; Duvaud, Séverine; Gasteiger, Elisabeth; Gateau, Alain; Veuthey, Anne-Lise; Bairoch, Amos
High-throughput proteomic studies produce a wealth of new information regarding post-translational modifications (PTMs). The Swiss-Prot knowledge base is faced with the challenge of including this information in a consistent and structured way, in order to facilitate easy retrieval and promote understanding by biologist expert users as well as computer programs. We are therefore standardizing the annotation of PTM features represented in Swiss-Prot. Indeed, a controlled vocabulary has been associated with every described PTM. In this paper, we present the major update of the feature annotation, and, by showing a few examples, explain how the annotation is implemented and what it means. Mod-Prot, a future companion database of Swiss-Prot, devoted to the biological aspects of PTMs (i.e., general description of the process, identity of the modification enzyme(s), taxonomic range, mass modification) is briefly described. Finally we encourage once again the scientific community (i.e., both individual researchers and database maintainers) to interact with us, so that we can continuously enhance the quality and swiftness of our services.
Full Text Available Limitations of Expert Evidence Edited by Stephen Leadbeatter MB ChB MCRPath ISBN 1 86016 029 8 Printed in Great Britain by Cathedral Print Services Ltd, Salisbury, 1996 Kitap 25 Ekim 1994 te The Royal College of Physicians ve The Royal College of Pathologists tarafından düzenlenen konferanstan sonra hekimlere ve avukatlara konuyu tartışmaya açmak için basılmış. Bilirkişi görüşünün temel filozofisinin, bu görevi yapanlar ve bu hizmeti alanların yapabileceklerinin sınırlarının tartışılması amaçlanmış.Seksen altı sayfadan oluşan kitabın fiatı on iki İngiliz Sterlini. Kitap üç bölüm ve bunların altında toplanan on ana başlıktan oluşmakta. Elinize aldığınızda küçük boyutu ve anlaşılır dili ile hemen okunup bitirelecek kitaplardan sanılıyor. En azından ben böyle düşünmüştüm. Ancak daha L A Tuınberg ve A J Bellinham’ın ön yazısında ben çarpıldım. Değerli yazarların kaleme aldığı başlıklar ve gündeme getirdiği tartışmaların tüm Adli Bilimlerle uğraşanların dikkatle okuması gereken cinsten olduğu kanısındayım. Birinci bölüm The Legal Perspective iki anabaşlıktan oluşuyor, The Criminal legal perspective Honour Judje Martin Stephens tarafından yazılmış,bilirkişi olarak görev yapabilmek için belgelenmiş bir eğitim olması gerektiği, mahkemelerde ya da yazılı raporlarda verilebilecek görüşlerin incelikleri tartışılmış. Bu bölümün ikinci anabaşlığı The civil legal perspective avukat Jennifer Cummin tarafından yazılmış. Toplum gözünde bilirkişinin anlamı ve mahkemenin bilirkişi görüşünü değişmez bilimsel doğru gibi algılayarak düştüğü bilimsel yanılgı ve raporlardaki kavram farkı dile getirilmiş. İkinci Bölüm The Medical And Scientific Perspective başlığı altında Roger C Evans MD Clinical evidence başlığında toplumun hasta tedavisi ve bilirkişilik hizmetinden beklentilerinin unrealistik olduğu ve
Torchia, M.; DuChez, J.
This annotated bibliography is a review of the scientific literature on the selection of asymptomatic patients for chest x-ray screening examinations. Selected articles cover a period of time from 1969 through 1979. The articles are organized under 10 main topics which correspond to various categories of chest x-ray screening examinations performed in the United States today. Within each main topic, the articles are presented in chronological order. To aid the reader in identifying specific citations, an author index and a list of citations by journal have been included for user reference. The standard format for each citation includes the title of each article, the author(s), journal, volume, page, date, and abstract
... the Experts | Diphtheria, Tetanus, Pertussis Ask the Experts Diphtheria, Tetanus, Pertussis Ask the Experts Home Administering Vaccines ... infants have died. How many doses of pediatric diphtheria-tetanus-acellular pertussis (DTaP) vaccine does an infant ...
Rhodes, W.; Szlapetis, I.; Hay, T.; Weihrer, S.
The review examines the use of human factors guidelines and methods in high technology applications, with emphasis on application to the nuclear industry. An extensive literature review was carried out identifying over 250 applicable documents, with 30 more documents identified during interviews with experts in human factors. Surveys were sent to 15 experts, of which 11 responded. The survey results indicated guidelines used and why these were favoured. Thirty-three of the most applicable guideline documents were described in detailed annotated bibliographies. A bibliographic list containing over 280 references was prepared. Thirty guideline documents were rated for their completeness, validity, applicability and practicality. The experts survey indicated the use of specific techniques. Ten human factors methods of analysis were described in general summaries, including procedures, applications, and specific techniques. Detailed descriptions of the techniques were prepared and each technique rated for applicability and practicality. Recommendations for further study of areas of importance to human factors in the nuclear field in Canada are given. (author). 8 tabs., 2 figs
Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957
Zvára, Karel; Tomečková, Marie; Peleška, Jan; Svátek, Vojtěch; Zvárová, Jana
Our main objective is to design a method of, and supporting software for, interactive correction and semantic annotation of narrative clinical reports, which would allow for their easier and less erroneous processing outside their original context: first, by physicians unfamiliar with the original language (and possibly also the source specialty), and second, by tools requiring structured information, such as decision-support systems. Our additional goal is to gain insights into the process of narrative report creation, including the errors and ambiguities arising therein, and also into the process of report annotation by clinical terms. Finally, we also aim to provide a dataset of ground-truth transformations (specific for Czech as the source language), set up by expert physicians, which can be reused in the future for subsequent analytical studies and for training automated transformation procedures. A three-phase preprocessing method has been developed to support secondary use of narrative clinical reports in electronic health record. Narrative clinical reports are narrative texts of healthcare documentation often stored in electronic health records. In the first phase a narrative clinical report is tokenized. In the second phase the tokenized clinical report is normalized. The normalized clinical report is easily readable for health professionals with the knowledge of the language used in the narrative clinical report. In the third phase the normalized clinical report is enriched with extracted structured information. The final result of the third phase is a semi-structured normalized clinical report where the extracted clinical terms are matched to codebook terms. Software tools for interactive correction, expansion and semantic annotation of narrative clinical reports has been developed and the three-phase preprocessing method validated in the cardiology area. The three-phase preprocessing method was validated on 49 anonymous Czech narrative clinical reports
Gonzelez, Avelino J.; Ragusa, James M.
Artificial intelligence (AI) technology, and in particular expert systems, has shown potential applicability in many areas of operation at the Kennedy Space Center (KSC). In an era of limited resources, the early identification of good expert system applications, and their segregation from inappropriate ones can result in a more efficient use of available NASA resources. On the other hand, the education of students in a highly technical area such as AI requires an extensive hands-on effort. The nature of expert systems is such that proper sample applications for the educational process are difficult to find. A pilot project between NASA-KSC and the University of Central Florida which was designed to simultaneously address the needs of both institutions at a minimum cost. This project, referred to as Expert Systems Prototype Training Project (ESPTP), provided NASA with relatively inexpensive development of initial prototype versions of certain applications. University students likewise benefit by having expertise on a non-trivial problem accessible to them at no cost. Such expertise is indispensible in a hands-on training approach to developing expert systems.
The US Nuclear Regulatory Commission (NRC) and the Electric Power Research Institute have initiated a broad-based exploration of means to evaluate the potential applications of expert systems in the nuclear industry. This exploratory effort will assess the use of expert systems to augment the diagnostic and decision-making capabilities of personnel with the goal of enhancing productivity, reliability, and performance. The initial research effort is the development and documentation of guidelines for verifying and validating (V and V) expert systems. An initial application of expert systems in the nuclear industry is to aid operations and maintenance personnel in decision-making tasks. The scope of the decision aiding covers all types of cognitive behavior consisting of skill, rule, and knowledge-based behavior. For example, procedure trackers were designed and tested to support rule-based behavior. Further, these systems automate many of the tedious, error-prone human monitoring tasks, thereby reducing the potential for human error. The paper version of the procedure contains the knowledge base and the rules and thus serves as the basis of the design verification of the procedure tracker. Person-in-the-loop tests serve as the basis for the validation of a procedure tracker. When conducting validation tests, it is important to ascertain that the human retains the locus of control in the use of the expert system
Choi, Young Sung; Lee, Sun Ho; Lee, Byong Whi
Public perception on nuclear energy is much influenced by subjective impressions mostly formed through sensational and dramatic news of mass media or anti-nuclear groups. However, nuclear experts, those who have more relevant knowledge and information about nuclear energy, may have reasonable opinion based on scientific facts or inferences. Thus their opinion and consensus should be examined and taken into account during the process of nuclear energy policy formulation. For the purpose of eliciting experts' opinion, the web-based on-line survey system (eBOSS) was developed. Using the survey system, experts' views on nuclear energy were tallied, analyzed and compared with the public's. Based on the survey results, the paper suggests some recommendations about the future direction of the public information program in Korea
Ludtke, P. R.
This register presents the names of approximately 235 individuals who are considered experts, or very knowledgeable, in various fields of technology related to hydrogen. Approximately 90 organizations are represented. Each person is listed by organizational affiliation, address, and principal area of expertise. The criteria for selection of names for the register are extensive experience in a given field of work, participation in or supervision of relevant research programs, contributions to the literature, or being recognized as an expert in a particular field. The purpose of the register is to present, in easy form, sources of dependable information regarding highly technical areas of hydrogen technology, with particular emphasis on safety. The register includes two indexes: an alphabetical listing of the experts and an alphabetical listing of the organizations with which they are affiliated.
Huang, Daisie I; Cronk, Quentin C B
Plann automates the process of annotating a plastome sequence in GenBank format for either downstream processing or for GenBank submission by annotating a new plastome based on a similar, well-annotated plastome. Plann is a Perl script to be executed on the command line. Plann compares a new plastome sequence to the features annotated in a reference plastome and then shifts the intervals of any matching features to the locations in the new plastome. Plann's output can be used in the National Center for Biotechnology Information's tbl2asn to create a Sequin file for GenBank submission. Unlike Web-based annotation packages, Plann is a locally executable script that will accurately annotate a plastome sequence to a locally specified reference plastome. Because it executes from the command line, it is ready to use in other software pipelines and can be easily rerun as a draft plastome is improved.
Morusiewicz, Linda; Valett, Jon D.
An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. All materials have been grouped into eight general subject areas for easy reference: The Software Engineering Laboratory; The Software Engineering Laboratory: Software Development Documents; Software Tools; Software Models; Software Measurement; Technology Evaluations; Ada Technology; and Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.
Full Text Available Abstract Background Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. Results GARNET (Gene Annotation Relationship NEtwork Tools is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules - gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. Conclusions GARNET (gene annotation relationship network tools is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/.
Full Text Available The eutherian comparative genomic analysis protocol annotated most comprehensive eutherian lysozyme gene data set. Among 209 potential coding sequences, the third party annotation gene data set of eutherian lysozyme genes included 116 complete coding sequences that first described seven major gene clusters. As one new framework of future experiments, the present integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new classification and nomenclature of eutherian lysozyme genes.
The eutherian comparative genomic analysis protocol annotated most comprehensive eutherian lysozyme gene data set. Among 209 potential coding sequences, the third party annotation gene data set of eutherian lysozyme genes included 116 complete coding sequences that first described seven major gene clusters. As one new framework of future experiments, the present integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new classification and nomencla...
Herold, Julia; Abouna, Sylvie; Zhou, Luxian; Pelengaris, Stella; Epstein, David B. A.; Khan, Michael; Nattkemper, Tim W.
In the last years, bioimaging has turned from qualitative measurements towards a high-throughput and highcontent modality, providing multiple variables for each biological sample analyzed. We present a system which combines machine learning based semantic image annotation and visual data mining to analyze such new multivariate bioimage data. Machine learning is employed for automatic semantic annotation of regions of interest. The annotation is the prerequisite for a biological object-oriented exploration of the feature space derived from the image variables. With the aid of visual data mining, the obtained data can be explored simultaneously in the image as well as in the feature domain. Especially when little is known of the underlying data, for example in the case of exploring the effects of a drug treatment, visual data mining can greatly aid the process of data evaluation. We demonstrate how our system is used for image evaluation to obtain information relevant to diabetes study and screening of new anti-diabetes treatments. Cells of the Islet of Langerhans and whole pancreas in pancreas tissue samples are annotated and object specific molecular features are extracted from aligned multichannel fluorescence images. These are interactively evaluated for cell type classification in order to determine the cell number and mass. Only few parameters need to be specified which makes it usable also for non computer experts and allows for high-throughput analysis.
Goeltz, R.; Purucker, S.; Tonn, B. (Oak Ridge National Lab., TN (USA)); Wiggen, T. (Oak Ridge Associated Universities, Inc., TN (USA)); MacGregor, D. (MacGregor-Bates, Inc., Eugene, OR (USA))
This report describes the Communications Alarm Processor (CAP), a prototype expert system developed for the Bonneville Power Administration by Oak Ridge National Laboratory. The system is designed to receive and diagnose alarms from Bonneville's Microwave Communications System (MCS). The prototype encompasses one of seven branches of the communications network and a subset of alarm systems and alarm types from each system. The expert system employs a backward chaining approach to diagnosing alarms. Alarms are fed into the expert system directly from the communication system via RS232 ports and sophisticated alarm filtering and mailbox software. Alarm diagnoses are presented to operators for their review and concurrence before the diagnoses are archived. Statistical software is incorporated to allow analysis of archived data for report generation and maintenance studies. The delivered system resides on a Digital Equipment Corporation VAX 3200 workstation and utilizes Nexpert Object and SAS for the expert system and statistical analysis, respectively. 11 refs., 23 figs., 7 tabs.
Cui, Meng; Yang, Shuo; Yu, Tong; Yang, Ce; Gao, Yonghong; Zhu, Haiyan
To design a model to capture information on the state and trends of knowledge creation, at both an individual and an organizational level, in order to enhance knowledge management. We designed a graph-theoretic knowledge model, the expert knowledge map (EKM), based on literature-based annotation. A case study in the domain of Traditional Chinese Medicine research was used to illustrate the usefulness of the model. The EKM successfully captured various aspects of knowledge and enhanced knowledge management within the case-study organization through the provision of knowledge graphs, expert graphs, and expert-knowledge biography. Our model could help to reveal the hot topics, trends, and products of the research done by an organization. It can potentially be used to facilitate knowledge learning, sharing and decision-making among researchers, academicians, students, and administrators of organizations.
Miller, R. Baxter; Butts, Tracy; Jones, Sharon
Contains an annotated bibliography of African American literature (published between 1989 and 1994), including anthologies, fiction, poetry, drama, criticism, cultural studies, biography, interviews, and letters. (TB)
Full Text Available SE40_AM1 PowerGet annotation In annotation process, KEGG, KNApSAcK and LipidMAPS ar...can assign, predicted molecular formulas are used for the annotation. MS/MS patterns was used to suggest fun...p/) and MS-MS Fragment Viewer (http://webs2.kazusa.or.jp/msmsfragmentviewer/) are used for ann...lcone, Nicotinamide, Nicotinate, Pantothenate, Phloretin, Prunin, Rutin, S-Adenosyl-L-methionine, Tomatine, UMP, Uridine) are used for annotation and identification of the compounds. ...
Full Text Available Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%.
, some program properties are beyond reach of such analysis for theoretical and practical reasons - but can be described by programmers. Three aspects are explored. The first is annotation of the source code. Two annotations are introduced. These allow more accurate modeling of parallelism...... and communication in embedded programs. Runtime checks are developed to ensure that annotations correctly describe observable program behavior. The performance impact of runtime checking is evaluated on several benchmark kernels and is negligible in all cases. The second aspect is compilation feedback. Annotations...
Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B
Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.
Simboura, Nomiki; Katsiaras, Nikolaos; Chatzigeorgiou, Giorgos; Arvanitidis, Christos
Abstract Background The last annotated checklist of marine polychaetes in Greece was published in 2001. Since then, global taxonomic progress, combined with many new species records for Greece, required a thorough review of the taxonomic, nomenclatural and biogeographic status of the national species list. This checklist revises the status of all extant polychaete species reported from the Greek Exclusive Economic Zone since 1832. The work was undertaken as part of the efforts on compiling a national species inventory (Greek Taxon Information System initiative) in the framework of the LifeWatchGreece Research Infrastructure. New information This checklist comprises an updated and annotated inventory of polychaete species in Greek waters, compiled from literature reports, online databases, museum collections and unpublished datasets. The list provides information on 836 species-level taxa from Greece, of which 142 are considered questionable. An additional 84 species reported in the past are currently considered absent from Greece; reasons for the exclusion of each species are given. Fourteen species are reported here for the first time from Greek waters. At least 52 species in the present list constitute in fact a complex of cryptic or pseudo-cryptic species. Forty-seven species are considered non-native to the area. In addition to the species-level taxa reported in this checklist, eleven genera have been recorded from Greece with no representatives identified to species level. One replacement name is introduced. For each species, a comprehensive bibliographic list of occurrence records in Greece and the synonyms used in these publications are provided as supplementary material. Where necessary, the taxonomic, nomenclatural or biogeographic status is discussed. Finally, the findings are discussed in the wider context of Mediterranean polychaete biogeography, taxonomic practice and worldwide research progress. PMID:29362552
May, John W.; James, A. Gordon; Steinbeck, Christoph
Summary: Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of t...
C++, and Microsoft C/C++ compilers. The personal edition is licensed for educational, research, and hobby use. Applications created with RT -Expert personal edition are not licensed for commercial purposes. Professional editions are available for commercial applications using DOS, Windows, and. Unix environments.
TNO Physics and Electronics laboratory, in collaboration with the University of Limburg and the Research Institute for Knowledge Systems, worked on a technology project named 'QUEST: Quality of Expert Systems' [FEL90]. QUEST was carried out under commision of the Dutch Ministry of Defence. A strong
The expert's role in the involvement in decisions on nuclear risks is discussed. The responsibility of scientists in ethics and in several sociological problems is highlighted. The mandates, the positivist reaction, way to knowledge, the scientist as a subject studying an object, and application in the domain of radioprotection are the main issues of the somewhat philosophical essay. (R.P.)
Buitelaar, T.; Larik, J.E.; Matta, A.
On 8 and 9 December 2015, The Hague Institute for Global Justice, in collaboration with the Ministry of Foreign Affairs of the Netherlands, organized both a public high-level discussion and a closed expert consultation on the EU’s forthcoming Global Strategy on Foreign and Security Policy. The
James P Balhoff
Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.
Full Text Available Background: Generating good training datasets is essential for machine learning-based nuclei detection methods. However, creating exhaustive nuclei contour annotations, to derive optimal training data from, is often infeasible. Methods: We compared different approaches for training nuclei detection methods solely based on nucleus center markers. Such markers contain less accurate information, especially with regard to nuclear boundaries, but can be produced much easier and in greater quantities. The approaches use different automated sample extraction methods to derive image positions and class labels from nucleus center markers. In addition, the approaches use different automated sample selection methods to improve the detection quality of the classification algorithm and reduce the run time of the training process. We evaluated the approaches based on a previously published generic nuclei detection algorithm and a set of Ki-67-stained breast cancer images. Results: A Voronoi tessellation-based sample extraction method produced the best performing training sets. However, subsampling of the extracted training samples was crucial. Even simple class balancing improved the detection quality considerably. The incorporation of active learning led to a further increase in detection quality. Conclusions: With appropriate sample extraction and selection methods, nuclei detection algorithms trained on the basis of simple center marker annotations can produce comparable quality to algorithms trained on conventionally created training sets.
Boiko, O. V.
Full Text Available A subject and maintenance of dissertations for the degree of Doctor and the Candidate of historical sciences which were defended in the specialized scientific advice D 08.051.14 in the Oles Honchar Dnipropetrovsk National University in 2014 is considered. For a year 4 dissertations for the degree of Doctor (specialty 07.00.01 – «Нistory of Ukraine» and 3 dissertations for the degree of the Candidate (specialty 07.00.01 – «Нistory of Ukraine» – 1 work, 07.00.06 – «Нistoriography, a source study and special historical disciplines» – 2 works were defended. 6 dissertations (besides thesis defended by A. V. Bortnikova were ratified by the Department of education and science of Ukraine. It is given the following information on every research work: theme, specialty, place (department of work implementation, date of defense of dissertation, scientific consultant (for doctoral thesis or leader (for candidate’s thesis, his scientific degree and rank, place of work, data about official opponents. Considerable attention is spared to the compressed review of the personal achievements of authors especially to scientific novelty of their researches.
Boyko, O. V.
Full Text Available A subject and maintenance of dissertations for the degree of Doctor and the Candidate of historical sciences which were defended in the specialized scientific advice D 08.051.14 in the Oles Honchar Dnipropetrovsk National University in 2013 is considered. Only for a year 6 dissertations for the degree of Doctor (specialty 07.00.01 – «Нistory of Ukraine» – 5 works; 07.00.02 – «World history» – 1 work and 16 dissertations for the degree of the Candidate (specialty 07.00.01 – «Нistory of Ukraine» – 10 works, 07.00.02 – «world history» – 4 works, 07.00.06 – «Нistoriography, a source study and special historical disciplines» – 2 works were defended. All dissertations were ratified by the Department of education and science of Ukraine. It is given the following information on every research work: theme, specialty, place (department of work implementation, date of defense of dissertation, scientific consultant (for doctoral thesis or leader (for candidate’s thesis, his scientific degree and rank, place of work, data about official opponents. Considerable attention is spared to the compressed review of the personal achievements of authors especially to scientific novelty of their researches.
Boyko, O. V.
Full Text Available A subject and maintenance of dissertations for the degree of Doctor and the Candidate of historical sciences which were defended in the specialized scientific advice D 08.051.14 in the Oles Honchar Dnipropetrovsk National University in 2015 is considered. For a year 2 dissertations for the degree of Doctor (specialty 07.00.01 "Нistory of Ukraine" and 4 dissertations for the degree of the Candidate (specialty 07.00.01 "Нistory of Ukraine" – 1 work, 07.00.06 "Нistoriography, a source study and special historical disciplines" – 3 works were defended. All dissertations were ratified by the Department of education and science of Ukraine. It is given the following information on every research work: theme, specialty, place (department of work implementation, date of defense of dissertation, scientific consultant (for doctoral thesis or leader (for candidate's thesis, his scientific degree and rank, place of work, data about official opponents. Considerable attention is spared to the compressed review of the personal achievements of authors especially to scientific novelty of their researches.
Garriga, Joan; Palmer, John R B; Oltra, Aitana; Bartumeus, Frederic
The growing capacity to process and store animal tracks has spurred the development of new methods to segment animal trajectories into elementary units of movement. Key challenges for movement trajectory segmentation are to (i) minimize the need of supervision, (ii) reduce computational costs, (iii) minimize the need of prior assumptions (e.g. simple parametrizations), and (iv) capture biologically meaningful semantics, useful across a broad range of species. We introduce the Expectation-Maximization binary Clustering (EMbC), a general purpose, unsupervised approach to multivariate data clustering. The EMbC is a variant of the Expectation-Maximization Clustering (EMC), a clustering algorithm based on the maximum likelihood estimation of a Gaussian mixture model. This is an iterative algorithm with a closed form step solution and hence a reasonable computational cost. The method looks for a good compromise between statistical soundness and ease and generality of use (by minimizing prior assumptions and favouring the semantic interpretation of the final clustering). Here we focus on the suitability of the EMbC algorithm for behavioural annotation of movement data. We show and discuss the EMbC outputs in both simulated trajectories and empirical movement trajectories including different species and different tracking methodologies. We use synthetic trajectories to assess the performance of EMbC compared to classic EMC and Hidden Markov Models. Empirical trajectories allow us to explore the robustness of the EMbC to data loss and data inaccuracies, and assess the relationship between EMbC output and expert label assignments. Additionally, we suggest a smoothing procedure to account for temporal correlations among labels, and a proper visualization of the output for movement trajectories. Our algorithm is available as an R-package with a set of complementary functions to ease the analysis.