scholarly journals Improving Automatic IPSyn Coding

2020 ◽  
Vol 51 (4) ◽  
pp. 1187-1189
Author(s):  
Brian MacWhinney ◽  
Jenny A. Roberts ◽  
Evelyn P. Altenberg ◽  
Madison Hunter
Keyword(s):  
Automatic Computation ◽  
Link Type ◽  
Language Analysis ◽  
High Level

Purpose The Computerized Language ANalysis–Index of Productive Syntax (CLAN-IPSyn) system is designed to facilitate automatic computation of the IPSyn measure of productive child syntax. Roberts et al. (2020) conducted a thorough comparison of hand-generated and automatic scores on the Index of Productive Syntax (IPSyn) measure (Scarborough, 1990) and found a high level of error for CLAN-IPSyn. We report on the use of the Roberts et al. analysis to reduce and eliminate errors in CLAN-IPSyn, to improve its accuracy. Method Scores provided by manual and machine scoring of the 20 transcripts used in Roberts et al. (2020) were compared. Divergences in point assignment were examined and significant modifications made to the CLAN-IPSyn program to increase its accuracy. Conclusion The currently available, free version of CLAN at https://talkbank.org is now significantly more correct in terms of exemplars produced, and should assist clinicians and researchers in using the revised IPSyn (Altenberg et al. 2018).

scholarly journals In vivo optical cellular diagnosis for uterine cervical or vaginal intraepithelial neoplasia using flexible gastrointestinal endocytoscopy -a prospective pilot study-

BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shoko Ono ◽  
Ayako Nozaki ◽  
Kana Matsuda ◽  
Emi Takakuwa ◽  
Naoya Sakamoto ◽  
...  
Keyword(s):  
Diagnostic Accuracy ◽  
Predictive Value ◽  
Intraepithelial Neoplasia ◽  
Observer Agreement ◽  
Optical Biopsy ◽  
Link Type ◽  
Guided Biopsy ◽  
Vaginal Intraepithelial Neoplasia ◽  
High Level

Abstract Backgrouund For patients with any kind of atypical squamous intraepithelial lesion of the uterine cervix or vagina, colposcopy and punch biopsy are common procedures for histological determination following cytology. However, colposcopy-guided biopsy does not provide a high level of diagnostic accuracy. The aim of this study was to determine the usefulness of optical biopsy in vivo using endocytoscopy compared with conventional procedures using colposcopy. Methods Between May 2018 and March 2019, patients who were scheduled for cervical conization or mapping biopsies of the vagina were prospectively enrolled. Endocytoscopy was performed by senior endoscopists prior to scheduled procedures, and endocytoscopic images and biopsy samples were taken from the most prominent site and surrounding area of the cervical or vaginal lesions. The collection process of images was randomized and anonymous, and three doctors separately evaluated the images according to the ECA classification. ECA 4 and 5 are indicative of endoscopic malignancy. The primary endpoint was diagnostic accuracy (benign or malignant: cervical intraepithelial neoplasia (CIN) 3 or vaginal intraepithelial neoplasia (VAIN) 3 or worse) of cell images at the most prominent site in each patient. Results A total of 28 consecutive patients were enrolled. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy of endocytoscopic images were 95.0% (84.8–98.6%), 87.5% (61.9–96.5%), 95.0% (84.8–98.6%), 87.5% (61.9–96.5%) and 92.9% (78.2–98.0%), respectively. Inter-observer agreement among three reviewers was 0.78 (0.08–9.88, P < 0.01). On the other hand, the accuracy of colposcopy-guided biopsy was 74.1% (64.0–84.0%). Conclusions Optical cell diagnosis of cervical or vaginal intraepithelial neoplasia using endocytoscopy provides a high level of diagnostic accuracy. Trial registration The study was registered with the UMIN database (ID: 000031712). UMIN000031712. Registered 16 March 2017,

scholarly journals Evidence That Runt Acts as a Counter-Repressor of Groucho During Drosophila melanogaster Primary Sex Determination

2020 ◽  
Vol 10 (7) ◽  
pp. 2487-2496
Author(s):  
Sharvani Mahadeveraju ◽  
Young-Ho Jung ◽  
James W. Erickson
Keyword(s):  
Drosophila Melanogaster ◽  
Sex Determination ◽  
Transcriptional Repression ◽  
Biological Effects ◽  
Regulatory Gene ◽  
Animal Cells ◽  
Interaction Domain ◽  
Link Type ◽  
High Level ◽  
Runx Proteins

Runx proteins are bifunctional transcription factors that both repress and activate transcription in animal cells. Typically, Runx proteins work in concert with other transcriptional regulators, including co-activators and co-repressors to mediate their biological effects. In Drosophila melanogaster the archetypal Runx protein, Runt, functions in numerous processes including segmentation, neurogenesis and sex determination. During primary sex determination Runt acts as one of four X-linked signal element (XSE) proteins that direct female-specific activation of the establishment promoter (Pe) of the master regulatory gene Sex-lethal (Sxl). Successful activation of SxlPe requires that the XSE proteins overcome the repressive effects of maternally deposited Groucho (Gro), a potent co-repressor of the Gro/TLE family. Runx proteins, including Runt, contain a C-terminal peptide, VWRPY, known to bind to Gro/TLE proteins to mediate transcriptional repression. We show that Runt’s VWRPY co-repressor-interaction domain is needed for Runt to activate SxlPe. Deletion of the Gro-interaction domain eliminates Runt-ability to activate SxlPe, whereas replacement with a higher affinity, VWRPW, sequence promotes Runt-mediated transcription. This suggests that Runt may activate SxlPe by antagonizing Gro function, a conclusion consistent with earlier findings that Runt is needed for Sxl expression only in embryonic regions with high Gro activity. Surprisingly we found that Runt is not required for the initial activation of SxlPe. Instead, Runt is needed to keep SxlPe active during the subsequent period of high-level Sxl transcription suggesting that Runt helps amplify the difference between female and male XSE signals by counter-repressing Gro in female, but not in male, embryos.

scholarly journals Using Computerized Language Analysis to Evaluate Grammatical Skills

2020 ◽  
Vol 51 (2) ◽  
pp. 184-204 ◽  
Author(s):  
Lizbeth H. Finestack ◽  
Bobbi Rohwer ◽  
Lisa Hilliard ◽  
Leonard Abbeduto
Keyword(s):  
Down Syndrome ◽  
Language Disorder ◽  
Treatment Goals ◽  
Developmental Language Disorder ◽  
Link Type ◽  
Language Analysis ◽  
Grammatical Skills ◽  
Computer Based ◽  
Language Assessments

Purpose Conducting in-depth grammatical analyses based on language samples can be time consuming. Developmental Sentence Scoring (DSS) and the Index of Productive Syntax (IPSyn) analyses provide detailed information regarding the grammatical profiles of children and can be conducted using free computer-based software. Here, we provide a tutorial to support clinicians' use of computer-based analyses to aid diagnosis and develop and monitor treatment goals. Method We analyzed language samples of a 5-year-old with developmental language disorder and an adolescent with Down syndrome using computer-based software, Computerized Language Analysis. We focused on DSS and IPSyn analyses. The tutorial includes step-by-step procedures for conducting the analyses. We also illustrate how the analyses may be used to assist in diagnosis, develop treatment goals focused on grammatical targets, and monitor progress on these treatment goals. Conclusion Clinicians should consider using Computerized Language Analysis's IPSyn and DSS analyses to support grammatical language assessments used to aid diagnosis, develop treatment goals, and monitor progress on these treatment goals. Supplemental Material https://doi.org/10.23641/asha.12021141

scholarly journals wft4galaxy: A Workflow Tester for Galaxy

2017 ◽  
Author(s):  
Marco Enrico Piras ◽  
Luca Pireddu ◽  
Gianluigi Zanetti
Keyword(s):  
Complex Analysis ◽  
Computer Programs ◽  
Supplementary Information ◽  
Automated Testing ◽  
Continuous Integration ◽  
Link Type ◽  
Scientific Analysis ◽  
The Galaxy ◽  
Supplementary Material ◽  
High Level

ABSTRACTMotivationWorkflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way exists to automatically test Galaxy workflows and ensure their correctness has appeared in the literature.ResultsWith wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container – the latter reducing installation effort to a minimum.Availabilitywft4galaxy is available online at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0.Supplementary informationSupplementary information is available at http://wft4galaxy.readthedocs.io.

scholarly journals Expectations for Carbon Pricing in Japan in the Global Climate Policy Context

2020 ◽  
pp. 1-21
Author(s):  
Satoshi Kojima ◽  
Kenji Asakawa
Keyword(s):  
Carbon Tax ◽  
Global Climate ◽  
Full Potential ◽  
Carbon Pricing ◽  
Policy Context ◽  
Link Type ◽  
Historical Progress ◽  
High Level ◽  
Pricing Schemes ◽  
Carbon Prices

Abstract Realizing a decarbonized society in consistent with the Paris Agreement, a fundamental transformation of the entire economic and social system is needed, and not only carbon intensive sectors but also all sectors and all stakeholders including households must be decarbonized. This chapter demonstrates increasing expectations for carbon pricing in Japan in this global policy context. After the review of the global trend of carbon pricing, historical progress of carbon pricing in Japan and the existing nation-wide carbon tax, i.e. the Global Warming Countermeasure Tax, is explained. There are also two sub-national carbon pricing schemes in Japan, Tokyo ETS and Saitama ETS, which are explained in Chaps. 10.1007/978-981-15-6964-7_6 and 10.1007/978-981-15-6964-7_7 respectively, and not focused in this chapter. We examine the claim that Japan has already implemented high level carbon pricing in terms of various forms of energy taxes. Based on the effective carbon rate which is defined by OECD as the sum of explicit carbon prices and fossil fuel taxes per carbon emission, the nationwide average effective carbon rate of Japan is lower than the average effective carbon rates of OECD countries and its key partner countries. The current carbon pricing schemes in Japan are too modest to realize decarbonization transition and there is a room to upgrade them to exploit full potential of carbon pricing. This chapter discusses adequate levels of carbon prices in compatible with decarbonization transition.

scholarly journals Mapfuser: an integrative toolbox for consensus map construction and Marey maps

2017 ◽  
Author(s):  
Dennis van Muijen ◽  
Ram K. Basnet ◽  
Nathalie N.J. Dek ◽  
Chris Maliepaard ◽  
Evert W. Gutteling
Keyword(s):  
R Package ◽  
Reproducible Research ◽  
Consensus Map ◽  
Link Type ◽  
Map Construction ◽  
Shiny App ◽  
Data Function ◽  
High Level ◽  
Automated Quality Control ◽  
Map Analysis

AbstractMotivationWhere standalone tools for genetic map visualisation, consensus map construction, and Marey map analysis offer useful analyses for research and breeding, no single tool combines the three. Manual data curation is part of each of these analyses, which is difficult to standardize and consequently error prone.ResultsMapfuser provides a high-level interface for common analyses in breeding programs and quantitative genetics. Combined with interactive visualisations and automated quality control, mapfuser provides a standardized and flexible toolbox and is available as Shiny app for biologists. Reproducible research in the R package is facilitated by storage of raw data, function parameters, and results in an R object. In the shiny app a rmarkdown report is available.AvailabilityMapfuser is available as R package at https://github.com/dmuijen/mapfuser under the GPL-3 License and is available for public use as Shiny application at https://plantbreeding.shinyapps.io/mapfuser. Documentation for the R package is available as package vignette. Shiny app documentation is integrated in the [email protected]

scholarly journals Genomic and temporal analyses of Mycobacterium bovis in southern Brazil

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Rudielle de Arruda Rodrigues ◽  
Flábio Ribeiro Araújo ◽  
Alberto Martín Rivera Dávila ◽  
Rodrigo Nestor Etges ◽  
Julian Parkhill ◽  
...  
Keyword(s):  
Population Structure ◽  
Mycobacterium Bovis ◽  
Type Species ◽  
Southern Brazil ◽  
Cattle Industry ◽  
Content Type ◽  
Cross Border ◽  
Link Type ◽  
High Level ◽  
The 19Th Century

Mycobacterium bovis is a causal agent of bovine tuberculosis (bTB), one of the most important diseases currently facing the cattle industry worldwide. Tracing the source of M. bovis infections of livestock is an important tool for understanding the epidemiology of bTB and defining control/eradication strategies. In this study, whole genome sequencing (WGS) of 74 M . bovis isolates sourced from naturally infected cattle in the State of Rio Grande do Sul (RS), southern Brazil, was used to evaluate the population structure of M. bovis in the region, identify potential transmission events and date the introduction of clonal complex (CC) European 2 (Eu2). In silico spoligotyping identified 11 distinct patterns including four new profiles and two CCs, European 1 (Eu1) and Eu2. The analyses revealed a high level of genetic diversity in the majority of herds and identified putative transmission clusters that suggested that within- and between-herd transmission is occurring in RS. In addition, a comparison with other published M. bovis isolates from Argentina, Brazil, Paraguay and Uruguay demonstrated some evidence for a possible cross-border transmission of CC Eu1 into RS from Uruguay or Argentina. An estimated date for the introduction of CC Eu2 into RS in the middle of the 19th century correlated with the historical introduction of cattle into RS to improve existing local breeds. These findings contribute to the understanding of the population structure of M. bovis in southern Brazil and highlight the potential of WGS in surveillance and helping to identify bTB transmission.

scholarly journals Displacement ventilation: a viable ventilation strategy for makeshift hospitals and public buildings to contain COVID-19 and other airborne diseases

2020 ◽  
Vol 7 (9) ◽  
pp. 200680
Author(s):  
Rajesh K. Bhagat ◽  
P. F. Linden
Keyword(s):  
Negative Pressure ◽  
Natural Ventilation ◽  
Public Spaces ◽  
Positive Pressure ◽  
Air Conditioner ◽  
Displacement Ventilation ◽  
Link Type ◽  
Building Ventilation ◽  
High Level ◽  
General Wards

The SARS-CoV-2 virus has so far infected more than 31 million people around the world, and its impact is being felt by all. Patients with diseases such as COVID-19 should ideally be treated in negative pressure isolation rooms. However, due to the overwhelming demand for hospital beds, patients have been treated in general wards, hospital corridors and makeshift hospitals. Adequate building ventilation in hospitals and public spaces is a crucial factor to contain the disease (Escombe et al. 2007 PLoS Med. 4 ; Escombe et al. 2019 BMC Infect. Dis. 19 , 88 ( doi:10.1186/s12879-019-3717-9 ); Morawska & Milton 2020 Clin. Infect. Dis . ciaa939. ( doi:10.1093/cid/ciaa939 )), to exit lockdown safely, and reduce the chance of subsequent waves of outbreaks. A recently reported air-conditioner-induced COVID-19 outbreak caused by an asymptomatic patient, in a restaurant in Guangzhou, China (Lu et al. 2020 Emerg. Infect. Dis. 26 ) exposes our vulnerability to future outbreaks linked to ventilation in public spaces. We argue that displacement ventilation (either mechanical or natural ventilation), where air intakes are at low level and extracts are at high level, is a viable alternative to negative pressure isolation rooms, which are often not available on site in hospital wards and makeshift hospitals. Displacement ventilation produces negative pressure at the occupant level, which draws fresh air from outdoors, and positive pressure near the ceiling, which expels the hot and contaminated air out. We acknowledge that, in both developed and developing countries, many modern large structures lack the openings required for natural ventilation. This lack of openings can be supplemented by installing extract fans. We have also discussed and addressed the issue of the ‘lock-up effect’. We provide guidelines for such mechanically assisted, naturally ventilated makeshift hospitals.

Mediation Spaces for Similarity-Based Semantic Web Services Selection

2011 ◽  
Vol 8 (1) ◽  
pp. 1-20 ◽  
Author(s):  
Stefan Dietze ◽  
Alessio Gugliotta ◽  
John Domingue ◽  
Michael Mrissa
Keyword(s):  
Web Services ◽  
Semantic Web ◽  
Service Providers ◽  
General Purpose ◽  
Semantic Web Services ◽  
Implicit Representation ◽  
Automatic Computation ◽  
Semantic Level ◽  
Automated Discovery ◽  
High Level

Semantic Web Services (SWS) aim at the automated discovery, selection and orchestration of Web services based on comprehensive, machine-interpretable semantic descriptions. The latter are, in principle, deployed by multiple possible actors (i.e., service providers and service consumers); thus, a high level of heterogeneity between distinct SWS annotations is expected. Therefore, mediation between concurrent semantic representations of services is a key requirement to fully implement the SWS vision. In this paper, the authors argue that “semantic-level mediation” is necessary to identify semantic similarities across distinct SWS representations. The authors formalize and implement a mediation approach based on “Mediation Spaces” (MS), which enables the implicit representation of semantic similarities among distinct SWS descriptions. As a result, given a specific SWS approach and the proposed MS, a general purpose algorithm is implemented to empower SWS selection with the automatic computation of semantic similarities between a given SWS request and a set of SWS offers. A prototypical application illustrates the approach and highlights the benefits w.r.t. current mediation approaches.

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