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Sample records for clinical lims software

  1. adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies.

    PubMed

    Calabria, Andrea; Spinozzi, Giulio; Benedicenti, Fabrizio; Tenderini, Erika; Montini, Eugenio

    2015-01-01

    Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Generation Sequencing (NGS) methods to perform high-throughput integration site monitoring in different clinical trials and scientific projects. Because of the huge amount of samples that we process every year, which result in hundreds of millions of sequencing reads, we need to standardize data management and tracking systems, building up a scalable and flexible structure with web-based interfaces, which are usually called Laboratory Information Management System (LIMS). We started collecting end-users' requirements, composed of desired functionalities of the system and Graphical User Interfaces (GUI), and then we evaluated available tools that could address our requirements, spanning from pure LIMS to Content Management Systems (CMS) up to enterprise information systems. Our analysis identified ADempiere ERP, an open source Enterprise Resource Planning written in Java J2EE, as the best software that also natively implements some highly desirable technological advances, such as the high usability and modularity that grants high use-case flexibility and software scalability for custom solutions. We extended and customized ADempiere ERP to fulfil LIMS requirements and we developed adLIMS. It has been validated by our end-users verifying functionalities and GUIs through test cases for PCRs samples and pre-sequencing data and it is currently in use in our laboratories. adLIMS implements authorization and authentication policies, allowing multiple users management and roles definition that enables specific permissions, operations and data views to each user. For example, adLIMS allows creating sample sheets from stored data using available exporting operations. This simplicity and process standardization may avoid manual errors and information backtracking, features

  2. LIMS and Clinical Data Management.

    PubMed

    Chen, Yalan; Lin, Yuxin; Yuan, Xuye; Shen, Bairong

    2016-01-01

    In order to achieve more accurate disease prevention, diagnosis, and treatment, clinical and genetic data need extensive and systematically associated study. As one way to achieve precision medicine, a laboratory information management system (LIMS) can effectively associate clinical data in a macrocosmic aspect and genomic data in a microcosmic aspect. This chapter summarizes the application of the LIMS in a clinical data management and implementation mode. It also discusses the principles of a LIMS in clinical data management, as well as the opportunities and challenges in the context of medical informatics.

  3. Principles and application of LIMS in mouse clinics.

    PubMed

    Maier, Holger; Schütt, Christine; Steinkamp, Ralph; Hurt, Anja; Schneltzer, Elida; Gormanns, Philipp; Lengger, Christoph; Griffiths, Mark; Melvin, David; Agrawal, Neha; Alcantara, Rafael; Evans, Arthur; Gannon, David; Holroyd, Simon; Kipp, Christian; Raj, Navis Pretheeba; Richardson, David; LeBlanc, Sophie; Vasseur, Laurent; Masuya, Hiroshi; Kobayashi, Kimio; Suzuki, Tomohiro; Tanaka, Nobuhiko; Wakana, Shigeharu; Walling, Alison; Clary, David; Gallegos, Juan; Fuchs, Helmut; de Angelis, Martin Hrabě; Gailus-Durner, Valerie

    2015-10-01

    Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.

  4. MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

    PubMed

    Grimes, Susan M; Ji, Hanlee P

    2014-08-27

    Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

  5. Recent advances in the rational design and development of LIM kinase inhibitors are not enough to enter clinical trials.

    PubMed

    Manetti, Fabrizio

    2018-06-08

    LIM kinases are involved in various pathophysiological processes that depend on actin organization. Alteration of microtubule dynamics by LIMK dysregulation is in fact related to tumor progression and metastasis, viral infection, and ocular diseases, such as glaucoma. As a consequence, many efforts have been done in recent years to rationally design small molecules able to inhibit LIMK activity selectively, without affecting other kinases. As a result, compounds optimized in terms of binding affinity and pharmacokinetic parameters have been discovered, that however failed to access clinical trials. In this review, a comprehensive survey of recent LIMK inhibitors is reported, together with SAR considerations and optimization processes. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  6. LIMS user acceptance testing.

    PubMed

    Klein, Corbett S

    2003-01-01

    Laboratory Information Management Systems (LIMS) play a key role in the pharmaceutical industry. Thorough and accurate validation of such systems is critical and is a regulatory requirement. LIMS user acceptance testing is one aspect of this testing and enables the user to make a decision to accept or reject implementation of the system. This paper discusses key elements in facilitating the development and execution of a LIMS User Acceptance Test Plan (UATP).

  7. Improving the Plasticity of LIMS Implementation: LIMS Extension through Microsoft Excel

    NASA Technical Reports Server (NTRS)

    Culver, Mark

    2017-01-01

    A Laboratory Information Management System (LIMS) is a databasing software with many built-in tools ideal for handling and documenting most laboratory processes in an accurate and consistent manner, making it an indispensable tool for the modern laboratory. However, a lot of LIMS end users will find that in the performance of analyses that have unique considerations such as standard curves, multiple stages incubations, or logical considerations, a base LIMS distribution may not ideally suit their needs. These considerations bring about the need for extension languages, which can extend the functionality of a LIMS. While these languages do provide the implementation team the functionality required to accommodate these special laboratory analyses, they are usually too complex for the end user to modify to compensate for natural changes in laboratory operations. The LIMS utilized by our laboratory offers a unique and easy-to-use choice for an extension language, one that is already heavily relied upon not only in science but also in most academic and business pursuits: Microsoft Excel. The validity of Microsoft Excel as a pseudo programming language and its usability and versatility as a LIMS extension language will be discussed. The NELAC implications and overall drawbacks of this LIMS configuration will also be discussed.

  8. Voice recognition software for clinical use.

    PubMed

    Korn, K

    1998-11-01

    The current generation voice recognition products truly offer the promise of voice recognition systems, that are financially and operationally acceptable for use in a health care facility. Although the initial capital outlay for the purchase of such equipment may be substantial, the long-term benefit is felt to outweigh the expense. The ability to utilize computer equipment for educational purposes and information management alone helps to rationalize the cost. In addition, it is important to remember that the Internet has become a substantial source of information which provides another functional use for this equipment. Although one can readily see the implication for such a program in clinical practice, other uses for the program should not be overlooked. Uses far beyond the writing of clinic notes and correspondence can be easily envisioned. Utilization of voice recognition software offers clinical practices the ability to produce quality printed records in a timely and cost-effective manner. After learning procedures for the selected product and appropriately formatting word processing software and printers, printed progress notes should be able to be produced in less time than traditional dictation and transcription methods. Although certain procedures and practices may need to be altered, or may preclude optimal utilization of this type of system, many advantages are apparent. It is recommended that facilities consider utilization of Voice Recognition products such as Dragon Systems Naturally Speaking Software, or at least consider a trial of this method with one of the limited-feature products, if current dictation practices are unsatisfactory or excessively costly. Free downloadable trial software or single user software can provide a reduced-cost method for trial evaluation of such products if a major commitment is not felt to be desired. A list of voice recognition software manufacturer web sites may be accessed through the following: http

  9. Open-source LIMS in Vietnam: The path toward sustainability and host country ownership.

    PubMed

    Landgraf, Kenneth M; Kakkar, Reshma; Meigs, Michelle; Jankauskas, Paul T; Phan, Thi Thu Huong; Nguyen, Viet Nga; Nguyen, Duy Thai; Duong, Thanh Tung; Nguyen, Thi Hoa; Bond, Kyle B

    2016-09-01

    The objectives of this case report are as follows: to describe the process of establishing a national laboratory information management system (LIMS) program for clinical and public health laboratories in Vietnam; to evaluate the outcomes and lessons learned; and to present a model for sustainability based on the program outcomes that could be applied to diverse laboratory programs. This case report comprises a review of program documentation and records, including planning and budgetary records of the donor, monthly reports from the implementer, direct observation, and ad-hoc field reports from technical advisors and governmental agencies. Additional data on program efficacy and user acceptance were collected from routine monitoring of laboratory policies and operational practices. LIMS software was implemented at 38 hospital, public health and HIV testing laboratories in Vietnam. This LIMS was accepted by users and program managers as a useful tool to support laboratory processes. Implementation cost per laboratory and average duration of deployment decreased over time, and project stakeholders initiated transition of financing (from the donor to local institutions) and of system maintenance functions (from the implementer to governmental and site-level staff). Collaboration between the implementer in Vietnam and the global LIMS user community was strongly established, and knowledge was successfully transferred to staff within Vietnam. Implementing open-sourced LIMS with local development and support was a feasible approach towards establishing a sustainable laboratory informatics program that met the needs of health laboratories in Vietnam. Further effort to institutionalize IT support capacity within key government agencies is ongoing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  10. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine

    PubMed Central

    2011-01-01

    Background Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. Results We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. Conclusions By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the immediate benefits of

  11. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine.

    PubMed

    Bath, Timothy G; Bozdag, Selcuk; Afzal, Vackar; Crowther, Daniel

    2011-05-13

    Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the immediate benefits of improved data visibility, audit and

  12. openBIS ELN-LIMS: an open-source database for academic laboratories.

    PubMed

    Barillari, Caterina; Ottoz, Diana S M; Fuentes-Serna, Juan Mariano; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian

    2016-02-15

    The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched. The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available. © The Author 2015. Published by Oxford University Press.

  13. A Study of Clinically Related Open Source Software Projects

    PubMed Central

    Hogarth, Michael A.; Turner, Stuart

    2005-01-01

    Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

  14. Using Clinical Decision Support Software in Health Insurance Company

    NASA Astrophysics Data System (ADS)

    Konovalov, R.; Kumlander, Deniss

    This paper proposes the idea to use Clinical Decision Support software in Health Insurance Company as a tool to reduce the expenses related to Medication Errors. As a prove that this class of software will help insurance companies reducing the expenses, the research was conducted in eight hospitals in United Arab Emirates to analyze the amount of preventable common Medication Errors in drug prescription.

  15. Thermography based prescreening software tool for veterinary clinics

    NASA Astrophysics Data System (ADS)

    Dahal, Rohini; Umbaugh, Scott E.; Mishra, Deependra; Lama, Norsang; Alvandipour, Mehrdad; Umbaugh, David; Marino, Dominic J.; Sackman, Joseph

    2017-05-01

    Under development is a clinical software tool which can be used in the veterinary clinics as a prescreening tool for these pathologies: anterior cruciate ligament (ACL) disease, bone cancer and feline hyperthyroidism. Currently, veterinary clinical practice uses several imaging techniques including radiology, computed tomography (CT), and magnetic resonance imaging (MRI). But, harmful radiation involved during imaging, expensive equipment setup, excessive time consumption and the need for a cooperative patient during imaging, are major drawbacks of these techniques. In veterinary procedures, it is very difficult for animals to remain still for the time periods necessary for standard imaging without resorting to sedation - which creates another set of complexities. Therefore, clinical application software integrated with a thermal imaging system and the algorithms with high sensitivity and specificity for these pathologies, can address the major drawbacks of the existing imaging techniques. A graphical user interface (GUI) has been created to allow ease of use for the clinical technician. The technician inputs an image, enters patient information, and selects the camera view associated with the image and the pathology to be diagnosed. The software will classify the image using an optimized classification algorithm that has been developed through thousands of experiments. Optimal image features are extracted and the feature vector is then used in conjunction with the stored image database for classification. Classification success rates as high as 88% for bone cancer, 75% for ACL and 90% for feline hyperthyroidism have been achieved. The software is currently undergoing preliminary clinical testing.

  16. Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

    PubMed

    Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

    2017-12-15

    This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

  17. A software tool to analyze clinical workflows from direct observations.

    PubMed

    Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

    2015-01-01

    Observational data of clinical processes need to be managed in a convenient way, so that process information is reliable, valid and viable for further analysis. However, existing tools for allocating observations fail in systematic data collection of specific workflow recordings. We present a software tool which was developed to facilitate the analysis of clinical process observations. The tool was successfully used in the project OntoHealth, to build, store and analyze observations of diabetes routine consultations.

  18. LIMS Version 6 Level 3 Dataset

    NASA Technical Reports Server (NTRS)

    Remsberg, Ellis E.; Lingenfelser, Gretchen

    2010-01-01

    This report describes the Limb Infrared Monitor of the Stratosphere (LIMS) Version 6 (V6) Level 3 data products and the assumptions used for their generation. A sequential estimation algorithm was used to obtain daily, zonal Fourier coefficients of the several parameters of the LIMS dataset for 216 days of 1978-79. The coefficients are available at up to 28 pressure levels and at every two degrees of latitude from 64 S to 84 N and at the synoptic time of 12 UT. Example plots were prepared and archived from the data at 10 hPa of January 1, 1979, to illustrate the overall coherence of the features obtained with the LIMS-retrieved parameters.

  19. Custom software development for use in a clinical laboratory

    PubMed Central

    Sinard, John H.; Gershkovich, Peter

    2012-01-01

    In-house software development for use in a clinical laboratory is a controversial issue. Many of the objections raised are based on outdated software development practices, an exaggeration of the risks involved, and an underestimation of the benefits that can be realized. Buy versus build analyses typically do not consider total costs of ownership, and unfortunately decisions are often made by people who are not directly affected by the workflow obstacles or benefits that result from those decisions. We have been developing custom software for clinical use for over a decade, and this article presents our perspective on this practice. A complete analysis of the decision to develop or purchase must ultimately examine how the end result will mesh with the departmental workflow, and custom-developed solutions typically can have the greater positive impact on efficiency and productivity, substantially altering the decision balance sheet. Involving the end-users in preparation of the functional specifications is crucial to the success of the process. A large development team is not needed, and even a single programmer can develop significant solutions. Many of the risks associated with custom development can be mitigated by a well-structured development process, use of open-source tools, and embracing an agile development philosophy. In-house solutions have the significant advantage of being adaptable to changing departmental needs, contributing to efficient and higher quality patient care. PMID:23372985

  20. Custom software development for use in a clinical laboratory.

    PubMed

    Sinard, John H; Gershkovich, Peter

    2012-01-01

    In-house software development for use in a clinical laboratory is a controversial issue. Many of the objections raised are based on outdated software development practices, an exaggeration of the risks involved, and an underestimation of the benefits that can be realized. Buy versus build analyses typically do not consider total costs of ownership, and unfortunately decisions are often made by people who are not directly affected by the workflow obstacles or benefits that result from those decisions. We have been developing custom software for clinical use for over a decade, and this article presents our perspective on this practice. A complete analysis of the decision to develop or purchase must ultimately examine how the end result will mesh with the departmental workflow, and custom-developed solutions typically can have the greater positive impact on efficiency and productivity, substantially altering the decision balance sheet. Involving the end-users in preparation of the functional specifications is crucial to the success of the process. A large development team is not needed, and even a single programmer can develop significant solutions. Many of the risks associated with custom development can be mitigated by a well-structured development process, use of open-source tools, and embracing an agile development philosophy. In-house solutions have the significant advantage of being adaptable to changing departmental needs, contributing to efficient and higher quality patient care.

  1. Enhancing outpatient clinics management software by reducing patients' waiting time.

    PubMed

    Almomani, Iman; AlSarheed, Ahlam

    The Kingdom of Saudi Arabia (KSA) gives great attention to improving the quality of services provided by health care sectors including outpatient clinics. One of the main drawbacks in outpatient clinics is long waiting time for patients-which affects the level of patient satisfaction and the quality of services. This article addresses this problem by studying the Outpatient Management Software (OMS) and proposing solutions to reduce waiting times. Many hospitals around the world apply solutions to overcome the problem of long waiting times in outpatient clinics such as hospitals in the USA, China, Sri Lanka, and Taiwan. These clinics have succeeded in reducing wait times by 15%, 78%, 60% and 50%, respectively. Such solutions depend mainly on adding more human resources or changing some business or management policies. The solutions presented in this article reduce waiting times by enhancing the software used to manage outpatient clinics services. Both quantitative and qualitative methods have been used to understand current OMS and examine level of patient's satisfaction. Five main problems that may cause high or unmeasured waiting time have been identified: appointment type, ticket numbering, doctor late arrival, early arriving patient and patients' distribution list. These problems have been mapped to the corresponding OMS components. Solutions to the above problems have been introduced and evaluated analytically or by simulation experiments. Evaluation of the results shows a reduction in patient waiting time. When late doctor arrival issues are solved, this can reduce the clinic service time by up to 20%. However, solutions for early arriving patients reduces 53.3% of vital time, 20% of the clinic time and overall 30.3% of the total waiting time. Finally, well patient-distribution lists make improvements by 54.2%. Improvements introduced to the patients' waiting time will consequently affect patients' satisfaction and improve the quality of health care services

  2. Implementation of Task-Tracking Software for Clinical IT Management.

    PubMed

    Purohit, Anne-Maria; Brutscheck, Clemens; Prokosch, Hans-Ulrich; Ganslandt, Thomas; Schneider, Martin

    2017-01-01

    Often in clinical IT departments, many different methods and IT systems are used for task-tracking and project organization. Based on managers' personal preferences and knowledge about project management methods, tools differ from team to team and even from employee to employee. This causes communication problems, especially when tasks need to be done in cooperation with different teams. Monitoring tasks and resources becomes impossible: there are no defined deliverables, which prevents reliable deadlines. Because of these problems, we implemented task-tracking software which is now in use across all seven teams at the University Hospital Erlangen. Over a period of seven months, a working group defined types of tasks (project, routine task, etc.), workflows, and views to monitor the tasks of the 7 divisions, 20 teams and 340 different IT services. The software has been in use since December 2016.

  3. [Development of integrated support software for clinical nutrition].

    PubMed

    Siquier Homar, Pedro; Pinteño Blanco, Manel; Calleja Hernández, Miguel Ángel; Fernández Cortés, Francisco; Martínez Sotelo, Jesús

    2015-09-01

    to develop an integrated computer software application for specialized nutritional support, integrated in the electronic clinical record, which detects automatically and early those undernourished patients or at risk of developing undernourishment, determining points of opportunity for improvement and evaluation of the results. the quality standards published by the Nutrition Work Group of the Spanish Society of Hospital Pharmacy (SEFH) and the recommendations by the Pharmacy Group of the Spanish Society of Parenteral and Enteral Nutrition (SENPE) have been taken into account. According to these quality standards, the nutritional support has to include the following healthcare stages or sub-processes: nutritional screening, nutritional assessment, plan for nutritional care, prescription, preparation and administration. this software allows to conduct, in an automated way, a specific nutritional assessment for those patients with nutritional risk, implementing, if necessary, a nutritional treatment plan, conducting follow-up and traceability of outcomes derived from the implementation of improvement actions, and quantifying to what extent our practice is close to the established standard. this software allows to standardize the specialized nutritional support from a multidisciplinary point of view, introducing the concept of quality control per processes, and including patient as the main customer. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  4. Towards Archetypes-Based Software Development

    NASA Astrophysics Data System (ADS)

    Piho, Gunnar; Roost, Mart; Perkins, David; Tepandi, Jaak

    We present a framework for the archetypes based engineering of domains, requirements and software (Archetypes-Based Software Development, ABD). An archetype is defined as a primordial object that occurs consistently and universally in business domains and in business software systems. An archetype pattern is a collaboration of archetypes. Archetypes and archetype patterns are used to capture conceptual information into domain specific models that are utilized by ABD. The focus of ABD is on software factories - family-based development artefacts (domain specific languages, patterns, frameworks, tools, micro processes, and others) that can be used to build the family members. We demonstrate the usage of ABD for developing laboratory information management system (LIMS) software for the Clinical and Biomedical Proteomics Group, at the Leeds Institute of Molecular Medicine, University of Leeds.

  5. Slip control for LIM propelled transit vehicles

    NASA Astrophysics Data System (ADS)

    Wallace, A. K.; Parker, J. H.; Dawson, G. E.

    1980-09-01

    Short stator linear induction motors, with an iron-backed aluminum sheet reaction rail and powered by a controlled inverter, have been selected as the propulsion system for transit vehicles in an intermediate capacity system (12-20,000 pphpd). The linear induction motor is capable of adhesion independent braking and acceleration levels which permit safe, close headways. In addition, simple control is possible allowing moving block automatic train control. This paper presents a slip frequency control scheme for the LIM. Experimental results for motoring and braking obtained from a test vehicle are also presented. These values are compared with theoretical predictions.

  6. Clinical genomics information management software linking cancer genome sequence and clinical decisions.

    PubMed

    Watt, Stuart; Jiao, Wei; Brown, Andrew M K; Petrocelli, Teresa; Tran, Ben; Zhang, Tong; McPherson, John D; Kamel-Reid, Suzanne; Bedard, Philippe L; Onetto, Nicole; Hudson, Thomas J; Dancey, Janet; Siu, Lillian L; Stein, Lincoln; Ferretti, Vincent

    2013-09-01

    Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reporting to clinicians. We describe a software application developed within a clinical genomics study, to support this entire process. The software application tracks patients, samples, genomic results, decisions and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of tumor mutation frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. By supporting the entire process, the application provides deep support for clinical decision making, enabling the generation of relevant guidance in reports for verification by an expert panel prior to forwarding to the treating physician. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Software.

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 1989

    1989-01-01

    Presented are reviews of two computer software packages for Apple II computers; "Organic Spectroscopy," and "Videodisc Display Program" for use with "The Periodic Table Videodisc." A sample spectrograph from "Organic Spectroscopy" is included. (CW)

  8. Principles of Contour Information: Reply to Lim and Leek (2012)

    ERIC Educational Resources Information Center

    Singh, Manish; Feldman, Jacob

    2012-01-01

    Lim and Leek (2012) presented a formalization of information along object contours, which they argued was an alternative to the approach taken in our article (Feldman & Singh, 2005). Here, we summarize the 2 approaches, showing that--notwithstanding Lim and Leek's (2012) critical rhetoric--their approach is substantially identical to ours,…

  9. Clinical software development for the Web: lessons learned from the BOADICEA project.

    PubMed

    Cunningham, Alex P; Antoniou, Antonis C; Easton, Douglas F

    2012-04-10

    In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web

  10. Clinical software development for the Web: lessons learned from the BOADICEA project

    PubMed Central

    2012-01-01

    Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers

  11. An emerging link between LIM domain proteins and nuclear receptors.

    PubMed

    Sala, Stefano; Ampe, Christophe

    2018-06-01

    Nuclear receptors are ligand-activated transcription factors that partake in several biological processes including development, reproduction and metabolism. Over the last decade, evidence has accumulated that group 2, 3 and 4 LIM domain proteins, primarily known for their roles in actin cytoskeleton organization, also partake in gene transcription regulation. They shuttle between the cytoplasm and the nucleus, amongst other as a consequence of triggering cells with ligands of nuclear receptors. LIM domain proteins act as important coregulators of nuclear receptor-mediated gene transcription, in which they can either function as coactivators or corepressors. In establishing interactions with nuclear receptors, the LIM domains are important, yet pleiotropy of LIM domain proteins and nuclear receptors frequently occurs. LIM domain protein-nuclear receptor complexes function in diverse physiological processes. Their association is, however, often linked to diseases including cancer.

  12. Laboratory Information Management System (LIMS): A case study

    NASA Technical Reports Server (NTRS)

    Crandall, Karen S.; Auping, Judith V.; Megargle, Robert G.

    1987-01-01

    In the late 70's, a refurbishment of the analytical laboratories serving the Materials Division at NASA Lewis Research Center was undertaken. As part of the modernization efforts, a Laboratory Information Management System (LIMS) was to be included. Preliminary studies indicated a custom-designed system as the best choice in order to satisfy all of the requirements. A scaled down version of the original design has been in operation since 1984. The LIMS, a combination of computer hardware, provides the chemical characterization laboratory with an information data base, a report generator, a user interface, and networking capabilities. This paper is an account of the processes involved in designing and implementing that LIMS.

  13. MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics.

    PubMed

    Hunter, Adam; Dayalan, Saravanan; De Souza, David; Power, Brad; Lorrimar, Rodney; Szabo, Tamas; Nguyen, Thu; O'Callaghan, Sean; Hack, Jeremy; Pyke, James; Nahid, Amsha; Barrero, Roberto; Roessner, Ute; Likic, Vladimir; Tull, Dedreia; Bacic, Antony; McConville, Malcolm; Bellgard, Matthew

    2017-01-01

    An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments. Here we present MASTR-MS, a downloadable and installable LIMS solution that can be deployed either within a single laboratory or used to link workflows across a multisite network. It comprises a Node Management System that can be used to link and manage projects across one or multiple collaborating laboratories; a User Management System which defines different user groups and privileges of users; a Quote Management System where client quotes are managed; a Project Management System in which metadata is stored and all aspects of project management, including experimental setup, sample tracking and instrument analysis, are defined, and a Data Management System that allows the automatic capture and storage of raw and processed data from the analytical instruments to the LIMS. MASTR-MS is a comprehensive LIMS solution specifically designed for metabolomics. It captures the entire lifecycle of a sample starting from project and experiment design to sample analysis, data capture and storage. It acts as an electronic notebook, facilitating project management within a single laboratory or a multi-node collaborative environment. This software is being developed in close consultation with members of the metabolomics research

  14. Usability study of clinical exome analysis software: top lessons learned and recommendations.

    PubMed

    Shyr, Casper; Kushniruk, Andre; Wasserman, Wyeth W

    2014-10-01

    New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis. Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience. We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to

  15. Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes

    SciTech Connect

    Bhati, Mugdha; Lee, Christopher; Nancarrow, Amy L.

    2008-09-03

    LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1{sub LBD}).more » Although the LIM interaction domain of Ldb1 (Ldb1{sub LID}) and Isl1{sub LBD} share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1{sub LBD} mimics Ldb1{sub LID}. These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events.« less

  16. Pros and Cons of Clinical Pathway Software Management: A Qualitative Study.

    PubMed

    Aarnoutse, M F; Brinkkemper, S; de Mul, M; Askari, M

    2018-01-01

    In this study we aimed to assess the perceived effectiveness of clinical pathway management software for healthcare professionals. A case study on the clinical pathway management software program Check-It was performed in three departments at an academic medical center. Four months after the implementation of the software, interviews were held with healthcare professionals who work with the system. The interview questions were posed in a semi-structured interview format and the participant were asked about the perceived positive or negative effects of Check-It, and whether they thought the software is effective for them. The interviews were recorded and transcribed based on grounded theory, using different coding techniques. Our results showed fewer overlooked tasks, pre-filled orders and letters, better overview, and increased protocol insight as positive aspects of using the software. Being not flexible enough was experienced as a negative aspect.

  17. [Software for illustrating a cost-quality balance carried out by clinical laboratory practice].

    PubMed

    Nishibori, Masahiro; Asayama, Hitoshi; Kimura, Satoshi; Takagi, Yasushi; Hagihara, Michio; Fujiwara, Mutsunori; Yoneyama, Akiko; Watanabe, Takashi

    2010-09-01

    We have no proper reference indicating the quality of clinical laboratory practice, which should clearly illustrates that better medical tests require more expenses. Japanese Society of Laboratory Medicine was concerned about recent difficult medical economy and issued a committee report proposing a guideline to evaluate the good laboratory practice. According to the guideline, we developed software that illustrate a cost-quality balance carried out by clinical laboratory practice. We encountered a number of controversial problems, for example, how to measure and weight each quality-related factor, how to calculate costs of a laboratory test and how to consider characteristics of a clinical laboratory. Consequently we finished only prototype software within the given period and the budget. In this paper, software implementation of the guideline and the above-mentioned problems are summarized. Aiming to stimulate these discussions, the operative software will be put on the Society's homepage for trial

  18. Automated pre-processing and multivariate vibrational spectra analysis software for rapid results in clinical settings

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, T.; Kumar, P.; Fillipe, L.

    2018-02-01

    Vibrational spectroscopy, especially FTIR and Raman, has shown enormous potential in disease diagnosis, especially in cancers. Their potential for detecting varied pathological conditions are regularly reported. However, to prove their applicability in clinics, large multi-center multi-national studies need to be undertaken; and these will result in enormous amount of data. A parallel effort to develop analytical methods, including user-friendly software that can quickly pre-process data and subject them to required multivariate analysis is warranted in order to obtain results in real time. This study reports a MATLAB based script that can automatically import data, preprocess spectra— interpolation, derivatives, normalization, and then carry out Principal Component Analysis (PCA) followed by Linear Discriminant Analysis (LDA) of the first 10 PCs; all with a single click. The software has been verified on data obtained from cell lines, animal models, and in vivo patient datasets, and gives results comparable to Minitab 16 software. The software can be used to import variety of file extensions, asc, .txt., .xls, and many others. Options to ignore noisy data, plot all possible graphs with PCA factors 1 to 5, and save loading factors, confusion matrices and other parameters are also present. The software can provide results for a dataset of 300 spectra within 0.01 s. We believe that the software will be vital not only in clinical trials using vibrational spectroscopic data, but also to obtain rapid results when these tools get translated into clinics.

  19. Statistical Validation for Clinical Measures: Repeatability and Agreement of Kinect™-Based Software

    PubMed Central

    Tello, Emanuel; Rodrigo, Alejandro; Valentinuzzi, Max E.

    2018-01-01

    Background The rehabilitation process is a fundamental stage for recovery of people's capabilities. However, the evaluation of the process is performed by physiatrists and medical doctors, mostly based on their observations, that is, a subjective appreciation of the patient's evolution. This paper proposes a tracking platform of the movement made by an individual's upper limb using Kinect sensor(s) to be applied for the patient during the rehabilitation process. The main contribution is the development of quantifying software and the statistical validation of its performance, repeatability, and clinical use in the rehabilitation process. Methods The software determines joint angles and upper limb trajectories for the construction of a specific rehabilitation protocol and quantifies the treatment evolution. In turn, the information is presented via a graphical interface that allows the recording, storage, and report of the patient's data. For clinical purposes, the software information is statistically validated with three different methodologies, comparing the measures with a goniometer in terms of agreement and repeatability. Results The agreement of joint angles measured with the proposed software and goniometer is evaluated with Bland-Altman plots; all measurements fell well within the limits of agreement, meaning interchangeability of both techniques. Additionally, the results of Bland-Altman analysis of repeatability show 95% confidence. Finally, the physiotherapists' qualitative assessment shows encouraging results for the clinical use. Conclusion The main conclusion is that the software is capable of offering a clinical history of the patient and is useful for quantification of the rehabilitation success. The simplicity, low cost, and visualization possibilities enhance the use of the software Kinect for rehabilitation and other applications, and the expert's opinion endorses the choice of our approach for clinical practice. Comparison of the new measurement

  20. Statistical Validation for Clinical Measures: Repeatability and Agreement of Kinect™-Based Software.

    PubMed

    Lopez, Natalia; Perez, Elisa; Tello, Emanuel; Rodrigo, Alejandro; Valentinuzzi, Max E

    2018-01-01

    The rehabilitation process is a fundamental stage for recovery of people's capabilities. However, the evaluation of the process is performed by physiatrists and medical doctors, mostly based on their observations, that is, a subjective appreciation of the patient's evolution. This paper proposes a tracking platform of the movement made by an individual's upper limb using Kinect sensor(s) to be applied for the patient during the rehabilitation process. The main contribution is the development of quantifying software and the statistical validation of its performance, repeatability, and clinical use in the rehabilitation process. The software determines joint angles and upper limb trajectories for the construction of a specific rehabilitation protocol and quantifies the treatment evolution. In turn, the information is presented via a graphical interface that allows the recording, storage, and report of the patient's data. For clinical purposes, the software information is statistically validated with three different methodologies, comparing the measures with a goniometer in terms of agreement and repeatability. The agreement of joint angles measured with the proposed software and goniometer is evaluated with Bland-Altman plots; all measurements fell well within the limits of agreement, meaning interchangeability of both techniques. Additionally, the results of Bland-Altman analysis of repeatability show 95% confidence. Finally, the physiotherapists' qualitative assessment shows encouraging results for the clinical use. The main conclusion is that the software is capable of offering a clinical history of the patient and is useful for quantification of the rehabilitation success. The simplicity, low cost, and visualization possibilities enhance the use of the software Kinect for rehabilitation and other applications, and the expert's opinion endorses the choice of our approach for clinical practice. Comparison of the new measurement technique with established

  1. Software for MR image overlay guided needle insertions: the clinical translation process

    NASA Astrophysics Data System (ADS)

    Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

    2013-03-01

    PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

  2. Evaluation of features to support safety and quality in general practice clinical software

    PubMed Central

    2011-01-01

    Background Electronic prescribing is now the norm in many countries. We wished to find out if clinical software systems used by general practitioners in Australia include features (functional capabilities and other characteristics) that facilitate improved patient safety and care, with a focus on quality use of medicines. Methods Seven clinical software systems used in general practice were evaluated. Fifty software features that were previously rated as likely to have a high impact on safety and/or quality of care in general practice were tested and are reported here. Results The range of results for the implementation of 50 features across the 7 clinical software systems was as follows: 17-31 features (34-62%) were fully implemented, 9-13 (18-26%) partially implemented, and 9-20 (18-40%) not implemented. Key findings included: Access to evidence based drug and therapeutic information was limited. Decision support for prescribing was available but varied markedly between systems. During prescribing there was potential for medicine mis-selection in some systems, and linking a medicine with its indication was optional. The definition of 'current medicines' versus 'past medicines' was not always clear. There were limited resources for patients, and some medicines lists for patients were suboptimal. Results were provided to the software vendors, who were keen to improve their systems. Conclusions The clinical systems tested lack some of the features expected to support patient safety and quality of care. Standards and certification for clinical software would ensure that safety features are present and that there is a minimum level of clinical functionality that clinicians could expect to find in any system.

  3. Extended cooperation in clinical studies through exchange of CDISC metadata between different study software solutions.

    PubMed

    Kuchinke, W; Wiegelmann, S; Verplancke, P; Ohmann, C

    2006-01-01

    Our objectives were to analyze the possibility of an exchange of an entire clinical study between two different and independent study software solutions. The question addressed was whether a software-independent transfer of study metadata can be performed without programming efforts and with software routinely used for clinical research. Study metadata was transferred with ODM standard (CDISC). Study software systems employed were MACRO (InferMed) and XTrial (XClinical). For the Proof of Concept, a test study was created with MACRO and exported as ODM. For modification and validation of the ODM export file XML-Spy (Altova) and ODM-Checker (XML4Pharma) were used. Through exchange of a complete clinical study between two different study software solutions, a Proof of Concept of the technical feasibility of a system-independent metadata exchange was conducted successfully. The interchange of study metadata between two different systems at different centers was performed with minimal expenditure. A small number of mistakes had to be corrected in order to generate a syntactically correct ODM file and a "vendor extension" had to be inserted. After these modifications, XTrial exhibited the study, including all data fields, correctly. However, the optical appearance of both CRFs (case report forms) was different. ODM can be used as an exchange format for clinical studies between different study software. Thus, new forms of cooperation through exchange of metadata seem possible, for example the joint creation of electronic study protocols or CRFs at different research centers. Although the ODM standard represents a clinical study completely, it contains no information about the representation of data fields in CRFs.

  4. Inclusion through Access to Outdoor Education: Learning in Motion (LIM)

    ERIC Educational Resources Information Center

    Brodin, Jane

    2009-01-01

    Learning in Motion (LIM) was a European project involving seven partners in five countries: Sweden, Finland, Latvia, Germany and Greece. The project focused on inclusion and access to outdoor education and was financed by the European Commission within the framework of the Socrates-Grundtvig Programme. The aim of the project was to explore if and…

  5. Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors

    PubMed Central

    Shyr, Casper; Kushniruk, Andre; van Karnebeek, Clara D.M.

    2016-01-01

    Background The transition of whole-exome and whole-genome sequencing (WES/WGS) from the research setting to routine clinical practice remains challenging. Objectives With almost no previous research specifically assessing interface designs and functionalities of WES and WGS software tools, the authors set out to ascertain perspectives from healthcare professionals in distinct domains on optimal clinical genomics user interfaces. Methods A series of semi-scripted focus groups, structured around professional challenges encountered in clinical WES and WGS, were conducted with bioinformaticians (n = 8), clinical geneticists (n = 9), genetic counselors (n = 5), and general physicians (n = 4). Results Contrary to popular existing system designs, bioinformaticians preferred command line over graphical user interfaces for better software compatibility and customization flexibility. Clinical geneticists and genetic counselors desired an overarching interactive graphical layout to prioritize candidate variants—a “tiered” system where only functionalities relevant to the user domain are made accessible. They favored a system capable of retrieving consistent representations of external genetic information from third-party sources. To streamline collaboration and patient exchanges, the authors identified user requirements toward an automated reporting system capable of summarizing key evidence-based clinical findings among the vast array of technical details. Conclusions Successful adoption of a clinical WES/WGS system is heavily dependent on its ability to address the diverse necessities and predilections among specialists in distinct healthcare domains. Tailored software interfaces suitable for each group is likely more appropriate than the current popular “one size fits all” generic framework. This study provides interfaces for future intervention studies and software engineering opportunities. PMID:26117142

  6. Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors.

    PubMed

    Shyr, Casper; Kushniruk, Andre; van Karnebeek, Clara D M; Wasserman, Wyeth W

    2016-03-01

    The transition of whole-exome and whole-genome sequencing (WES/WGS) from the research setting to routine clinical practice remains challenging. With almost no previous research specifically assessing interface designs and functionalities of WES and WGS software tools, the authors set out to ascertain perspectives from healthcare professionals in distinct domains on optimal clinical genomics user interfaces. A series of semi-scripted focus groups, structured around professional challenges encountered in clinical WES and WGS, were conducted with bioinformaticians (n = 8), clinical geneticists (n = 9), genetic counselors (n = 5), and general physicians (n = 4). Contrary to popular existing system designs, bioinformaticians preferred command line over graphical user interfaces for better software compatibility and customization flexibility. Clinical geneticists and genetic counselors desired an overarching interactive graphical layout to prioritize candidate variants--a "tiered" system where only functionalities relevant to the user domain are made accessible. They favored a system capable of retrieving consistent representations of external genetic information from third-party sources. To streamline collaboration and patient exchanges, the authors identified user requirements toward an automated reporting system capable of summarizing key evidence-based clinical findings among the vast array of technical details. Successful adoption of a clinical WES/WGS system is heavily dependent on its ability to address the diverse necessities and predilections among specialists in distinct healthcare domains. Tailored software interfaces suitable for each group is likely more appropriate than the current popular "one size fits all" generic framework. This study provides interfaces for future intervention studies and software engineering opportunities. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

  7. VARK Learning Preferences and Mobile Anatomy Software Application Use in Pre-Clinical Chiropractic Students

    ERIC Educational Resources Information Center

    Meyer, Amanda J.; Stomski, Norman J.; Innes, Stanley I.; Armson, Anthony J.

    2016-01-01

    Ubiquitous smartphone ownership and reduced face-to-face teaching time may lead to students making greater use of mobile technologies in their learning. This is the first study to report on the prevalence of mobile gross anatomy software applications (apps) usage in pre-clinical chiropractic students and to ascertain if a relationship exists…

  8. SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

    SciTech Connect

    Jiang, S; Dolly, S; Cai, B

    Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deepmore » modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality

  9. Visual and computer software-aided estimates of Dupuytren's contractures: correlation with clinical goniometric measurements.

    PubMed

    Smith, R P; Dias, J J; Ullah, A; Bhowal, B

    2009-05-01

    Corrective surgery for Dupuytren's disease represents a significant proportion of a hand surgeon's workload. The decision to go ahead with surgery and the success of surgery requires measuring the degree of contracture of the diseased finger(s). This is performed in clinic with a goniometer, pre- and postoperatively. Monitoring the recurrence of the contracture can inform on surgical outcome, research and audit. We compared visual and computer software-aided estimation of Dupuytren's contractures to clinical goniometric measurements in 60 patients with Dupuytren's disease. Patients' hands were digitally photographed. There were 76 contracted finger joints--70 proximal interphalangeal joints and six distal interphalangeal joints. The degrees of contracture of these images were visually assessed by six orthopaedic staff of differing seniority and re-assessed with computer software. Across assessors, the Pearson correlation between the goniometric measurements and the visual estimations was 0.83 and this significantly improved to 0.88 with computer software. Reliability with intra-class correlations achieved 0.78 and 0.92 for the visual and computer-aided estimations, respectively, and with test-retest analysis, 0.92 for visual estimation and 0.95 for computer-aided measurements. Visual estimations of Dupuytren's contractures correlate well with actual clinical goniometric measurements and improve further if measured with computer software. Digital images permit monitoring of contracture after surgery and may facilitate research into disease progression and auditing of surgical technique.

  10. [Evaluation of Web-based software applications for administrating and organising an ophthalmological clinical trial site].

    PubMed

    Kortüm, K; Reznicek, L; Leicht, S; Ulbig, M; Wolf, A

    2013-07-01

    The importance and complexity of clinical trials is continuously increasing, especially in innovative specialties like ophthalmology. Therefore an efficient clinical trial site organisational structure is essential. In modern internet times, this can be accomplished by web-based applications. In total, 3 software applications (Vibe on Prem, Sharepoint and open source software) were evaluated in a clinical trial site in ophthalmology. Assessment criteria were set; they were: reliability, easiness of administration, usability, scheduling, task list, knowledge management, operating costs and worldwide availability. Vibe on Prem customised by the local university met the assessment criteria best. Other applications were not as strong. By introducing a web-based application for administrating and organising an ophthalmological trial site, studies can be conducted in a more efficient and reliable manner. Georg Thieme Verlag KG Stuttgart · New York.

  11. The effect of advertising in clinical software on general practitioners' prescribing behaviour.

    PubMed

    Henderson, Joan; Miller, Graeme; Pan, Ying; Britt, Helena

    2008-01-07

    To assess the effect of pharmaceutical advertising embedded in clinical software on the prescribing behaviour of general practitioners. Secondary analysis of data from a random sample of 1336 Australian GPs who participated in Bettering the Evaluation and Care of Health, a national continuous cross-sectional survey of general practice activity, between November 2003 and March 2005. The prescribing behaviour of participants who used the advertising software was compared with that of participants who did not, for seven pharmaceutical products advertised continually throughout the study period. Prescription for advertised product as a proportion (%) of prescriptions for all pharmaceutical products in the same generic class or group. GP age, practice location, accreditation status, patient bulk-billing status and hours worked were significantly associated (P < 0.05) with use of advertising software. We found no significant differences, either before or after adjustment for these confounders, in the prescribing rate of Lipitor (adjusted odds ratio [AOR], 0.90; P = 0.26); Micardis (AOR, 0.98; P = 0.91); Mobic (AOR, 1.02; P = 0.89); Norvasc (AOR, 1.02; P = 0.91); Natrilix (AOR, 0.80; P = 0.32); or Zanidip (AOR, 0.88; P = 0.47). GPs using advertising software prescribed Nexium significantly less often than those not using advertising software (AOR, 0.78; P = 0.02). When all advertised products were combined and compared with products that were not advertised, no difference in the overall prescribing behaviour was demonstrated (AOR, 0.96; P = 0.42). Exposure to advertisements in clinical software has little influence on the prescribing behaviour of GPs.

  12. Semi-Automatic Segmentation Software for Quantitative Clinical Brain Glioblastoma Evaluation

    PubMed Central

    Zhu, Y; Young, G; Xue, Z; Huang, R; You, H; Setayesh, K; Hatabu, H; Cao, F; Wong, S.T.

    2012-01-01

    Rationale and Objectives Quantitative measurement provides essential information about disease progression and treatment response in patients with Glioblastoma multiforme (GBM). The goal of this paper is to present and validate a software pipeline for semi-automatic GBM segmentation, called AFINITI (Assisted Follow-up in NeuroImaging of Therapeutic Intervention), using clinical data from GBM patients. Materials and Methods Our software adopts the current state-of-the-art tumor segmentation algorithms and combines them into one clinically usable pipeline. Both the advantages of the traditional voxel-based and the deformable shape-based segmentation are embedded into the software pipeline. The former provides an automatic tumor segmentation scheme based on T1- and T2-weighted MR brain data, and the latter refines the segmentation results with minimal manual input. Results Twenty six clinical MR brain images of GBM patients were processed and compared with manual results. The results can be visualized using the embedded graphic user interface (GUI). Conclusion Validation results using clinical GBM data showed high correlation between the AFINITI results and manual annotation. Compared to the voxel-wise segmentation, AFINITI yielded more accurate results in segmenting the enhanced GBM from multimodality MRI data. The proposed pipeline could be used as additional information to interpret MR brain images in neuroradiology. PMID:22591720

  13. Laboratory and software applications for clinical trials: the global laboratory environment.

    PubMed

    Briscoe, Chad

    2011-11-01

    The Applied Pharmaceutical Software Meeting is held annually. It is sponsored by The Boston Society, a not-for-profit organization that coordinates a series of meetings within the global pharmaceutical industry. The meeting generally focuses on laboratory applications, but in recent years has expanded to include some software applications for clinical trials. The 2011 meeting emphasized the global laboratory environment. Global clinical trials generate massive amounts of data in many locations that must be centralized and processed for efficient analysis. Thus, the meeting had a strong focus on establishing networks and systems for dealing with the computer infrastructure to support such environments. In addition to the globally installed laboratory information management system, electronic laboratory notebook and other traditional laboratory applications, cloud computing is quickly becoming the answer to provide efficient, inexpensive options for managing the large volumes of data and computing power, and thus it served as a central theme for the meeting.

  14. Clinical, information and business process modeling to promote development of safe and flexible software.

    PubMed

    Liaw, Siaw-Teng; Deveny, Elizabeth; Morrison, Iain; Lewis, Bryn

    2006-09-01

    Using a factorial vignette survey and modeling methodology, we developed clinical and information models - incorporating evidence base, key concepts, relevant terms, decision-making and workflow needed to practice safely and effectively - to guide the development of an integrated rule-based knowledge module to support prescribing decisions in asthma. We identified workflows, decision-making factors, factor use, and clinician information requirements. The Unified Modeling Language (UML) and public domain software and knowledge engineering tools (e.g. Protégé) were used, with the Australian GP Data Model as the starting point for expressing information needs. A Web Services service-oriented architecture approach was adopted within which to express functional needs, and clinical processes and workflows were expressed in the Business Process Execution Language (BPEL). This formal analysis and modeling methodology to define and capture the process and logic of prescribing best practice in a reference implementation is fundamental to tackling deficiencies in prescribing decision support software.

  15. Treatment delivery software for a new clinical grade ultrasound system for thermoradiotherapy.

    PubMed

    Novák, Petr; Moros, Eduardo G; Straube, William L; Myerson, Robert J

    2005-11-01

    A detailed description of a clinical grade Scanning Ultrasound Reflector Linear Array System (SURLAS) applicator was given in a previous paper [Med. Phys. 32, 230-240 (2005)]. In this paper we concentrate on the design, development, and testing of the personal computer (PC) based treatment delivery software that runs the therapy system. The SURLAS requires the coordinated interaction between the therapy applicator and several peripheral devices for its proper and safe operation. One of the most important tasks was the coordination of the input power sequences for the elements of two parallel opposed ultrasound arrays (eight 1.5 cm x 2 cm elements/array, array 1 and 2 operate at 1.9 and 4.9 MHz, respectively) in coordination with the position of a dual-face scanning acoustic reflector. To achieve this, the treatment delivery software can divide the applicator's treatment window in up to 64 sectors (minimum size of 2 cm x 2 cm), and control the power to each sector independently by adjusting the power output levels from the channels of a 16-channel radio-frequency generator. The software coordinates the generator outputs with the position of the reflector as it scans back and forth between the arrays. Individual sector control and dual frequency operation allows the SURLAS to adjust power deposition in three dimensions to superficial targets coupled to its treatment window. The treatment delivery software also monitors and logs several parameters such as temperatures acquired using a 16-channel thermocouple thermometry unit. Safety (in particular to patients) was the paramount concern and design criterion. Failure mode and effects analysis (FMEA) was applied to the applicator as well as to the entire therapy system in order to identify safety issues and rank their relative importance. This analysis led to the implementation of several safety mechanisms and a software structure where each device communicates with the controlling PC independently of the others. In case

  16. LIM kinase function and renal growth: Potential role for LIM kinases in fetal programming of kidney development.

    PubMed

    Sparrow, Alexander J; Sweetman, Dylan; Welham, Simon J M

    2017-10-01

    Maternal dietary restriction during pregnancy impairs nephron development and results in offspring with fewer nephrons. Cell turnover in the early developing kidney is altered by exposure to maternal dietary restriction and may be regulated by the LIM-kinase family of enzymes. We set out to establish whether disturbance of LIM-kinase activity might play a role in the impairment of nephron formation. E12.5 metanephric kidneys and HK2 cells were grown in culture with the pharmacological LIM-kinase inhibitor BMS5. Organs were injected with DiI, imaged and cell numbers measured over 48h to assess growth. Cells undergoing mitosis were visualised by pH3 labelling. Growth of cultured kidneys reduced to 83% of controls after exposure to BMS5 and final cell number to 25% of control levels after 48h. Whilst control and BMS5 treated organs showed cells undergoing mitosis (100±11 cells/field vs 113±18 cells/field respectively) the proportion in anaphase was considerably diminished with BMS5 treatment (7.8±0.8% vs 0.8±0.6% respectively; P<0.01). This was consistent with effects on HK2 cells highlighting a severe impact of BMS5 on formation of the mitotic spindle and centriole positioning. DiI labelled cells migrated in 100% of control cultures vs 0% BMS5 treated organs. The number of nephrogenic precursor cells appeared depleted in whole organs and formation of new nephrons was blocked by exposure to BMS5. Pharmacological blockade of LIM-kinase function in the early developing kidney results in failure of renal development. This is likely due to prevention of dividing cells from completion of mitosis with their resultant loss. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Clinical records anonymisation and text extraction (CRATE): an open-source software system.

    PubMed

    Cardinal, Rudolf N

    2017-04-26

    Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.

  18. Perceptions of clinical utility of an Augmented Reality musical software among health care professionals.

    PubMed

    Corrêa, Ana Grasielle Dionísio; de Assis, Gilda Aparecida; do Nascimento, Marilena; de Deus Lopes, Roseli

    2017-04-01

    Augmented Reality musical software (GenVirtual) is a technology, which primarily allows users to develop music activities for rehabilitation. This study aimed to analyse the perceptions of health care professionals regarding the clinical utility of GenVirtual. A second objective was to identify improvements to GenVirtual software and similar technologies. Music therapists, occupational therapists, physiotherapists and speech and language therapist who assist people with physical and cognitive disabilities were enrolled in three focus groups. The quantitative and qualitative data were collected through inductive thematic analysis. Three main themes were identified: the use of GenVirtual in health care areas; opportunities for realistic application of GenVirtual; and limitations in the use of GenVirtual. The registration units identified were: motor stimulation, cognitive stimulation, verbal learning, recreation activity, musicality, accessibility, motivation, sonic accuracy, interference of lighting, poor sound, children and adults. This research suggested that the GenVirtual is a complementary tool to conventional clinical practice and has great potential to motor and cognitive rehabilitation of children and adults. Implications for Rehabilitation Gaining health professional' perceptions of the Augmented Reality musical game (GenVirtual) give valuable information as to the clinical utility of the software. GenVirtual was perceived as a tool that could be used as enhancing the motor and cognitive rehabilitation process. GenVirtual was viewed as a tool that could enhance clinical practice and communication among various agencies, but it was suggested that it should be used with caution to avoid confusion and replacement of important services.

  19. Ease of adoption of clinical natural language processing software: An evaluation of five systems.

    PubMed

    Zheng, Kai; Vydiswaran, V G Vinod; Liu, Yang; Wang, Yue; Stubbs, Amber; Uzuner, Özlem; Gururaj, Anupama E; Bayer, Samuel; Aberdeen, John; Rumshisky, Anna; Pakhomov, Serguei; Liu, Hongfang; Xu, Hua

    2015-12-01

    In recognition of potential barriers that may inhibit the widespread adoption of biomedical software, the 2014 i2b2 Challenge introduced a special track, Track 3 - Software Usability Assessment, in order to develop a better understanding of the adoption issues that might be associated with the state-of-the-art clinical NLP systems. This paper reports the ease of adoption assessment methods we developed for this track, and the results of evaluating five clinical NLP system submissions. A team of human evaluators performed a series of scripted adoptability test tasks with each of the participating systems. The evaluation team consisted of four "expert evaluators" with training in computer science, and eight "end user evaluators" with mixed backgrounds in medicine, nursing, pharmacy, and health informatics. We assessed how easy it is to adopt the submitted systems along the following three dimensions: communication effectiveness (i.e., how effective a system is in communicating its designed objectives to intended audience), effort required to install, and effort required to use. We used a formal software usability testing tool, TURF, to record the evaluators' interactions with the systems and 'think-aloud' data revealing their thought processes when installing and using the systems and when resolving unexpected issues. Overall, the ease of adoption ratings that the five systems received are unsatisfactory. Installation of some of the systems proved to be rather difficult, and some systems failed to adequately communicate their designed objectives to intended adopters. Further, the average ratings provided by the end user evaluators on ease of use and ease of interpreting output are -0.35 and -0.53, respectively, indicating that this group of users generally deemed the systems extremely difficult to work with. While the ratings provided by the expert evaluators are higher, 0.6 and 0.45, respectively, these ratings are still low indicating that they also experienced

  20. Evaluation of DICOM viewer software for workflow integration in clinical trials

    NASA Astrophysics Data System (ADS)

    Haak, Daniel; Page, Charles E.; Kabino, Klaus; Deserno, Thomas M.

    2015-03-01

    The digital imaging and communications in medicine (DICOM) protocol is nowadays the leading standard for capture, exchange and storage of image data in medical applications. A broad range of commercial, free, and open source software tools supporting a variety of DICOM functionality exists. However, different from patient's care in hospital, DICOM has not yet arrived in electronic data capture systems (EDCS) for clinical trials. Due to missing integration, even just the visualization of patient's image data in electronic case report forms (eCRFs) is impossible. Four increasing levels for integration of DICOM components into EDCS are conceivable, raising functionality but also demands on interfaces with each level. Hence, in this paper, a comprehensive evaluation of 27 DICOM viewer software projects is performed, investigating viewing functionality as well as interfaces for integration. Concerning general, integration, and viewing requirements the survey involves the criteria (i) license, (ii) support, (iii) platform, (iv) interfaces, (v) two-dimensional (2D) and (vi) three-dimensional (3D) image viewing functionality. Optimal viewers are suggested for applications in clinical trials for 3D imaging, hospital communication, and workflow. Focusing on open source solutions, the viewers ImageJ and MicroView are superior for 3D visualization, whereas GingkoCADx is advantageous for hospital integration. Concerning workflow optimization in multi-centered clinical trials, we suggest the open source viewer Weasis. Covering most use cases, an EDCS and PACS interconnection with Weasis is suggested.

  1. Quantitative Neuroimaging Software for Clinical Assessment of Hippocampal Volumes on MR Imaging

    PubMed Central

    Ahdidan, Jamila; Raji, Cyrus A.; DeYoe, Edgar A.; Mathis, Jedidiah; Noe, Karsten Ø.; Rimestad, Jens; Kjeldsen, Thomas K.; Mosegaard, Jesper; Becker, James T.; Lopez, Oscar

    2015-01-01

    Background: Multiple neurological disorders including Alzheimer’s disease (AD), mesial temporal sclerosis, and mild traumatic brain injury manifest with volume loss on brain MRI. Subtle volume loss is particularly seen early in AD. While prior research has demonstrated the value of this additional information from quantitative neuroimaging, very few applications have been approved for clinical use. Here we describe a US FDA cleared software program, NeuroreaderTM, for assessment of clinical hippocampal volume on brain MRI. Objective: To present the validation of hippocampal volumetrics on a clinical software program. Method: Subjects were drawn (n = 99) from the Alzheimer Disease Neuroimaging Initiative study. Volumetric brain MR imaging was acquired in both 1.5 T (n = 59) and 3.0 T (n = 40) scanners in participants with manual hippocampal segmentation. Fully automated hippocampal segmentation and measurement was done using a multiple atlas approach. The Dice Similarity Coefficient (DSC) measured the level of spatial overlap between NeuroreaderTM and gold standard manual segmentation from 0 to 1 with 0 denoting no overlap and 1 representing complete agreement. DSC comparisons between 1.5 T and 3.0 T scanners were done using standard independent samples T-tests. Results: In the bilateral hippocampus, mean DSC was 0.87 with a range of 0.78–0.91 (right hippocampus) and 0.76–0.91 (left hippocampus). Automated segmentation agreement with manual segmentation was essentially equivalent at 1.5 T (DSC = 0.879) versus 3.0 T (DSC = 0.872). Conclusion: This work provides a description and validation of a software program that can be applied in measuring hippocampal volume, a biomarker that is frequently abnormal in AD and other neurological disorders. PMID:26484924

  2. Sustainable Land Management in the Lim River Basin

    NASA Astrophysics Data System (ADS)

    Grujic, Gordana; Petkovic, Sava; Tatomir, Uros

    2017-04-01

    In the cross-border belt between Serbia and Montenegro are located more than one hundred torrential water flows that belong to the Lim River Basin. Under extreme climate events they turned into floods of destructive power and great energy causing enormous damage on the environment and socio-economic development in the wider region of the Western Balkans. In addition, anthropogenic factors influence the land instability, erosion of river beds and loss of topsoil. Consequently, this whole area is affected by pluvial and fluvial erosion of various types and intensity. Terrain on the slopes over 5% is affected by intensive degree of erosion, while strong to medium degree covers 70% of the area. Moreover, in the Lim River Basin were built several hydro-energetic systems and accumulations which may to a certain extent successfully regulate the water regime downstream and to reduce the negative impact on the processes of water erosion. However, siltation of accumulation reduces their useful volume and threatens the basic functions (water reservoirs), especially those ones for water supply, irrigation and energy production that have lost a significant part of the usable volume due to accumulated sediments. Facing the negative impacts of climate change and human activities on the process of land degradation in the Lim River basin imposes urgent need of adequate preventive and protective measures at the local and regional level, which can be effectively applied only through enhanced cross-border cooperation among affected communities in the region. The following set of activities were analyzed to improve the actual management of river catchment: Identifying priorities in the spatial planning, land use and water resources management while respecting the needs of local people and the communities in the cross border region; development of cooperation and partnership between the local population, owners and users of real estate (pastures, agricultural land, forests, fisheries

  3. Randomization in clinical trials: stratification or minimization? The HERMES free simulation software.

    PubMed

    Fron Chabouis, Hélène; Chabouis, Francis; Gillaizeau, Florence; Durieux, Pierre; Chatellier, Gilles; Ruse, N Dorin; Attal, Jean-Pierre

    2014-01-01

    Operative clinical trials are often small and open-label. Randomization is therefore very important. Stratification and minimization are two randomization options in such trials. The first aim of this study was to compare stratification and minimization in terms of predictability and balance in order to help investigators choose the most appropriate allocation method. Our second aim was to evaluate the influence of various parameters on the performance of these techniques. The created software generated patients according to chosen trial parameters (e.g., number of important prognostic factors, number of operators or centers, etc.) and computed predictability and balance indicators for several stratification and minimization methods over a given number of simulations. Block size and proportion of random allocations could be chosen. A reference trial was chosen (50 patients, 1 prognostic factor, and 2 operators) and eight other trials derived from this reference trial were modeled. Predictability and balance indicators were calculated from 10,000 simulations per trial. Minimization performed better with complex trials (e.g., smaller sample size, increasing number of prognostic factors, and operators); stratification imbalance increased when the number of strata increased. An inverse correlation between imbalance and predictability was observed. A compromise between predictability and imbalance still has to be found by the investigator but our software (HERMES) gives concrete reasons for choosing between stratification and minimization; it can be downloaded free of charge. This software will help investigators choose the appropriate randomization method in future two-arm trials.

  4. Development of preoperative planning software for transforaminal endoscopic surgery and the guidance for clinical applications.

    PubMed

    Chen, Xiaojun; Cheng, Jun; Gu, Xin; Sun, Yi; Politis, Constantinus

    2016-04-01

    Preoperative planning is of great importance for transforaminal endoscopic techniques applied in percutaneous endoscopic lumbar discectomy. In this study, a modular preoperative planning software for transforaminal endoscopic surgery was developed and demonstrated. The path searching method is based on collision detection, and the oriented bounding box was constructed for the anatomical models. Then, image reformatting algorithms were developed for multiplanar reconstruction which provides detailed anatomical information surrounding the virtual planned path. Finally, multithread technique was implemented to realize the steady-state condition of the software. A preoperative planning software for transforaminal endoscopic surgery (TE-Guider) was developed; seven cases of patients with symptomatic lumbar disc herniations were planned preoperatively using TE-Guider. The distances to the midlines and the direction of the optimal paths were exported, and each result was in line with the empirical value. TE-Guider provides an efficient and cost-effective way to search the ideal path and entry point for the puncture. However, more clinical cases will be conducted to demonstrate its feasibility and reliability.

  5. MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs.

    PubMed

    Heinle, Cassie Elizabeth; Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M

    2017-06-01

    As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. © The Authors 2017. Published by Oxford University Press.

  6. MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs

    PubMed Central

    Gaultier, Nicolas Paul Eugène; Miller, Dana; Purbojati, Rikky Wenang; Lauro, Federico M.

    2017-01-01

    Abstract Background: As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. Findings: MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. Conclusions: MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers. PMID:28430964

  7. PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

    PubMed

    Moody, George B; Mark, Roger G; Goldberger, Ary L

    2011-01-01

    PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

  8. PhenoTips: patient phenotyping software for clinical and research use.

    PubMed

    Girdea, Marta; Dumitriu, Sergiu; Fiume, Marc; Bowdin, Sarah; Boycott, Kym M; Chénier, Sébastien; Chitayat, David; Faghfoury, Hanna; Meyn, M Stephen; Ray, Peter N; So, Joyce; Stavropoulos, Dimitri J; Brudno, Michael

    2013-08-01

    We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our software combines an easy-to-use interface, compatible with any device that runs a Web browser, with a standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and additional notes. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. PhenoTips supports accurate diagnosis by analyzing the entered data, then suggesting additional clinical investigations and providing Online Mendelian Inheritance in Man (OMIM) links to likely disorders. By collecting, classifying, and analyzing phenotypic information during the patient encounter, PhenoTips allows for streamlining of clinic workflow, efficient data entry, improved diagnosis, standardization of collected patient phenotypes, and sharing of anonymized patient phenotype data for the study of rare disorders. Our source code and a demo version of PhenoTips are available at http://phenotips.org. © 2013 WILEY PERIODICALS, INC.

  9. RARtool: A MATLAB Software Package for Designing Response-Adaptive Randomized Clinical Trials with Time-to-Event Outcomes.

    PubMed

    Ryeznik, Yevgen; Sverdlov, Oleksandr; Wong, Weng Kee

    2015-08-01

    Response-adaptive randomization designs are becoming increasingly popular in clinical trial practice. In this paper, we present RARtool , a user interface software developed in MATLAB for designing response-adaptive randomized comparative clinical trials with censored time-to-event outcomes. The RARtool software can compute different types of optimal treatment allocation designs, and it can simulate response-adaptive randomization procedures targeting selected optimal allocations. Through simulations, an investigator can assess design characteristics under a variety of experimental scenarios and select the best procedure for practical implementation. We illustrate the utility of our RARtool software by redesigning a survival trial from the literature.

  10. The LIM Protein Zyxin Binds CARP-1 and Promotes Apoptosis

    PubMed Central

    Hervy, Martial; Hoffman, Laura M.; Jensen, Christopher C.; Smith, Mark; Beckerle, Mary C.

    2010-01-01

    Zyxin is a dual-function LIM domain protein that regulates actin dynamics in response to mechanical stress and shuttles between focal adhesions and the cell nucleus. Here we show that zyxin contributes to UV-induced apoptosis. Exposure of wild-type fibroblasts to UV-C irradiation results in apoptotic cell death, whereas cells harboring a homozygous disruption of the zyxin gene display a statistically significant survival advantage. To gain insight into the molecular mechanism by which zyxin promotes apoptotic signaling, we expressed an affinity-tagged zyxin variant in zyxin-null cells and isolated zyxin-associated proteins from cell lysates under physiological conditions. A 130-kDa protein that was co-isolated with zyxin was identified by microsequence analysis as the Cell Cycle and Apoptosis Regulator Protein-1 (CARP-1). CARP-1 associates with the LIM region of zyxin. Zyxin lacking the CARP-1 binding region shows reduced proapoptotic activity in response to UV-C irradiation. We demonstrate that CARP-1 is a nuclear protein. Zyxin is modified by phosphorylation in cells exposed to UV-C irradiation, and nuclear accumulation of zyxin is induced by UV-C exposure. These findings highlight a novel mechanism for modulating the apoptotic response to UV irradiation. PMID:20852740

  11. A guide for the laboratory information management system (LIMS) for light stable isotopes--Versions 7 and 8

    USGS Publications Warehouse

    Coplen, Tyler B.

    2000-01-01

    The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program, the Laboratory Information Management System (LIMS) for Light Stable Isotopes, is presented herein. Major benefits of this system include (i) a dramatic improvement in quality assurance, (ii) an increase in laboratory efficiency, (iii) a reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) a decrease in errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for laboratories. LIMS for Light Stable Isotopes is available for both Microsoft Office 97 Professional and Microsoft Office 2000 Professional as versions 7 and 8, respectively. Both source code (mdb file) and precompiled executable files (mde) are available. Numerous improvements have been made for continuous flow isotopic analysis in this version (specifically 7.13 for Microsoft Access 97 and 8.13 for Microsoft Access 2000). It is much easier to import isotopic results from Finnigan ISODAT worksheets, even worksheets on which corrections for amount of sample (linearity corrections) have been added. The capability to determine blank corrections using isotope mass balance from analyses of elemental analyzer samples has been added. It is now possible to calculate and apply drift corrections to isotopic

  12. Photogrammetric method to measure the discrepancy between clinical and software-designed positions of implants.

    PubMed

    Rivara, Federico; Lumetti, Simone; Calciolari, Elena; Toffoli, Andrea; Forlani, Gianfranco; Manfredi, Edoardo

    2016-06-01

    The position of dental implants placed with software-guided systems should be highly accurate in order to ensure safety and a passive fit of the immediate prosthesis. The purpose of this study was to measure the discrepancy between the clinical and software-planned position of dental implants by applying a photogrammetric method. Two casts were obtained, 1 from the surgical template and 1 from the actual position of the implants on the alveolar ridge of a patient. Photogrammetry was then applied to precisely locate the position of each implant on the casts. Because this mathematical technique required the identification of image points and of the relative spatial coordinates, 4 marks were drilled on the implant screw. The position of the implants was then identified as the geometric center of the 4 marks, while the orientation of the implant axis was represented by a vector normal to the plane fitting the points. A series of 16 convergent images all around the object was made using a high-resolution digital camera. A mathematical method called "rototranslation" was used to superimpose the cast images for the comparison. The tests performed on the casts resulted in an average precision level of 4 μm for the locations and less than 1 degree for the axis of the implants. A series of empirical and numerical tests were performed to assess the performance of the procedure and of the measurement protocol. The photogrammetric method is reproducible and can be used to measure the discrepancy between the software-planned and the real position of dental implants. Considering that the average precision level required for an implant-based prosthesis is approximately 50 μm, the error associated with this method can be considered as negligible. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

  13. OxMaR: open source free software for online minimization and randomization for clinical trials.

    PubMed

    O'Callaghan, Christopher A

    2014-01-01

    Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

  14. [Software-based visualization of patient flow at a university eye clinic].

    PubMed

    Greb, O; Abou Moulig, W; Hufendiek, K; Junker, B; Framme, C

    2017-03-01

    This article presents a method for visualization and navigation of patient flow in outpatient eye clinics with a high level of complexity. A network-based software solution was developed targeting long-term process optimization by structural analysis and temporal coordination of process navigation. Each examination unit receives a separate waiting list of patients in which the patient flow for every patient is recorded in a timeline. Time periods and points in time can be executed by mouse clicks and the desired diagnostic procedure can be entered. Recent progress in any of these diagnostic requests, as well as a variety of information on patient progress are collated and drawn into the corresponding timeline which can be viewed by any of the personnel involved. The software called TimeElement has been successfully tested in the practical implemenation for several months. As an example the patient flow regarding time stamps of defined events for intravitreous injections on 250 patients was recorded and an average attendance time of 169.71 min was found, whereby the time was also automatically recorded for each individual stage. Recording of patient flow data is a fundamental component of patient flow management, waiting time reduction, patient flow navigation with time and coordination in particular regarding timeline-based visualization for each individual patient. Long-term changes in process management can be planned and evaluated by comparing patient flow data. As using the software itself causes structural changes within the organization, a questionnaire is being planned for appraisal by the personnel involved.

  15. Clinical Severity Classification using Automated Conjunctival Hyperemia Analysis Software in Patients with Superior Limbic Keratoconjunctivitis.

    PubMed

    Kurita, Junki; Shoji, Jun; Inada, Noriko; Yoneda, Tsuyoshi; Sumi, Tamaki; Kobayashi, Masahiko; Hoshikawa, Yasuhiro; Fukushima, Atsuki; Yamagami, Satoru

    2018-06-01

    Digitization of clinical observation is necessary for assessing the severity of superior limbic keratoconjunctivitis (SLK). This study aimed to use a novel quantitative marker to examine hyperemia in patients with SLK. We included six eyes of six patients with both dry eye disease and SLK (SLK group) and eight eyes of eight patients with Sjögren syndrome (SS group). We simultaneously obtained the objective finding scores by using slit-lamp examination and calculated the superior hyperemia index (SHI) with an automated conjunctival hyperemia analysis software by using photographs of the anterior segment. Three objective finding scores, including papillary formation of the superior palpebral conjunctiva, superior limbal hyperemia and swelling, and superior corneal epitheliopathy, were determined. The SHI was calculated as the superior/temporal ratio of bulbar conjunctival hyperemia by using the software. Fisher's exact test was used to compare a high SHI (≥1.07) ratio between the SLK and SS groups. P-Values < 0.05 were considered statistically significant. The SHI (mean ± standard deviation) in the SLK and SS groups was 1.19 ± 0.50 and 0.69 ± 0.24, respectively. The number of patients with a high SHI (≥1.07) was significantly higher in the SLK group than in the SS group (p < 0.05). The sensitivity and specificity of the SHI in the differential diagnosis between SS and SLK were 66.7% and 87.5%, respectively. An analysis of the association between the objective finding scores and SHI showed that the SHI had a tendency to indicate the severity of superior limbal hyperemia and swelling score in the SLK group. The SHI calculated using the automated conjunctival hyperemia analysis software could successfully quantify superior bulbar conjunctival hyperemia and may be a useful tool for the differential diagnosis between SS and SLK and for the quantitative follow-up of patients with SLK.

  16. Molecular Characterization of abLIM, a Novel Actin-binding and Double Zinc Finger Protein

    PubMed Central

    Roof, Dorothy J.; Hayes, Annmarie; Adamian, Michael; Chishti, Athar H.; Li, Tiansen

    1997-01-01

    Molecules that couple the actin-based cytoskeleton to intracellular signaling pathways are central to the processes of cellular morphogenesis and differentiation. We have characterized a novel protein, the actin-binding LIM (abLIM) protein, which could mediate such interactions between actin filaments and cytoplasmic targets. abLIM protein consists of a COOH-terminal cytoskeletal domain that is fused to an NH2-terminal domain consisting of four double zinc finger motifs. The cytoskeletal domain is ∼50% identical to erythrocyte dematin, an actin-bundling protein of the red cell membrane skeleton, while the zinc finger domains conform to the LIM motif consensus sequence. In vitro expression studies demonstrate that abLIM protein can bind to F-actin through the dematin-like domain. Transcripts corresponding to three distinct isoforms have a widespread tissue distribution. However, a polypeptide corresponding to the full-length isoform is found exclusively in the retina and is enriched in biochemical extracts of retinal rod inner segments. abLIM protein also undergoes extensive phosphorylation in light-adapted retinas in vivo, and its developmental expression in the retina coincides with the elaboration of photoreceptor inner and outer segments. Based on the composite primary structure of abLIM protein, actin-binding capacity, potential regulation via phosphorylation, and isoform expression pattern, we speculate that abLIM may play a general role in bridging the actin-based cytoskeleton with an array of potential LIM protein-binding partners. The developmental time course of abLIM expression in the retina suggests that the retina-specific isoform may have a specialized role in the development or elaboration of photoreceptor inner and outer segments. PMID:9245787

  17. Global lower mesospheric water vapor revealed by LIMS observations

    NASA Technical Reports Server (NTRS)

    Gordley, L. L.; Russell, J. M., III; Remsberg, E. E.

    1985-01-01

    The Limb Infrared Monitor of the Stratospheric water vapor channel data analysis has been extended from the 1. mb level (about 48 km) to the .3 mb level (about 60 km) through a radiance averaging procedure and better understanding of systematic errors. The data show H2O mixing ratio peaks near the .5 mb level varying from 4 to 7 ppmv with latitude and season. Above this level the mixing ratio drops off quickly with altitude, but, due to experimental uncertainties, at an uncertain rate. The stratospheric results are virtually the same as determined from the archived LIMS results with a tropical hygropause and enhanced H2O concentration in the lower levels at high winter latitudes.

  18. Lightning Mapping and Leader Propagation Reconstruction using LOFAR-LIM

    NASA Astrophysics Data System (ADS)

    Hare, B.; Ebert, U.; Rutjes, C.; Scholten, O.; Trinh, G. T. N.

    2017-12-01

    LOFAR (LOw Frequency ARray) is a radio telescope that consists of a large number of dual-polarized antennas spread over the northern Netherlands and beyond. The LOFAR for Lightning Imaging project (LOFAR-LIM) has successfully used LOFAR to map out lightning in the Netherlands. Since LOFAR covers a large frequency range (10-90 MHz), has antennas spread over a large area, and saves the raw trace data from the antennas, LOFAR-LIM can combine all the strongest aspects of both lightning mapping arrays and lightning interferometers. These aspects include a nanosecond resolution between pulses, nanosecond timing accuracy, and an ability to map lightning in all 3 spatial dimensions and time. LOFAR should be able to map out overhead lightning with a spatial accuracy on the order of meters. The large amount of complex data provide by LOFAR has presented new data processing challenges, such as handling the time offsets between stations with large baselines and locating as many sources as possible. New algorithms to handle these challenges have been developed and will be discussed. Since the antennas are dual-polarized, all three components of the electric field can be extracted and the structure of the R.F. pulses can be investigated at a large number of distances and angles relative to the lightning source, potentially allowing for modeling of lightning current distributions relevant to the 10 to 90 MHz frequency range. R.F. pulses due to leader propagation will be presented, which show a complex sub-structure, indicating intricate physics that could potentially be reconstructed.

  19. A manual for a laboratory information management system (LIMS) for light stable isotopes

    USGS Publications Warehouse

    Coplen, Tyler B.

    1997-01-01

    The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program is presented herein. Major benefits of this system include (i) an increase in laboratory efficiency, (ii) reduction in the use of paper, (iii) reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) decreased errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for stable isotope laboratories. Since the original publication of the manual for LIMS for Light Stable Isotopes, the isotopes 3 H, 3 He, and 14 C, and the chlorofluorocarbons (CFCs), CFC-11, CFC-12, and CFC-113, have been added to this program.

  20. A manual for a Laboratory Information Management System (LIMS) for light stable isotopes

    USGS Publications Warehouse

    Coplen, Tyler B.

    1998-01-01

    The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program is presented herein. Major benefits of this system include (i) an increase in laboratory efficiency, (ii) reduction in the use of paper, (iii) reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) decreased errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for stable isotope laboratories. Since the original publication of the manual for LIMS for Light Stable Isotopes, the isotopes 3 H, 3 He, and 14 C, and the chlorofluorocarbons (CFCs), CFC-11, CFC-12, and CFC-113, have been added to this program.

  1. Comprehensive, powerful, efficient, intuitive: a new software framework for clinical imaging applications

    NASA Astrophysics Data System (ADS)

    Augustine, Kurt E.; Holmes, David R., III; Hanson, Dennis P.; Robb, Richard A.

    2006-03-01

    One of the greatest challenges for a software engineer is to create a complex application that is comprehensive enough to be useful to a diverse set of users, yet focused enough for individual tasks to be carried out efficiently with minimal training. This "powerful yet simple" paradox is particularly prevalent in advanced medical imaging applications. Recent research in the Biomedical Imaging Resource (BIR) at Mayo Clinic has been directed toward development of an imaging application framework that provides powerful image visualization/analysis tools in an intuitive, easy-to-use interface. It is based on two concepts very familiar to physicians - Cases and Workflows. Each case is associated with a unique patient and a specific set of routine clinical tasks, or a workflow. Each workflow is comprised of an ordered set of general-purpose modules which can be re-used for each unique workflow. Clinicians help describe and design the workflows, and then are provided with an intuitive interface to both patient data and analysis tools. Since most of the individual steps are common to many different workflows, the use of general-purpose modules reduces development time and results in applications that are consistent, stable, and robust. While the development of individual modules may reflect years of research by imaging scientists, new customized workflows based on the new modules can be developed extremely fast. If a powerful, comprehensive application is difficult to learn and complicated to use, it will be unacceptable to most clinicians. Clinical image analysis tools must be intuitive and effective or they simply will not be used.

  2. The Clinical Utilisation of Respiratory Elastance Software (CURE Soft): a bedside software for real-time respiratory mechanics monitoring and mechanical ventilation management.

    PubMed

    Szlavecz, Akos; Chiew, Yeong Shiong; Redmond, Daniel; Beatson, Alex; Glassenbury, Daniel; Corbett, Simon; Major, Vincent; Pretty, Christopher; Shaw, Geoffrey M; Benyo, Balazs; Desaive, Thomas; Chase, J Geoffrey

    2014-09-30

    Real-time patient respiratory mechanics estimation can be used to guide mechanical ventilation settings, particularly, positive end-expiratory pressure (PEEP). This work presents a software, Clinical Utilisation of Respiratory Elastance (CURE Soft), using a time-varying respiratory elastance model to offer this ability to aid in mechanical ventilation treatment. CURE Soft is a desktop application developed in JAVA. It has two modes of operation, 1) Online real-time monitoring decision support and, 2) Offline for user education purposes, auditing, or reviewing patient care. The CURE Soft has been tested in mechanically ventilated patients with respiratory failure. The clinical protocol, software testing and use of the data were approved by the New Zealand Southern Regional Ethics Committee. Using CURE Soft, patient's respiratory mechanics response to treatment and clinical protocol were monitored. Results showed that the patient's respiratory elastance (Stiffness) changed with the use of muscle relaxants, and responded differently to ventilator settings. This information can be used to guide mechanical ventilation therapy and titrate optimal ventilator PEEP. CURE Soft enables real-time calculation of model-based respiratory mechanics for mechanically ventilated patients. Results showed that the system is able to provide detailed, previously unavailable information on patient-specific respiratory mechanics and response to therapy in real-time. The additional insight available to clinicians provides the potential for improved decision-making, and thus improved patient care and outcomes.

  3. Free software to analyse the clinical relevance of drug interactions with antiretroviral agents (SIMARV®) in patients with HIV/AIDS.

    PubMed

    Giraldo, N A; Amariles, P; Monsalve, M; Faus, M J

    Highly active antiretroviral therapy has extended the expected lifespan of patients with HIV/AIDS. However, the therapeutic benefits of some drugs used simultaneously with highly active antiretroviral therapy may be adversely affected by drug interactions. The goal was to design and develop a free software to facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. A comprehensive Medline/PubMed database search of drug interactions was performed. Articles that recognized any drug interactions in HIV disease were selected. The publications accessed were limited to human studies in English or Spanish, with full texts retrieved. Drug interactions were analyzed, assessed, and grouped into four levels of clinical relevance according to gravity and probability. Software to systematize the information regarding drug interactions and their clinical relevance was designed and developed. Overall, 952 different references were retrieved and 446 selected; in addition, 67 articles were selected from the citation lists of identified articles. A total of 2119 pairs of drug interactions were identified; of this group, 2006 (94.7%) were drug-drug interactions, 1982 (93.5%) had an identified pharmacokinetic mechanism, and 1409 (66.5%) were mediated by enzyme inhibition. In terms of clinical relevance, 1285 (60.6%) drug interactions were clinically significant in patients with HIV (levels 1 and 2). With this information, a software program that facilitates identification and assessment of the clinical relevance of antiretroviral drug interactions (SIMARV ® ) was developed. A free software package with information on 2119 pairs of antiretroviral drug interactions was designed and developed that could facilitate analysis, assessment, and clinical decision making according to the clinical relevance of drug interactions in patients with HIV/AIDS. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Occupational therapists' perceptions about the clinical utility of the 3D interior design software.

    PubMed

    Atwa, Anita; Money, Arthur G; Spiliotopoulou, Georgia; Mcintyre, Anne

    2013-07-01

    The 3D interior design software (3DIDS) is a technology, which primarily allows users to simulate their homes and visualize any changes prior to implementing them. This feasibility study aimed to examine occupational therapists' perceptions about the clinical utility of the 3DIDS. A secondary aim was to explore the attitudes of occupational therapists towards technology in general. Three focus groups were conducted with 25 occupational therapists working with older people in the UK. The qualitative data were analysed using inductive thematic analysis. The three main themes that were identified were usage and attitudes of technology, opportunities for realistic application of the 3DIDS and related threats and benefits for the occupational therapy profession. Occupational therapists had a positive attitude towards technology. They suggested that the 3DIDS could be used in discharge planning and in rehabilitation. They viewed it as a tool that could enhance their status within the health care profession and improve communication, but not as a tool that should replace the role of the occupational therapist. This research offers new and important findings about the utilization of the 3DIDS by occupational therapists and provides information as to where this technology should be trialled.

  5. The LIM protein LIMD1 influences osteoblast differentiation and function

    SciTech Connect

    Luderer, Hilary F.; Bai Shuting; Longmore, Gregory D.

    2008-09-10

    The balance between bone resorption and bone formation involves the coordinated activities of osteoblasts and osteoclasts. Communication between these two cell types is essential for maintenance of normal bone homeostasis; however, the mechanisms regulating this cross talk are not completely understood. Many factors that mediate differentiation and function of both osteoblasts and osteoclasts have been identified. The LIM protein Limd1 has been implicated in the regulation of stress osteoclastogenesis through an interaction with the p62/sequestosome protein. Here we show that Limd1 also influences osteoblast progenitor numbers, differentiation, and function. Limd1{sup -/-} calvarial osteoblasts display increased mineralization and accelerated differentiation. Whilemore » no significant differences in osteoblast number or function were detected in vivo, bone marrow stromal cells isolated from Limd1{sup -/-} mice contain significantly more osteoblast progenitors compared to wild type controls when cultured ex vivo. Furthermore, we observed a significant increase in nuclear {beta}-catenin staining in differentiating Limd1{sup -/-} calvarial osteoblasts suggesting that Limd1 is a negative regulator of canonical Wnt signaling in osteoblasts. These results demonstrate that Limd1 influences not only stress osteoclastogenesis but also osteoblast function and osteoblast progenitor commitment. Together, these data identify Limd1 as a novel regulator of both bone osetoclast and bone osteoblast development and function.« less

  6. Nociceptive DRG neurons express muscle lim protein upon axonal injury.

    PubMed

    Levin, Evgeny; Andreadaki, Anastasia; Gobrecht, Philipp; Bosse, Frank; Fischer, Dietmar

    2017-04-04

    Muscle lim protein (MLP) has long been regarded as a cytosolic and nuclear muscular protein. Here, we show that MLP is also expressed in a subpopulation of adult rat dorsal root ganglia (DRG) neurons in response to axonal injury, while the protein was not detectable in naïve cells. Detailed immunohistochemical analysis of L4/L5 DRG revealed ~3% of MLP-positive neurons 2 days after complete sciatic nerve crush and maximum ~10% after 4-14 days. Similarly, in mixed cultures from cervical, thoracic, lumbar and sacral DRG ~6% of neurons were MLP-positive after 2 days and maximal 17% after 3 days. In both, histological sections and cell cultures, the protein was detected in the cytosol and axons of small diameter cells, while the nucleus remained devoid. Moreover, the vast majority could not be assigned to any of the well characterized canonical DRG subpopulations at 7 days after nerve injury. However, further analysis in cell culture revealed that the largest population of MLP expressing cells originated from non-peptidergic IB4-positive nociceptive neurons, which lose their ability to bind the lectin upon axotomy. Thus, MLP is mostly expressed in a subset of axotomized nociceptive neurons and can be used as a novel marker for this population of cells.

  7. Four and a half LIM domain protein signaling and cardiomyopathy.

    PubMed

    Liang, Yan; Bradford, William H; Zhang, Jing; Sheikh, Farah

    2018-06-20

    Four and a half LIM domain (FHL) protein family members, FHL1 and FHL2, are multifunctional proteins that are enriched in cardiac muscle. Although they both localize within the cardiomyocyte sarcomere (titin N2B), they have been shown to have important yet unique functions within the context of cardiac hypertrophy and disease. Studies in FHL1-deficient mice have primarily uncovered mitogen-activated protein kinase (MAPK) scaffolding functions for FHL1 as part of a novel biomechanical stretch sensor within the cardiomyocyte sarcomere, which acts as a positive regulator of pressure overload-mediated cardiac hypertrophy. New data have highlighted a novel role for the serine/threonine protein phosphatase (PP5) as a deactivator of the FHL1-based biomechanical stretch sensor, which has implications in not only cardiac hypertrophy but also heart failure. In contrast, studies in FHL2-deficient mice have primarily uncovered an opposing role for FHL2 as a negative regulator of adrenergic-mediated signaling and cardiac hypertrophy, further suggesting unique functions targeted by FHL proteins in the "stressed" cardiomyocyte. In this review, we provide current knowledge of the role of FHL1 and FHL2 in cardiac muscle as it relates to their actions in cardiac hypertrophy and cardiomyopathy. A specific focus will be to dissect the pathways and protein-protein interactions that underlie FHLs' signaling role in cardiac hypertrophy as well as provide a comprehensive list of FHL mutations linked to cardiac disease, using evidence gained from genetic mouse models and human genetic studies.

  8. Molecular cloning, structure, and chromosomal localization of the mouse LIM/homeobox gene Lhx5

    SciTech Connect

    Bertuzzi, S.; Sheng, Hui Z.; Westphal, H.

    1996-09-01

    Lhx5, the mouse ortholog of the Xenopus Xlim-5, is a LIM/homeobox gene expressed in the central nervous system during both embryonic development and adulthood. During development its domain of expression is mainly localized at the most anterior portion of the neural tube, and it precedes the morphological differentiation of the forebrain; for this reason we believe that Lhx5 could play an important role in forebrain patterning. Here we present the structural organization and the chromosomal localization of the Lhx5 gene. The gene is composed of five exons spanning more than 10 kb of genomic sequence. The first and second LIMmore » domains are encoded by the first and second exon, while the codons of the homeobox are split between the third and the fourth exons. The structure of Lhx5 is similar to that of other LIM/homeodomain proteins, Lxh1/lim1 and Lhx3/lim3, but differs from that of other LIM genes, such as mec3 and LMO1/Rbtn1, in which the codons for the LIM domains are interrupted by introns. We have mapped Lhx5 to the central region of mouse chromosome 5. 38 refs., 4 figs.« less

  9. A data model for clinical legal medicine practice and the development of a dedicated software for both practitioners and researchers.

    PubMed

    Dang, Catherine; Phuong, Thomas; Beddag, Mahmoud; Vega, Anabel; Denis, Céline

    2018-07-01

    To present a data model for clinical legal medicine and the software based on that data model for both practitioners and researchers. The main functionalities of the presented software are computer-assisted production of medical certificates and data capture, storage and retrieval. The data model and the software were jointly developed by the department of forensic medicine of the Jean Verdier Hospital (Bondy, France) and an bioinformatics laboratory (LIMICS, Paris universities 6-13) between November 2015 and May 2016. The data model was built based on four sources: i) a template used in our department for producing standardised medical certificates; ii) a random sample of medical certificates produced by the forensic department; iii) anterior consensus between four healthcare professionals (two forensic practitioners, a psychologist and a forensic psychiatrist) and iv) anatomical dictionaries. The trial version of the open source software was first designed for examination of physical assault survivors. An UML-like data model dedicated to clinical legal practice was built. The data model describes the terminology for examinations of sexual assault survivors, physical assault survivors, individuals kept in police custody and undocumented migrants for age estimation. A trial version of a software relying on the data model was developed and tested by three physicians. The software allows files archiving, standardised data collection, extraction and assistance for certificate generation. It can be used for research purpose, by data exchange and analysis. Despite some current limitations of use, it is a tool which can be shared and used by other departments of forensic medicine and other specialties, improving data management and exploitation. Full integration with external sources, analytics software and use of a semantic interoperability framework are planned for the next months. Copyright © 2016 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights

  10. VARK learning preferences and mobile anatomy software application use in pre-clinical chiropractic students.

    PubMed

    Meyer, Amanda J; Stomski, Norman J; Innes, Stanley I; Armson, Anthony J

    2016-05-06

    Ubiquitous smartphone ownership and reduced face-to-face teaching time may lead to students making greater use of mobile technologies in their learning. This is the first study to report on the prevalence of mobile gross anatomy software applications (apps) usage in pre-clinical chiropractic students and to ascertain if a relationship exists between preferred learning styles as determined by the validated VARK(©) questionnaire and use of mobile anatomy apps. The majority of the students who completed the VARK questionnaire were multimodal learners with kinesthetic and visual preferences. Sixty-seven percent (73/109) of students owned one or more mobile anatomy apps which were used by 57 students. Most of these students owned one to five apps and spent less than 30 minutes per week using them. Six of the top eight mobile anatomy apps owned and recommended by the students were developed by 3D4Medical. Visual learning preferences were not associated with time spent using mobile anatomy apps (OR = 0.40, 95% CI 0.12-1.40). Similarly, kinesthetic learning preferences (OR = 1.88, 95% CI 0.18-20.2), quadmodal preferences (OR = 0.71, 95% CI 0.06-9.25), or gender (OR = 1.51, 95% CI 0.48-4.81) did not affect the time students' spent using mobile anatomy apps. Learning preferences do not appear to influence students' time spent using mobile anatomy apps. Anat Sci Educ 9: 247-254. © 2015 American Association of Anatomists. © 2015 American Association of Anatomists.

  11. SU-F-T-22: Clinical Implications When Using TG-186 (ACE) Heterogeneity Software

    SciTech Connect

    Likhacheva, A; Grade, E; Sadeghi, A

    Purpose: The purpose of this study is to compare dosimetric calculations using traditional TG-43 formalism and Oncentra Brachy Advanced Collapsed cone Engine (ACE) TG-186 calculation algorithm in clinical setting. Methods: We analyzed dosimetry of four patients treated with accelerated partial breast irradiation using a multi-channel intracavitary device (SAVI). All patients were treated to 34 Gy in 10 fractions using a high-dose-rate (192) Ir source. The plans were designed and treated using the TG-43 model. ACE was used to assess the effect heterogeneity correction on various dosimetric parameters. Mass density was estimated using Hounsfield units. Results: Compared to TG-43 formalism, ACEmore » estimated lower doses to targets and organs at risk. The mean difference was 19.8% (range 15.3–24.1%) for PTV-eval V200, 12.0% (range 9.7–17.7%) for PTV-eval V150, 4.3% (range 3.3–6.5%) for PTV-eval D95, 3.3% (range 1.4–5.4%) for PTV-eval D90, 5.4% (range 2.9–9.9%) for maximum rib dose, and 5.7% (2.4–7.4%) for maximum skin dose. There was no correlation between the magnitude of the difference and the PTV-eval volume, air volume, or tissue-applicator conformance. Conclusion: Based on our preliminary study, the TG-43 algorithm appears to overestimate the dose to targets and organs at risk when compared to the ACE TG-186 software. We hypothesize that air adjacent to the SAVI struts contributes to lack of scatter thereby contributing a significant difference in dose calculation when using ACE. We believe that ACE calculation provides a more realistic isodose distribution than TG-43. We plan to further investigate the impact of heterogeneity correction on brachytherapy planning for a wide variety of clinical scenarios, include skin, cervix/uterus, prostate, and lung.« less

  12. 77 FR 6782 - In the Matter of: Kok Tong Lim, a/k/a Thomas Lim Blk 258A Compassvale Road #07-551 Singapore...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-09

    ... (50 U.S.C. 1701 et seq. (2000)) (``IEEPA''). Specifically, Lim conspired to illegally export wound... the Internal Security Act of 1950 (50 U.S.C. 783(b)), or section 38 of the Arms Export Control Act (22... Export Administration Act (50 U.S.C. app. Sec. Sec. 2401-2420 (2000)) (``EAA''). Since August 21, 2001...

  13. Impact of computer-based treatment planning software on clinical judgment of dental students for planning prosthodontic rehabilitation

    PubMed Central

    Deshpande, Saee; Chahande, Jayashree

    2014-01-01

    Purpose Successful prosthodontic rehabilitation involves making many interrelated clinical decisions which have an impact on each other. Self-directed computer-based training has been shown to be a very useful tool to develop synthetic and analytical problem-solving skills among students. Thus, a computer-based case study and treatment planning (CSTP) software program was developed which would allow students to work through the process of comprehensive, multidisciplinary treatment planning for patients in a structured and logical manner. The present study was aimed at assessing the effect of this CSTP software on the clinical judgment of dental students while planning prosthodontic rehabilitation and to assess the students’ perceptions about using the program for its intended use. Methods A CSTP software program was developed and validated. The impact of this program on the clinical decision making skills of dental graduates was evaluated by real life patient encounters, using a modified and validated mini-CEX. Students’ perceptions about the program were obtained by a pre-validated feedback questionnaire. Results The faculty assessment scores of clinical judgment improved significantly after the use of this program. The majority of students felt it was an informative, useful, and innovative way of learning and they strongly felt that they had learnt the logical progression of planning, the insight into decision making, and the need for flexibility in treatment planning after using this program. Conclusion CSTP software was well received by the students. There was significant improvement in students’ clinical judgment after using this program. It should thus be envisaged fundamentally as an adjunct to conventional teaching techniques to improve students’ decision making skills and confidence. PMID:25170288

  14. A Manual for a Laboratory Information Management System (LIMS) For Light Stable Isotopes - Version 7.0

    DTIC Science & Technology

    1998-01-01

    A MANUAL FOR A LABORATORY INFORMATION MANAGEMENT SYSTEM (LIMS) FOR LIGHT STABLE ISOTOPES— VERSION 7.0 U.S. GEOLOGICAL SURVEY Open-File Report 98-284...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 A MANUAL FOR A LABORATORY INFORMATION MANAGEMENT SYSTEM (LIMS) FOR LIGHT STABLE...Europa Scientific ..................................................120 1 A MANUAL FOR A LABORATORY INFORMATION MANAGEMENT SYSTEM (LIMS) FOR LIGHT STABLE

  15. Agreement between clinical estimation and a new quantitative analysis by Photoshop software in fundus and angiographic image variables.

    PubMed

    Ramezani, Alireza; Ahmadieh, Hamid; Azarmina, Mohsen; Soheilian, Masoud; Dehghan, Mohammad H; Mohebbi, Mohammad R

    2009-12-01

    To evaluate the validity of a new method for the quantitative analysis of fundus or angiographic images using Photoshop 7.0 (Adobe, USA) software by comparing with clinical evaluation. Four hundred and eighteen fundus and angiographic images of diabetic patients were evaluated by three retina specialists and then by computing using Photoshop 7.0 software. Four variables were selected for comparison: amount of hard exudates (HE) on color pictures, amount of HE on red-free pictures, severity of leakage, and the size of the foveal avascular zone (FAZ). The coefficient of agreement (Kappa) between the two methods in the amount of HE on color and red-free photographs were 85% (0.69) and 79% (0.59), respectively. The agreement for severity of leakage was 72% (0.46). In the two methods for the evaluation of the FAZ size using the magic and lasso software tools, the agreement was 54% (0.09) and 89% (0.77), respectively. Agreement in the estimation of the FAZ size by the lasso magnetic tool was excellent and was almost as good in the quantification of HE on color and on red-free images. Considering the agreement of this new technique for the measurement of variables in fundus images using Photoshop software with the clinical evaluation, this method seems to have sufficient validity to be used for the quantitative analysis of HE, leakage, and FAZ size on the angiograms of diabetic patients.

  16. Dosimetric and workflow evaluation of first commercial synthetic CT software for clinical use in pelvis

    NASA Astrophysics Data System (ADS)

    Tyagi, Neelam; Fontenla, Sandra; Zhang, Jing; Cloutier, Michelle; Kadbi, Mo; Mechalakos, Jim; Zelefsky, Michael; Deasy, Joe; Hunt, Margie

    2017-04-01

    To evaluate a commercial synthetic CT (syn-CT) software for use in prostate radiotherapy. Twenty-five prostate patients underwent CT and MR simulation scans in treatment position on a 3T MR scanner. A commercially available MR protocol was used that included a T2w turbo spin-echo sequence for soft-tissue contrast and a dual echo 3D mDIXON fast field echo (FFE) sequence for generating syn-CT. A dual-echo 3D FFE B 0 map was used for patient-induced susceptibility distortion analysis and a new 3D balanced-FFE sequence was evaluated for identification of implanted gold fiducial markers and subsequent image-guidance during radiotherapy delivery. Tissues were classified as air, adipose, water, trabecular/spongy bone and compact/cortical bone and assigned bulk HU values. The accuracy of syn-CT for treatment planning was analyzed by transferring the structures and plan from planning CT to syn-CT and recalculating the dose. Accuracy of localization at the treatment machine was evaluated by comparing registration of kV radiographs to either digitally reconstructed radiographs (DRRs) generated from syn-CT or traditional DRRs generated from the planning CT. Similarly, accuracy of setup using CBCT and syn-CT was compared to that using the planning CT. Finally, a MR-only simulation workflow was established and end-to-end testing was completed on five patients undergoing MR-only simulation. Dosimetric comparison between the original CT and syn-CT plans was within 0.5% on average for all structures. The de-novo optimized plans on the syn-CT met institutional clinical objectives for target and normal structures. Patient-induced susceptibility distortion based on B 0 maps was within 1 mm and 0.5 mm in the body and prostate respectively. DRR and CBCT localization based on MR-localized fiducials showed a standard deviation of  <1 mm. End-to-end testing and MR simulation workflow was successfully validated. MRI derived synthetic CT can be successfully used for a MR

  17. Software-based evaluation of toric IOL orientation in a multicenter clinical study.

    PubMed

    Kasthurirangan, Sanjeev; Feuchter, Lucas; Smith, Pamela; Nixon, Donald

    2014-12-01

    To evaluate the rotational stability of a new one-piece hydrophobic acrylic toric intraocular lens (IOL) using a custom-developed software for analysis of slit-lamp photographs. In a prospective, multicenter study, 174 eyes were implanted with the TECNIS Toric IOL (Abbott Medical Optics, Inc., Santa Ana, CA). A custom-developed software was used to analyze high-resolution slit-lamp photographs of 156 eyes taken at day 1 (baseline) and 1, 3, and 6 months postoperatively. The software uses iris and sclera landmarks to align the baseline image and later images for comparison. Validation of software was performed through repeated analyses of protractor images rotated from 0.1° to 10.0° and randomly selected photographs of 20 eyes. Software validation showed precision (repeatability plus reproducibility variation) of 0.02° using protractor images and 2.22° using slit-lamp photographs. Good quality slit-lamp images and clear landmarks were necessary for precise measurements. At 6 months, 94.2% of eyes had 5° or less change in IOL orientation versus baseline; only 2 eyes (1.4%) had axis shift greater than 30°. Most eyes were within 5° or less of rotation between 1 and 3 months (92.9%) and 3 and 6 months (94.1%). Mean absolute axis change (± standard deviation) from 1 day to 6 months was 2.70° ± 5.51°. The new custom software was precise and quick in analyzing slit-lamp photographs to determine postoperative toric IOL rotation. Copyright 2014, SLACK Incorporated.

  18. Evaluation of a deidentification (De-Id) software engine to share pathology reports and clinical documents for research.

    PubMed

    Gupta, Dilip; Saul, Melissa; Gilbertson, John

    2004-02-01

    We evaluated a comprehensive deidentification engine at the University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, that uses a complex set of rules, dictionaries, pattern-matching algorithms, and the Unified Medical Language System to identify and replace identifying text in clinical reports while preserving medical information for sharing in research. In our initial data set of 967 surgical pathology reports, the software did not suppress outside (103), UPMC (47), and non-UPMC (56) accession numbers; dates (7); names (9) or initials (25) of case pathologists; or hospital or laboratory names (46). In 150 reports, some clinical information was suppressed inadvertently (overmarking). The engine retained eponymic patient names, eg, Barrett and Gleason. In the second evaluation (1,000 reports), the software did not suppress outside (90) or UPMC (6) accession numbers or names (4) or initials (2) of case pathologists. In the third evaluation, the software removed names of patients, hospitals (297/300), pathologists (297/300), transcriptionists, residents and physicians, dates of procedures, and accession numbers (298/300). By the end of the evaluation, the system was reliably and specifically removing safe-harbor identifiers and producing highly readable deidentified text without removing important clinical information. Collaboration between pathology domain experts and system developers and continuous quality assurance are needed to optimize ongoing deidentification processes.

  19. Comparison of Southern Hemisphere radiosonde and LIMS temperatures at 100 mb. [limb infrared monitor of stratosphere

    NASA Technical Reports Server (NTRS)

    Miles, T.; Grose, W. L.; Russell, J. M., III; Remsberg, E. E.

    1987-01-01

    Radiosonde (RS)and satellite-derived (Nimbus-7 LIMS) 100-mb temperatures over New Zealand at 12 GMT are compared for the 1978-79 summer. The colocated LIMS temperature information consists of synoptically mapped values (for 12 GMT), as well as the primary nighttime orbital retrievals valid at about 1030 GMT. The RS time series of temperature is dominated by temporal fluctuations associated mainly with the eastward passage of waves which have characteristic periods of 4-5 and 11-12 days and peak-to-peak amplitudes of 10-15 K. The LIMS temperatures and the corresponding temperature time series are also found to exhibit quite close agreement (in terms of temporal phase for the latter) with the RS data. However, the LIMS-mapped temperature fluctuations suffer from a noticeable attenuation in amplitude (approaching 50 percent for higher-frequency fluctuations), which will affect the accuracy of LIMS-derived estimates of dynamical quantities such as wind velocity and relative vorticity in the lower stratosphere.

  20. Phase coexistence and exchange-bias effect in LiM n2O4 nanorods

    NASA Astrophysics Data System (ADS)

    Zhang, X. K.; Yuan, J. J.; Xie, Y. M.; Yu, Y.; Kuang, F. G.; Yu, H. J.; Zhu, X. R.; Shen, H.

    2018-03-01

    In this paper, the magnetic properties of LiM n2O4 nanorods with an average diameter of ˜100 nm and length of ˜1 μ m are investigated. The temperature dependences of dc and ac susceptibility measurements show that LiM n2O4 nanorods experience multiple magnetic phase transitions upon cooling, i.e., paramagnetic (PM), antiferromagnetic (AFM), canted antiferromagnetic (CAFM), and cluster spin glass (SG). The coexistence between a long-range ordered AFM phase due to a M n4 +-M n4 + interaction and a cluster SG phase originating from frozen AFM clusters at low temperature in LiM n2O4 nanorods is elucidated. Field-cooled hysteresis loops (FC loops) and magnetic training effect (TE) measurements confirm the presence of an exchange-bias (EB) effect in LiM n2O4 nanorods below the Néel temperature (TN˜60 K ) . Furthermore, by analyzing the TE, we conclude that the observed EB effect originates completely from an exchange coupling interaction at the interface between the AFM and cluster SG states. A phenomenological model based on phase coexistence is proposed to interpret the origin of the EB effect below 60 K in the present compound. In turn, the appearance of the EB effect further supports the coexistence of AFM order along with a cluster SG state in LiM n2O4 nanorods.

  1. Cyclic Testing of the 6-Strand Tang and Modified Lim-Tsai Flexor Tendon Repair Techniques.

    PubMed

    Kang, Gavrielle Hui-Ying; Wong, Yoke-Rung; Lim, Rebecca Qian-Ru; Loke, Austin Mun-Kitt; Tay, Shian-Chao

    2018-03-01

    In this study, we compared the Tang repair technique with the 6-strand modified Lim-Tsai repair technique under cyclic testing conditions. Twenty fresh-frozen porcine flexor tendons were randomized into 2 groups for repair with either the modified Lim-Tsai or the Tang technique using Supramid 4-0 core sutures and Ethilon 6-0 epitendinous running suture. The repaired tendons were subjected to 2 stage cyclic loading. The survival rate and gap formation at the repair site were recorded. Tendons repaired by the Tang technique achieved an 80% survival rate. None of the modified Lim-Tsai repairs survived. The mean gap formed at the end of 1000 cycles was 1.09 mm in the Tang repairs compared with 4.15 mm in the modified Lim-Tsai repairs. The Tang repair is biomechanically stronger than the modified Lim-Tsai repair under cyclic loading. The Tang repair technique may exhibit a higher tolerance for active mobilization after surgery with less propensity for gap formation. Copyright © 2018 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  2. Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

    PubMed Central

    Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

    2018-01-01

    Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with

  3. SMITH: a LIMS for handling next-generation sequencing workflows.

    PubMed

    Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

    2014-01-01

    Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available

  4. SMITH: a LIMS for handling next-generation sequencing workflows

    PubMed Central

    2014-01-01

    Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The

  5. Development of computer tablet software for clinical quantification of lateral knee compartment translation during the pivot shift test.

    PubMed

    Muller, Bart; Hofbauer, Marcus; Rahnemai-Azar, Amir Ata; Wolf, Megan; Araki, Daisuke; Hoshino, Yuichi; Araujo, Paulo; Debski, Richard E; Irrgang, James J; Fu, Freddie H; Musahl, Volker

    2016-01-01

    The pivot shift test is a commonly used clinical examination by orthopedic surgeons to evaluate knee function following injury. However, the test can only be graded subjectively by the examiner. Therefore, the purpose of this study is to develop software for a computer tablet to quantify anterior translation of the lateral knee compartment during the pivot shift test. Based on the simple image analysis method, software for a computer tablet was developed with the following primary design constraint - the software should be easy to use in a clinical setting and it should not slow down an outpatient visit. Translation of the lateral compartment of the intact knee was 2.0 ± 0.2 mm and for the anterior cruciate ligament-deficient knee was 8.9 ± 0.9 mm (p < 0.001). Intra-tester (ICC range = 0.913 to 0.999) and inter-tester (ICC = 0.949) reliability were excellent for the repeatability assessments. Overall, the average percent error of measuring simulated translation of the lateral knee compartment with the tablet parallel to the monitor increased from 2.8% at 50 cm distance to 7.7% at 200 cm. Deviation from the parallel position of the tablet did not have a significant effect until a tablet angle of 45°. Average percent error during anterior translation of the lateral knee compartment of 6mm was 2.2% compared to 6.2% for 2 mm of translation. The software provides reliable, objective, and quantitative data on translation of the lateral knee compartment during the pivot shift test and meets the design constraints posed by the clinical setting.

  6. Towards integration of clinical decision support in commercial hospital information systems using distributed, reusable software and knowledge components.

    PubMed

    Müller, M L; Ganslandt, T; Eich, H P; Lang, K; Ohmann, C; Prokosch, H U

    2001-12-01

    Clinicians' acceptance of clinical decision support depends on its workflow-oriented, context-sensitive accessibility and availability at the point of care, integrated into the Electronic Patient Record (EPR). Commercially available Hospital Information Systems (HIS) often focus on administrative tasks and mostly do not provide additional knowledge based functionality. Their traditionally monolithic and closed software architecture encumbers integration of and interaction with external software modules. Our aim was to develop methods and interfaces to integrate knowledge sources into two different commercial hospital information systems to provide the best decision support possible within the context of available patient data. An existing, proven standalone scoring system for acute abdominal pain was supplemented by a communication interface. In both HIS we defined data entry forms and developed individual and reusable mechanisms for data exchange with external software modules. We designed an additional knowledge support frontend which controls data exchange between HIS and the knowledge modules. Finally, we added guidelines and algorithms to the knowledge library. Despite some major drawbacks which resulted mainly from the HIS' closed software architectures we showed exemplary, how external knowledge support can be integrated almost seamlessly into different commercial HIS. This paper describes the prototypical design and current implementation and discusses our experiences.

  7. Technical Considerations in Remote LIMS Access via the World Wide Web

    PubMed Central

    Schlabach, David M.

    2005-01-01

    The increased dependency on the World Wide Web by both laboratories and their customers has led LIMS developers to take advantage of thin-client web applications that provide both remote data entry and manipulation, along with remote reporting functionality. Use of an LIMS through a web browser allows a person to interact with a distant application, providing both remote administration and real-time analytical result delivery from virtually anywhere in the world. While there are many benefits of web-based LIMS applications, some concern must be given to these new methods of system architecture before justifying them as a suitable replacement for their traditional client-server systems. Developers and consumers alike must consider the security aspects of introducing a wide area network capable system into a production environment, as well as the concerns of data integrity and usability. PMID:18924736

  8. On the Quality of the Nimbus 7 LIMS Version 6 Water Vapor Profiles and Distributions

    NASA Technical Reports Server (NTRS)

    Remsberg, E. E.; Natarajan, M.; Lingenfelser, G. S.; Thompson, R. E.; Marshall, B. T.; Gordley, L. L.

    2009-01-01

    This report describes the quality of the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS) water vapor (H2O) profiles of 1978/79 that were processed with a Version 6 (V6) algorithm and archived in 2002. The V6 profiles incorporate a better knowledge of the instrument attitude for the LIMS measurements along its orbits, leading to improvements for its temperature profiles and for the registration of its water vapor radiances with pressure. As a result, the LIMS V6 zonal-mean distributions of H2O exhibit better hemispheric symmetry than was the case from the original Version 5 (V5) dataset that was archived in 1982. Estimates of the precision and accuracy of the V6 H2O profiles are developed and provided. Individual profiles have a precision of order 5% and an estimated accuracy of about 19% at 3 hPa, 14% at 10 hPa, and 26% at 50 hPa. Profile segments within about 2 km of the tropopause are often affected by emissions from clouds that appear in the finite field-of-view of the detector for the LIMS H2O channel. Zonally-averaged distributions of the LIMS V6 H2O are compared with those from the more recent Microwave Limb Sounder (MLS) satellite experiment for November, February, and May of 2004/2005. The patterns and values of their respective distributions are similar in many respects. Effects of a strengthened Brewer-Dobson circulation are indicated in the MLS distributions of the recent decade versus those of LIMS from 1978/79. A tropical tape recorder signal is present in the 7-month time series of LIMS V6 H2O with lowest values in February 1979, and the estimated, annually-averaged "entry-level" H2O is 3.5 to 3.8 ppmv. It is judged that this historic LIMS water vapor dataset is of good quality for studies of the near global-scale chemistry and transport for pressure levels from 3 hPa to about 70 to 100 hPa.

  9. The first clinical application of planning software for laparoscopic microwave thermosphere ablation of malignant liver tumours

    PubMed Central

    Berber, Eren

    2015-01-01

    Background Liver tumour ablation is an operator-dependent procedure. The determination of the optimum needle trajectory and correct ablation parameters could be challenging. The aim of this study was to report the utility of a new, procedure planning software for microwave ablation (MWA) of liver tumours. Methods This was a feasibility study in a pilot group of five patients with nine metastatic liver tumours who underwent laparoscopic MWA. Pre-operatively, parameters predicting the desired ablation zones were calculated for each tumour. Intra-operatively, this planning strategy was followed for both antenna placement and energy application. Post-operative 2-week computed tomography (CT) scans were performed to evaluate complete tumour destruction. Results The patients had an average of two tumours (range 1–4), measuring 1.9 ± 0.4 cm (range 0.9–4.4 cm). The ablation time was 7.1 ± 1.3 min (range 2.5–10 min) at 100W. There were no complications or mortality. The patients were discharged home on post-operative day (POD) 1. At 2-week CT scans, there were no residual tumours, with a complete ablation demonstrated in all lesions. Conclusions This study describes and validates pre-treatment planning software for MWA of liver tumours. This software was found useful to determine precisely the ablation parameters and needle placement to create a predicted zone of ablation. PMID:25980481

  10. The first clinical application of planning software for laparoscopic microwave thermosphere ablation of malignant liver tumours.

    PubMed

    Berber, Eren

    2015-07-01

    Liver tumour ablation is an operator-dependent procedure. The determination of the optimum needle trajectory and correct ablation parameters could be challenging. The aim of this study was to report the utility of a new, procedure planning software for microwave ablation (MWA) of liver tumours. This was a feasibility study in a pilot group of five patients with nine metastatic liver tumours who underwent laparoscopic MWA. Pre-operatively, parameters predicting the desired ablation zones were calculated for each tumour. Intra-operatively, this planning strategy was followed for both antenna placement and energy application. Post-operative 2-week computed tomography (CT) scans were performed to evaluate complete tumour destruction. The patients had an average of two tumours (range 1-4), measuring 1.9 ± 0.4 cm (range 0.9-4.4 cm). The ablation time was 7.1 ± 1.3 min (range 2.5-10 min) at 100W. There were no complications or mortality. The patients were discharged home on post-operative day (POD) 1. At 2-week CT scans, there were no residual tumours, with a complete ablation demonstrated in all lesions. This study describes and validates pre-treatment planning software for MWA of liver tumours. This software was found useful to determine precisely the ablation parameters and needle placement to create a predicted zone of ablation. © 2015 International Hepato-Pancreato-Biliary Association.

  11. Internet-based virtual classroom and educational management software enhance students' didactic and clinical experiences in perfusion education programs.

    PubMed

    Riley, Jeffrey B; Austin, Jon W; Holt, David W; Searles, Bruce E; Darling, Edward M

    2004-09-01

    A challenge faced by many university-based perfusion education (PE) programs is the need for student clinical rotations at hospital locations that are geographically disparate from the main educational campus. The problem has been addressed through the employment of distance-learning environments. The purpose of this educational study is to evaluate the effectiveness of this teaching model as it is applied to PE. Web-based virtual classroom (VC) environments and educational management system (EMS) software were implemented independently and as adjuncts to live, interactive Internet-based audio/video transmission from classroom to classroom in multiple university-based PE programs. These Internet environments have been used in a variety of ways including: 1) forum for communication between the university faculty, students, and preceptors at clinical sites, 2) didactic lectures from expert clinicians to students assigned to distant clinical sites, 3) small group problem-based-learning modules designed to enhance students analytical skills, and 4) conversion of traditional face-to-face lectures to asynchronous learning modules. Hypotheses and measures of student and faculty satisfaction, clinical experience, and learning outcomes are proposed, and some early student feedback was collected. For curricula that emphasize both didactic and clinical education, the use of Internet-based VC and EMS software provides significant advancements over traditional models. Recognized advantages include: 1) improved communications between the college faculty and the students and clinical preceptors, 2) enhanced access to a national network of clinical experts in specialized techniques, 3) expanded opportunity for student distant clinical rotations with continued didactic course work, and 4) improved continuity and consistency of clinical experiences between students through implementation of asynchronous learning modules. Students recognize the learning efficiency of on

  12. Clinical Data Systems to Support Public Health Practice: A National Survey of Software and Storage Systems Among Local Health Departments.

    PubMed

    McCullough, J Mac; Goodin, Kate

    2016-01-01

    Numerous software and data storage systems are employed by local health departments (LHDs) to manage clinical and nonclinical data needs. Leveraging electronic systems may yield improvements in public health practice. However, information is lacking regarding current usage patterns among LHDs. To analyze clinical and nonclinical data storage and software types by LHDs. Data came from the 2015 Informatics Capacity and Needs Assessment Survey, conducted by Georgia Southern University in collaboration with the National Association of County and City Health Officials. A total of 324 LHDs from all 50 states completed the survey (response rate: 50%). Outcome measures included LHD's primary clinical service data system, nonclinical data system(s) used, and plans to adopt electronic clinical data system (if not already in use). Predictors of interest included jurisdiction size and governance type, and other informatics capacities within the LHD. Bivariate analyses were performed using χ and t tests. Up to 38.4% of LHDs reported using an electronic health record (EHR). Usage was common especially among LHDs that provide primary care and/or dental services. LHDs serving smaller populations and those with state-level governance were both less likely to use an EHR. Paper records were a common data storage approach for both clinical data (28.9%) and nonclinical data (59.4%). Among LHDs without an EHR, 84.7% reported implementation plans. Our findings suggest that LHDs are increasingly using EHRs as a clinical data storage solution and that more LHDs are likely to adopt EHRs in the foreseeable future. Yet use of paper records remains common. Correlates of electronic system usage emerged across a range of factors. Program- or system-specific needs may be barriers or facilitators to EHR adoption. Policy makers can tailor resources to address barriers specific to LHD size, governance, service portfolio, existing informatics capabilities, and other pertinent characteristics.

  13. Clinical values of intraoperative indocyanine green fluorescence video angiography with Flow 800 software in cerebrovascular surgery.

    PubMed

    Ye, Xun; Liu, Xing-Ju; Ma, Li; Liu, Ling-Tong; Wang, Wen-Lei; Wang, Shuo; Cao, Yong; Zhang, Dong; Wang, Rong; Zhao, Ji-Zong; Zhao, Yuan-Li

    2013-11-01

    Microscope-integrated near-infrared indocyanine green video angiography (ICG-VA) has been used in neurosurgery for a decade. This study aimed to assess the value of intraoperative indocyanine green (ICG) video angiography with Flow 800 software in cerebrovascular surgery and to discover its hemodynamic features and changes of cerebrovascular diseases during surgery. A total of 87 patients who received ICG-VA during various surgical procedures were enrolled in this study. Among them, 45 cases were cerebral aneurysms, 25 were cerebral arteriovenous malformations (AVMs), and 17 were moyamoya disease (MMD). A surgical microscope integrating an infrared fluorescence module was used to confirm the residual aneurysms and blocking of perforating arteries in aneurysms. Feeder arteries, draining veins, and normal cortical vessels were identified by the time delay color mode of Flow 800 software. Hemodynamic parameters were recorded. All data were analyzed by SPSS version 18.0 (SPSS Inc., USA). T-test was used to analyze the hemodynamic features of AVMs and MMDs, the influence on peripheral cortex after resection in AVMs, and superficial temporal artery to middle cerebral artery (STA-MCA) bypass in MMDs. The visual delay map obtained by Flow 800 software had more advantages than the traditional playback mode in identifying the feeder arteries, draining veins, and their relations to normal cortex vessels. The maximum fluorescence intensity (MFI) and the slope of ICG fluorescence curve of feeder arteries and draining veins were higher than normal peripheral vessels (MFI: 584.24±85.86 vs. 382.94 ± 91.50, slope: 144.95 ± 38.08 vs. 69.20 ± 13.08, P < 0.05). The arteriovenous transit time in AVM was significantly shorter than in normal cortical vessels ((0.60 ± 0.27) vs. (2.08 ± 1.42) seconds, P < 0.05). After resection of AVM, the slope of artery in the cortex increased, which reflected the increased cerebral flow. In patients with MMD, after STA-MCA bypass, cortex perfusion

  14. Automated matching software for clinical trials eligibility: measuring efficiency and flexibility.

    PubMed

    Penberthy, Lynne; Brown, Richard; Puma, Federico; Dahman, Bassam

    2010-05-01

    Clinical trials (CT) serve as the media that translates clinical research into standards of care. Low or slow recruitment leads to delays in delivery of new therapies to the public. Determination of eligibility in all patients is one of the most important factors to assure unbiased results from the clinical trials process and represents the first step in addressing the issue of under representation and equal access to clinical trials. This is a pilot project evaluating the efficiency, flexibility, and generalizibility of an automated clinical trials eligibility screening tool across 5 different clinical trials and clinical trial scenarios. There was a substantial total savings during the study period in research staff time spent in evaluating patients for eligibility ranging from 165h to 1329h. There was a marked enhancement in efficiency with the automated system for all but one study in the pilot. The ratio of mean staff time required per eligible patient identified ranged from 0.8 to 19.4 for the manual versus the automated process. The results of this study demonstrate that automation offers an opportunity to reduce the burden of the manual processes required for CT eligibility screening and to assure that all patients have an opportunity to be evaluated for participation in clinical trials as appropriate. The automated process greatly reduces the time spent on eligibility screening compared with the traditional manual process by effectively transferring the load of the eligibility assessment process to the computer. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  15. Multiattribute selection of acute stroke imaging software platform for Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) clinical trial.

    PubMed

    Churilov, Leonid; Liu, Daniel; Ma, Henry; Christensen, Soren; Nagakane, Yoshinari; Campbell, Bruce; Parsons, Mark W; Levi, Christopher R; Davis, Stephen M; Donnan, Geoffrey A

    2013-04-01

    The appropriateness of a software platform for rapid MRI assessment of the amount of salvageable brain tissue after stroke is critical for both the validity of the Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) Clinical Trial of stroke thrombolysis beyond 4.5 hours and for stroke patient care outcomes. The objective of this research is to develop and implement a methodology for selecting the acute stroke imaging software platform most appropriate for the setting of a multi-centre clinical trial. A multi-disciplinary decision making panel formulated the set of preferentially independent evaluation attributes. Alternative Multi-Attribute Value Measurement methods were used to identify the best imaging software platform followed by sensitivity analysis to ensure the validity and robustness of the proposed solution. Four alternative imaging software platforms were identified. RApid processing of PerfusIon and Diffusion (RAPID) software was selected as the most appropriate for the needs of the EXTEND trial. A theoretically grounded generic multi-attribute selection methodology for imaging software was developed and implemented. The developed methodology assured both a high quality decision outcome and a rational and transparent decision process. This development contributes to stroke literature in the area of comprehensive evaluation of MRI clinical software. At the time of evaluation, RAPID software presented the most appropriate imaging software platform for use in the EXTEND clinical trial. The proposed multi-attribute imaging software evaluation methodology is based on sound theoretical foundations of multiple criteria decision analysis and can be successfully used for choosing the most appropriate imaging software while ensuring both robust decision process and outcomes. © 2012 The Authors. International Journal of Stroke © 2012 World Stroke Organization.

  16. A Couple of "Lim (h[right arrow]0)-Is-Missing" Problems

    ERIC Educational Resources Information Center

    Lau, Ko Hin

    2007-01-01

    Since most students "hate" the concept of limit, in order to make them "happier," this article suggests a couple of naive "lim (h[right arrow]0)-is-missing" problems for them to try for fun. Indeed, differential functional equations that are related to difference quotients in calculus are studied in this paper. In particular, two interesting…

  17. A novel muscle LIM-only protein is generated from the paxillin gene locus in Drosophila.

    PubMed

    Yagi, R; Ishimaru, S; Yano, H; Gaul, U; Hanafusa, H; Sabe, H

    2001-09-01

    Paxillin is a protein containing four LIM domains, and functions in integrin signaling. We report here that two transcripts are generated from the paxillin gene locus in Drosophila; one encodes a protein homolog of the vertebrate Paxillin (DPxn37), and the other a protein with only three LIM domains, partly encoded by its own specific exon (PDLP). At the myotendinous junctions of Drosophila embryos where integrins play important roles, both DPxn37 and PDLP are highly expressed with different patterns; DPxn37 is predominantly concentrated at the center of the junctions, whereas PDLP is highly enriched at neighboring sides of the junction centers, primarily expressed in the mesodermal myotubes. Northern blot analysis revealed that DPxn37 is ubiquitously expressed throughout the life cycle, whereas PDLP expression exhibits a biphasic pattern during development, largely concomitant with muscle generation and remodeling. Our results collectively reveal that a unique system exists in Drosophila for the generation of a novel type of LIM-only protein, highly expressed in the embryonic musculature, largely utilizing the Paxillin LIM domains.

  18. Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

    PubMed

    Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

    2018-04-13

    Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test

  19. The Transcription Factors Islet and Lim3 Combinatorially Regulate Ion Channel Gene Expression

    PubMed Central

    Wolfram, Verena; Southall, Tony D.; Günay, Cengiz; Prinz, Astrid A.; Brand, Andrea H.

    2014-01-01

    Expression of appropriate ion channels is essential to allow developing neurons to form functional networks. Our previous studies have identified LIM-homeodomain (HD) transcription factors (TFs), expressed by developing neurons, that are specifically able to regulate ion channel gene expression. In this study, we use the technique of DNA adenine methyltransferase identification (DamID) to identify putative gene targets of four such TFs that are differentially expressed in Drosophila motoneurons. Analysis of targets for Islet (Isl), Lim3, Hb9, and Even-skipped (Eve) identifies both ion channel genes and genes predicted to regulate aspects of dendritic and axonal morphology. Significantly, some ion channel genes are bound by more than one TF, consistent with the possibility of combinatorial regulation. One such gene is Shaker (Sh), which encodes a voltage-dependent fast K+ channel (Kv1.1). DamID reveals that Sh is bound by both Isl and Lim3. We used body wall muscle as a test tissue because in conditions of low Ca2+, the fast K+ current is carried solely by Sh channels (unlike neurons in which a second fast K+ current, Shal, also contributes). Ectopic expression of isl, but not Lim3, is sufficient to reduce both Sh transcript and Sh current level. By contrast, coexpression of both TFs is additive, resulting in a significantly greater reduction in both Sh transcript and current compared with isl expression alone. These observations provide evidence for combinatorial activity of Isl and Lim3 in regulating ion channel gene expression. PMID:24523544

  20. Architecture Design of Healthcare Software-as-a-Service Platform for Cloud-Based Clinical Decision Support Service

    PubMed Central

    Oh, Sungyoung; Cha, Jieun; Ji, Myungkyu; Kang, Hyekyung; Kim, Seok; Heo, Eunyoung; Han, Jong Soo; Kang, Hyunggoo; Chae, Hoseok; Hwang, Hee

    2015-01-01

    Objectives To design a cloud computing-based Healthcare Software-as-a-Service (SaaS) Platform (HSP) for delivering healthcare information services with low cost, high clinical value, and high usability. Methods We analyzed the architecture requirements of an HSP, including the interface, business services, cloud SaaS, quality attributes, privacy and security, and multi-lingual capacity. For cloud-based SaaS services, we focused on Clinical Decision Service (CDS) content services, basic functional services, and mobile services. Microsoft's Azure cloud computing for Infrastructure-as-a-Service (IaaS) and Platform-as-a-Service (PaaS) was used. Results The functional and software views of an HSP were designed in a layered architecture. External systems can be interfaced with the HSP using SOAP and REST/JSON. The multi-tenancy model of the HSP was designed as a shared database, with a separate schema for each tenant through a single application, although healthcare data can be physically located on a cloud or in a hospital, depending on regulations. The CDS services were categorized into rule-based services for medications, alert registration services, and knowledge services. Conclusions We expect that cloud-based HSPs will allow small and mid-sized hospitals, in addition to large-sized hospitals, to adopt information infrastructures and health information technology with low system operation and maintenance costs. PMID:25995962

  1. Architecture Design of Healthcare Software-as-a-Service Platform for Cloud-Based Clinical Decision Support Service.

    PubMed

    Oh, Sungyoung; Cha, Jieun; Ji, Myungkyu; Kang, Hyekyung; Kim, Seok; Heo, Eunyoung; Han, Jong Soo; Kang, Hyunggoo; Chae, Hoseok; Hwang, Hee; Yoo, Sooyoung

    2015-04-01

    To design a cloud computing-based Healthcare Software-as-a-Service (SaaS) Platform (HSP) for delivering healthcare information services with low cost, high clinical value, and high usability. We analyzed the architecture requirements of an HSP, including the interface, business services, cloud SaaS, quality attributes, privacy and security, and multi-lingual capacity. For cloud-based SaaS services, we focused on Clinical Decision Service (CDS) content services, basic functional services, and mobile services. Microsoft's Azure cloud computing for Infrastructure-as-a-Service (IaaS) and Platform-as-a-Service (PaaS) was used. The functional and software views of an HSP were designed in a layered architecture. External systems can be interfaced with the HSP using SOAP and REST/JSON. The multi-tenancy model of the HSP was designed as a shared database, with a separate schema for each tenant through a single application, although healthcare data can be physically located on a cloud or in a hospital, depending on regulations. The CDS services were categorized into rule-based services for medications, alert registration services, and knowledge services. We expect that cloud-based HSPs will allow small and mid-sized hospitals, in addition to large-sized hospitals, to adopt information infrastructures and health information technology with low system operation and maintenance costs.

  2. Software for illustrative presentation of basic clinical characteristics of laboratory tests--GraphROC for Windows.

    PubMed

    Kairisto, V; Poola, A

    1995-01-01

    GraphROC for Windows is a program for clinical test evaluation. It was designed for the handling of large datasets obtained from clinical laboratory databases. In the user interface, graphical and numerical presentations are combined. For simplicity, numerical data is not shown unless requested. Relevant numbers can be "picked up" from the graph by simple mouse operations. Reference distributions can be displayed by using automatically optimized bin widths. Any percentile of the distribution with corresponding confidence limits can be chosen for display. In sensitivity-specificity analysis, both illness- and health-related distributions are shown in the same graph. The following data for any cutoff limit can be shown in a separate click window: clinical sensitivity and specificity with corresponding confidence limits, positive and negative likelihood ratios, positive and negative predictive values and efficiency. Predictive values and clinical efficiency of the cutoff limit can be updated for any prior probability of disease. Receiver Operating Characteristics (ROC) curves can be generated and combined into the same graph for comparison of several different tests. The area under the curve with corresponding confidence interval is calculated for each ROC curve. Numerical results of analyses and graphs can be printed or exported to other Microsoft Windows programs. GraphROC for Windows also employs a new method, developed by us, for the indirect estimation of health-related limits and change limits from mixed distributions of clinical laboratory data.

  3. Using Minitel Network and New Software Engineering Techniques for Randomized Clinical Trials Management

    PubMed Central

    Lepage, E.; Tavernier, H.; Bouhaddou, O.; Jais, JP.; Gisselbrecht, C.; Aurengo, A.; Boiron, M.

    1989-01-01

    The usual Randomized Clinical Trials (RCT) management using an anachronic procedure involving a flowsheet exchange between the remote centers and the coordinating center presents a number of inadequacies. Eligibility criteria are not always verified by the coordinating center before inclusion in the trial and randomization. Laboratory tests and therapeutic adjustments are frequently decided from memory by the clinician which often leads to data oversight and variability of therapeutic decisions. This results in protocol deviations and alteration of the efficiency of the RCT. HICREN is a medical consultation system designed to take into account the different difficulties encountered during RCT driving. The system integrates a clinical database with artificial intelligence technics to manage clinical trial data on non-expensive and widely available Minitel® terminals. Randomization is then possible, after eligibility criteria are satisfied, anytime and anywhere in France through the national telematic network. HICREN also includes an intuitive graphic interface to increase physician's compliance: a user friendly dialogue manager supports on line data entry with multi-windowing facilities and pull down menus. Interactive data validation is achieved through an interface to dedicated C programs. Patient follow up is achieved by an expert system that proposes appropriate dose of treatment according to the rules defined in the trial. At present, HICREN is implemented on the CISARC system for conducting three randomized clinical trials and one epidemiologic study.

  4. Clinical evaluation of reducing acquisition time on single-photon emission computed tomography image quality using proprietary resolution recovery software.

    PubMed

    Aldridge, Matthew D; Waddington, Wendy W; Dickson, John C; Prakash, Vineet; Ell, Peter J; Bomanji, Jamshed B

    2013-11-01

    A three-dimensional model-based resolution recovery (RR) reconstruction algorithm that compensates for collimator-detector response, resulting in an improvement in reconstructed spatial resolution and signal-to-noise ratio of single-photon emission computed tomography (SPECT) images, was tested. The software is said to retain image quality even with reduced acquisition time. Clinically, any improvement in patient throughput without loss of quality is to be welcomed. Furthermore, future restrictions in radiotracer supplies may add value to this type of data analysis. The aims of this study were to assess improvement in image quality using the software and to evaluate the potential of performing reduced time acquisitions for bone and parathyroid SPECT applications. Data acquisition was performed using the local standard SPECT/CT protocols for 99mTc-hydroxymethylene diphosphonate bone and 99mTc-methoxyisobutylisonitrile parathyroid SPECT imaging. The principal modification applied was the acquisition of an eight-frame gated data set acquired using an ECG simulator with a fixed signal as the trigger. This had the effect of partitioning the data such that the effect of reduced time acquisitions could be assessed without conferring additional scanning time on the patient. The set of summed data sets was then independently reconstructed using the RR software to permit a blinded assessment of the effect of acquired counts upon reconstructed image quality as adjudged by three experienced observers. Data sets reconstructed with the RR software were compared with the local standard processing protocols; filtered back-projection and ordered-subset expectation-maximization. Thirty SPECT studies were assessed (20 bone and 10 parathyroid). The images reconstructed with the RR algorithm showed improved image quality for both full-time and half-time acquisitions over local current processing protocols (P<0.05). The RR algorithm improved image quality compared with local processing

  5. From data to the decision: A software architecture to integrate predictive modelling in clinical settings.

    PubMed

    Martinez-Millana, A; Fernandez-Llatas, C; Sacchi, L; Segagni, D; Guillen, S; Bellazzi, R; Traver, V

    2015-08-01

    The application of statistics and mathematics over large amounts of data is providing healthcare systems with new tools for screening and managing multiple diseases. Nonetheless, these tools have many technical and clinical limitations as they are based on datasets with concrete characteristics. This proposition paper describes a novel architecture focused on providing a validation framework for discrimination and prediction models in the screening of Type 2 diabetes. For that, the architecture has been designed to gather different data sources under a common data structure and, furthermore, to be controlled by a centralized component (Orchestrator) in charge of directing the interaction flows among data sources, models and graphical user interfaces. This innovative approach aims to overcome the data-dependency of the models by providing a validation framework for the models as they are used within clinical settings.

  6. Clinical Application of an Open-Source 3D Volume Rendering Software to Neurosurgical Approaches.

    PubMed

    Fernandes de Oliveira Santos, Bruno; Silva da Costa, Marcos Devanir; Centeno, Ricardo Silva; Cavalheiro, Sergio; Antônio de Paiva Neto, Manoel; Lawton, Michael T; Chaddad-Neto, Feres

    2018-02-01

    Preoperative recognition of the anatomic individualities of each patient can help to achieve more precise and less invasive approaches. It also may help to anticipate potential complications and intraoperative difficulties. Here we describe the use, accuracy, and precision of a free tool for planning microsurgical approaches using 3-dimensional (3D) reconstructions from magnetic resonance imaging (MRI). We used the 3D volume rendering tool of a free open-source software program for 3D reconstruction of images of surgical sites obtained by MRI volumetric acquisition. We recorded anatomic reference points, such as the sulcus and gyrus, and vascularization patterns for intraoperative localization of lesions. Lesion locations were confirmed during surgery by intraoperative ultrasound and/or electrocorticography and later by postoperative MRI. Between August 2015 and September 2016, a total of 23 surgeries were performed using this technique for 9 low-grade gliomas, 7 high-grade gliomas, 4 cortical dysplasias, and 3 arteriovenous malformations. The technique helped delineate lesions with an overall accuracy of 2.6 ± 1.0 mm. 3D reconstructions were successfully performed in all patients, and images showed sulcus, gyrus, and venous patterns corresponding to the intraoperative images. All lesion areas were confirmed both intraoperatively and at the postoperative evaluation. With the technique described herein, it was possible to successfully perform 3D reconstruction of the cortical surface. This reconstruction tool may serve as an adjunct to neuronavigation systems or may be used alone when such a system is unavailable. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. A Framework for Software Reuse in Safety-Critical System of Systems

    DTIC Science & Technology

    2008-03-01

    environment.8 Pressman , on the other hand, defines a software component as a unit of composition with contractually specified and explicit context...2005, p654. 9 R.S. Pressman ., Software Engineering A Practitioner’s Approach, Sixth Edition, New York, NY.: McGraw-Hill, 2005, p817. 10 W.C. Lim...index.php. 79 Pressman , R.S., Software Engineering A Practitioner’s Approach, Sixth Edition, New York, NY.: McGraw-Hill, 2005. Radio Technical

  8. Open-source Software for Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis.

    PubMed

    Mohammed, Emad A; Naugler, Christopher

    2017-01-01

    Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. This tool will allow anyone with historic test volume data to model future demand.

  9. Open-source Software for Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis

    PubMed Central

    Mohammed, Emad A.; Naugler, Christopher

    2017-01-01

    Background: Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. Method: In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. Results: This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. Conclusion: This tool will allow anyone with historic test volume data to model future demand. PMID:28400996

  10. A software tool for pure‑tone audiometry. Classification of audiograms for inclusion of patients in clinical trials. English version.

    PubMed

    Rahne, T; Buthut, F; Plößl, S; Plontke, S K

    2016-03-01

    Selecting subjects for clinical trials on hearing loss therapies relies on the patient meeting the audiological inclusion criteria. In studies on the treatment of idiopathic sudden sensorineural hearing loss, the patient's acute audiogram is usually compared with a previous audiogram, the audiogram of the non-affected ear, or a normal audiogram according to an ISO standard. Generally, many more patients are screened than actually fulfill the particular inclusion criteria. The inclusion criteria often require a calculation of pure-tone averages, selection of the most affected frequencies, and calculation of hearing loss differences. A software tool was developed to simplify and accelerate this inclusion procedure for investigators to estimate the possible recruitment rate during the planning phase of a clinical trial and during the actual study. This tool is Microsoft Excel-based and easy to modify to meet the particular inclusion criteria of a specific clinical trial. The tool was retrospectively evaluated on 100 patients with acute hearing loss comparing the times for classifying automatically and manually. The study sample comprised 100 patients with idiopathic sudden sensorineural hearing loss. The age- and sex-related normative audiogram was calculated automatically by the tool and the hearing impairment was graded. The estimated recruitment rate of our sample was quickly calculated. Information about meeting the inclusion criteria was provided instantaneously. A significant reduction of 30 % in the time required for classifying (30 s per patient) was observed.

  11. Objective Assessment of Joint Stiffness: A Clinically Oriented Hardware and Software Device with an Application to the Shoulder Joint.

    PubMed

    McQuade, Kevin; Price, Robert; Liu, Nelson; Ciol, Marcia A

    2012-08-30

    Examination of articular joints is largely based on subjective assessment of the "end-feel" of the joint in response to manually applied forces at different joint orientations. This technical report aims to describe the development of an objective method to examine joints in general, with specific application to the shoulder, and suitable for clinical use. We adapted existing hardware and developed laptop-based software to objectively record the force/displacement behavior of the glenohumeral joint during three common manual joint examination tests with the arm in six positions. An electromagnetic tracking system recorded three-dimensional positions of sensors attached to a clinician examiner and a patient. A hand-held force transducer recorded manually applied translational forces. The force and joint displacement were time-synchronized and the joint stiffness was calculated as a quantitative representation of the joint "end-feel." A methodology and specific system checks were developed to enhance clinical testing reproducibility and precision. The device and testing protocol were tested on 31 subjects (15 with healthy shoulders, and 16 with a variety of shoulder impairments). Results describe the stiffness responses, and demonstrate the feasibility of using the device and methods in clinical settings.

  12. Usefulness of the automatic quantitative estimation tool for cerebral blood flow: clinical assessment of the application software tool AQCEL.

    PubMed

    Momose, Mitsuhiro; Takaki, Akihiro; Matsushita, Tsuyoshi; Yanagisawa, Shin; Yano, Kesato; Miyasaka, Tadashi; Ogura, Yuka; Kadoya, Masumi

    2011-01-01

    AQCEL enables automatic reconstruction of single-photon emission computed tomogram (SPECT) without image degradation and quantitative analysis of cerebral blood flow (CBF) after the input of simple parameters. We ascertained the usefulness and quality of images obtained by the application software AQCEL in clinical practice. Twelve patients underwent brain perfusion SPECT using technetium-99m ethyl cysteinate dimer at rest and after acetazolamide (ACZ) loading. Images reconstructed using AQCEL were compared with those reconstructed using conventional filtered back projection (FBP) method for qualitative estimation. Two experienced nuclear medicine physicians interpreted the image quality using the following visual scores: 0, same; 1, slightly superior; 2, superior. For quantitative estimation, the mean CBF values of the normal hemisphere of the 12 patients using ACZ calculated by the AQCEL method were compared with those calculated by the conventional method. The CBF values of the 24 regions of the 3-dimensional stereotaxic region of interest template (3DSRT) calculated by the AQCEL method at rest and after ACZ loading were compared to those calculated by the conventional method. No significant qualitative difference was observed between the AQCEL and conventional FBP methods in the rest study. The average score by the AQCEL method was 0.25 ± 0.45 and that by the conventional method was 0.17 ± 0.39 (P = 0.34). There was a significant qualitative difference between the AQCEL and conventional methods in the ACZ loading study. The average score for AQCEL was 0.83 ± 0.58 and that for the conventional method was 0.08 ± 0.29 (P = 0.003). During quantitative estimation using ACZ, the mean CBF values of 12 patients calculated by the AQCEL method were 3-8% higher than those calculated by the conventional method. The square of the correlation coefficient between these methods was 0.995. While comparing the 24 3DSRT regions of 12 patients, the squares of the correlation

  13. Optimized conditions for selective gold flotation by ToF-SIMS and ToF-LIMS

    NASA Astrophysics Data System (ADS)

    Chryssoulis, S. L.; Dimov, S. S.

    2004-06-01

    This work describes a comprehensive characterization of the factors controlling the floatability of free gold from flotation test using reagents (collectors) at plant concentration levels. A relationship between the collectors loadings on gold particles and their surface composition has been established. The findings of this study show that silver activates gold flotation and there is a strong correlation between the surface concentration of silver and the loading of certain collectors. The organic surface analysis was done by ToF-SIMS while the inorganic surface analysis was carried out by time-of-flight laser ionization mass spectrometry (ToF-LIMS). The developed testing protocol based on ToF-LIMS and ToF-SIMS complementary surface analysis allows for optimization of the flotation scheme and hence improved gold recovery.

  14. Comparison of horizontal winds from the LIMS satellite instrument with rocket measurements

    NASA Technical Reports Server (NTRS)

    Smith, A. K.; Bailey, P. L.

    1985-01-01

    Statistical results are given for a comparison between horizontal geostrophic winds computed from satellite height data and all available in situ rocket wind soundings during a 7-month period. The satellite data are the daily mapped fields from the Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS) instrument, which extend from 100 to 0.1 mbar. Results indicate that in both the tropics and the extratropical Northern Hemisphere, the average zonal and meridional wind speeds agree to within 2-4 m/s throughout the stratosphere. The rms differences are much larger, with values of 5-10 m/s in the lower stratosphere, increasing to 20-40 m/s in the lower mesosphere. Time series show that LIMS and rocketsonde zonal wind speeds show coherent variations with temporal periods of 1-2 weeks and more, and both exhibit irregular variations on time scales of less than one week.

  15. Dynamic contrast-enhanced MRI: Study of inter-software accuracy and reproducibility using simulated and clinical data.

    PubMed

    Beuzit, Luc; Eliat, Pierre-Antoine; Brun, Vanessa; Ferré, Jean-Christophe; Gandon, Yves; Bannier, Elise; Saint-Jalmes, Hervé

    2016-06-01

    To test the reproducibility and accuracy of pharmacokinetic parameter measurements on five analysis software packages (SPs) for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), using simulated and clinical data. This retrospective study was Institutional Review Board-approved. Simulated tissues consisted of pixel clusters of calculated dynamic signal changes for combinations of Tofts model pharmacokinetic parameters (volume transfer constant [K(trans) ], extravascular extracellular volume fraction [ve ]), longitudinal relaxation time (T1 ). The clinical group comprised 27 patients treated for rectal cancer, with 36 3T DCE-MR scans performed between November 2012 and February 2014, including dual-flip-angle T1 mapping and a dynamic postcontrast T1 -weighted, 3D spoiled gradient-echo sequence. The clinical and simulated images were postprocessed with five SPs to measure K(trans) , ve , and the initial area under the gadolinium curve (iAUGC). Modified Bland-Altman analysis was conducted, intraclass correlation coefficients (ICCs) and within-subject coefficients of variation were calculated. Thirty-one examinations from 23 patients were of sufficient technical quality and postprocessed. Measurement errors were observed on the simulated data for all the pharmacokinetic parameters and SPs, with a bias ranging from -0.19 min(-1) to 0.09 min(-1) for K(trans) , -0.15 to 0.01 for ve , and -0.65 to 1.66 mmol.L(-1) .min for iAUGC. The ICC between SPs revealed moderate agreement for the simulated data (K(trans) : 0.50; ve : 0.67; iAUGC: 0.77) and very poor agreement for the clinical data (K(trans) : 0.10; ve : 0.16; iAUGC: 0.21). Significant errors were found in the calculated DCE-MRI pharmacokinetic parameters for the perfusion analysis SPs, resulting in poor inter-software reproducibility. J. Magn. Reson. Imaging 2016;43:1288-1300. © 2015 Wiley Periodicals, Inc.

  16. World Workshop on Oral Medicine VI: Utilization of Oral Medicine-specific software for support of clinical care, research, and education: current status and strategy for broader implementation.

    PubMed

    Brailo, Vlaho; Firriolo, Francis John; Tanaka, Takako Imai; Varoni, Elena; Sykes, Rosemary; McCullough, Michael; Hua, Hong; Sklavounou, Alexandra; Jensen, Siri Beier; Lockhart, Peter B; Mattsson, Ulf; Jontell, Mats

    2015-08-01

    To assess the current scope and status of Oral Medicine-specific software (OMSS) utilized to support clinical care, research, and education in Oral Medicine and to propose a strategy for broader implementation of OMSS within the global Oral Medicine community. An invitation letter explaining the objectives was sent to the global Oral Medicine community. Respondents were interviewed to obtain information about different aspects of OMSS functionality. Ten OMSS tools were identified. Four were being used for clinical care, one was being used for research, two were being used for education, and three were multipurpose. Clinical software was being utilized as databases developed to integrate of different type of clinical information. Research software was designed to facilitate multicenter research. Educational software represented interactive, case-orientated technology designed for clinical training in Oral Medicine. Easy access to patient data was the most commonly reported advantage. Difficulty of use and poor integration with other software was the most commonly reported disadvantage. The OMSS presented in this paper demonstrate how information technology (IT) can have an impact on the quality of patient care, research, and education in the field of Oral Medicine. A strategy for broader implementation of OMSS is proposed. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Expression of LIM-homeodomain transcription factors in the developing and mature mouse retina

    PubMed Central

    Balasubramanian, Revathi; Bui, Andrew; Ding, Qian; Gan, Lin

    2014-01-01

    LIM-homeodomain (LIM-HD) transcription factors have been extensively studied for their role in the development of the central nervous system. Their function is key to several developmental events like cell proliferation, differentiation and subtype specification. However, their roles in retinal neurogenesis remain largely unknown. Here we report a detailed expression study of LIM-HD transcription factors LHX9 and LHX2, LHX3 and LHX4, and LHX6 in the developing and mature mouse retina using immunohistochemistry and in situ hybridization techniques. We show that LHX9 is expressed during the early stages of development in the retinal ganglion cell layer and the inner nuclear layer. We also show that LHX9 is expressed in a subset of amacrine cells in the adult retina. LHX2 is known to be expressed in retinal progenitor cells during development and in Müller glial cells and a subset of amacrine cells in the adult retina. We found that the LHX2 subset of amacrine cells is not cholinergic and that a very few of LHX2 amacrine cells express calretinin. LHX3 and LHX4 are expressed in a subset of bipolar cells in the adult retina. LHX6 is expressed in cells in the ganglion cell layer and the neuroblast layer starting at embryonic stage 13.5 (E13.5) and continues to be expressed in cells in the ganglion cell layer and inner nuclear layer, postnatally, suggesting its likely expression in amacrine cells or a subset thereof. Taken together, our comprehensive assay of expression patterns of LIM-HD transcription factors during mouse retinal development will help further studies elucidating their biological functions in the differentiation of retinal cell subtypes. PMID:24333658

  18. ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics.

    PubMed

    Helsens, Kenny; Colaert, Niklaas; Barsnes, Harald; Muth, Thilo; Flikka, Kristian; Staes, An; Timmerman, Evy; Wortelkamp, Steffi; Sickmann, Albert; Vandekerckhove, Joël; Gevaert, Kris; Martens, Lennart

    2010-03-01

    MS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims (http://genesis.UGent.be/ms_lims), a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses.

  19. Oracle, a novel PDZ-LIM domain protein expressed in heart and skeletal muscle.

    PubMed

    Passier, R; Richardson, J A; Olson, E N

    2000-04-01

    In order to identify novel genes enriched in adult heart, we performed a subtractive hybridization for genes expressed in mouse heart but not in skeletal muscle. We identified two alternative splicing variants of a novel PDZ-LIM domain protein, which we named Oracle. Both variants contain a PDZ domain at the amino-terminus and three LIM domains at the carboxy-terminus. Highest homology of Oracle was found with the human and rat enigma proteins in the PDZ domain (62 and 61%, respectively) and in the LIM domains (60 and 69%, respectively). By Northern hybridization analysis, we showed that expression is highest in adult mouse heart, low in skeletal muscle and undetectable in other adult mouse tissues. In situ hybridization in mouse embryos confirmed and extended these data by showing high expression of Oracle mRNA in atrial and ventricular myocardial cells from E8.5. From E9.5 low expression of Oracle mRNA was detectable in myotomes. These data suggest a role for Oracle in the early development and function of heart and skeletal muscle.

  20. Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A.

    PubMed

    Boëda, Batiste; Knowles, Phillip P; Briggs, David C; Murray-Rust, Judith; Soriano, Erika; Garvalov, Boyan K; McDonald, Neil Q; Way, Michael

    2011-04-01

    Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized "orphan" Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1-65(Arp7A)·LIM2-3(Tes)·EVH1(Mena) complex reveals that residues 28-49 of Arp7A contact the LIM2-3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2-3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.

  1. Chromatin Immunoprecipitation and DNA Sequencing Identified a LIMS1/ILK Pathway Regulated by LMO1 in Neuroblastoma.

    PubMed

    Saeki, Norihisa; Saito, Akira; Sugaya, Yuki; Amemiya, Mitsuhiro; Ono, Hiroe; Komatsuzaki, Rie; Yanagihara, Kazuyoshi; Sasaki, Hiroki

    2018-01-01

    Overall survival for the high-risk group of neuroblastoma (NB) remains at 40-50%. An integrative genomics study revealed that LIM domain only 1 (LMO1) encoding a transcriptional regulator to be an NB-susceptibility gene with a tumor-promoting activity, that needs to be revealed. We conducted chromatin immunoprecipitation and DNA sequencing analyses and cell proliferation assays on two NB cell lines. We identified three genes regulated by LMO1 in the cells, LIM and senescent cell antigen-like domains 1 (LIMS1), Ras suppressor protein 1 (RSU1) and relaxin 2 (RLN2). LIMS1 and RSU1 encode proteins functioning with integrin-linked kinase (ILK), and inhibition of LIMS1, ILK or RLN2 by shRNA reduced cell proliferation of the NB cells, which was also suppressed with an ILK inhibiting compound Cpd 22. The downstream of LMO1-regulatory cascade includes a tumor-promoting LIMS1/ILK pathway, which has a potential to be a novel therapeutic target. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  2. AJUBA LIM Proteins Limit Hippo Activity in Proliferating Cells by Sequestering the Hippo Core Kinase Complex in the Cytosol.

    PubMed

    Jagannathan, Radhika; Schimizzi, Gregory V; Zhang, Kun; Loza, Andrew J; Yabuta, Norikazu; Nojima, Hitoshi; Longmore, Gregory D

    2016-10-15

    The Hippo pathway controls organ growth and is implicated in cancer development. Whether and how Hippo pathway activity is limited to sustain or initiate cell growth when needed is not understood. The members of the AJUBA family of LIM proteins are negative regulators of the Hippo pathway. In mammalian epithelial cells, we found that AJUBA LIM proteins limit Hippo regulation of YAP, in proliferating cells only, by sequestering a cytosolic Hippo kinase complex in which LATS kinase is inhibited. At the plasma membranes of growth-arrested cells, AJUBA LIM proteins do not inhibit or associate with the Hippo kinase complex. The ability of AJUBA LIM proteins to inhibit YAP regulation by Hippo and to associate with the kinase complex directly correlate with their capacity to limit Hippo signaling during Drosophila wing development. AJUBA LIM proteins did not influence YAP activity in response to cell-extrinsic or cell-intrinsic mechanical signals. Thus, AJUBA LIM proteins limit Hippo pathway activity in contexts where cell proliferation is needed. Copyright © 2016 Jagannathan et al.

  3. AJUBA LIM Proteins Limit Hippo Activity in Proliferating Cells by Sequestering the Hippo Core Kinase Complex in the Cytosol

    PubMed Central

    Jagannathan, Radhika; Schimizzi, Gregory V.; Zhang, Kun; Loza, Andrew J.; Yabuta, Norikazu; Nojima, Hitoshi

    2016-01-01

    The Hippo pathway controls organ growth and is implicated in cancer development. Whether and how Hippo pathway activity is limited to sustain or initiate cell growth when needed is not understood. The members of the AJUBA family of LIM proteins are negative regulators of the Hippo pathway. In mammalian epithelial cells, we found that AJUBA LIM proteins limit Hippo regulation of YAP, in proliferating cells only, by sequestering a cytosolic Hippo kinase complex in which LATS kinase is inhibited. At the plasma membranes of growth-arrested cells, AJUBA LIM proteins do not inhibit or associate with the Hippo kinase complex. The ability of AJUBA LIM proteins to inhibit YAP regulation by Hippo and to associate with the kinase complex directly correlate with their capacity to limit Hippo signaling during Drosophila wing development. AJUBA LIM proteins did not influence YAP activity in response to cell-extrinsic or cell-intrinsic mechanical signals. Thus, AJUBA LIM proteins limit Hippo pathway activity in contexts where cell proliferation is needed. PMID:27457617

  4. Ex-vivo transduced autologous skin fibroblasts expressing human Lim Mineralization Protein-3 efficiently form new bone in animal models

    PubMed Central

    Lattanzi, Wanda; Parrilla, Claudio; Fetoni, Annarita; Logroscino, Giandomenico; Straface, Giuseppe; Pecorini, Giovanni; Stigliano, Egidio; Tampieri, Anna; Bedini, Rossella; Pecci, Raffaella; Michetti, Fabrizio; Gambotto, Andrea; Robbins, Paul D.; Pola, Enrico

    2012-01-01

    Local gene transfer of the human LIM Mineralization Protein (LMP), a novel intracellular positive regulator of the osteoblast differentiation program, can induce efficient bone formation in rodents. In order to develop a clinically relevant gene therapy approach to facilitate bone healing, we have used primary dermal fibroblasts transduced ex vivo with Ad.LMP3 and seeded on an hydroxyapatite/collagen matrix prior to autologous implantation. Here we demonstrate that genetically modified autologous dermal fibroblasts expressing Ad.LMP-3 are able to induce ectopic bone formation following implantation of the matrix into the mouse triceps and paravertebral muscles. Moreover, implantation of the Ad.LMP-3-modified dermal fibroblasts into a rat mandibular bone critical size defect model results in efficient healing as determined by X-ray, histology and three dimensional micro computed tomography (3DμCT). These results demonstrate the effectiveness of the non-secreted intracellular osteogenic factor LMP-3, in inducing bone formation in vivo. Moreover, the utilization of autologous dermal fibroblasts implanted on a biomaterial represents a promising approach for possible future clinical applications aimed at inducing new bone formation. PMID:18633445

  5. Clinical value of CT-based preoperative software assisted lung lobe volumetry for predicting postoperative pulmonary function after lung surgery

    NASA Astrophysics Data System (ADS)

    Wormanns, Dag; Beyer, Florian; Hoffknecht, Petra; Dicken, Volker; Kuhnigk, Jan-Martin; Lange, Tobias; Thomas, Michael; Heindel, Walter

    2005-04-01

    This study was aimed to evaluate a morphology-based approach for prediction of postoperative forced expiratory volume in one second (FEV1) after lung resection from preoperative CT scans. Fifteen Patients with surgically treated (lobectomy or pneumonectomy) bronchogenic carcinoma were enrolled in the study. A preoperative chest CT and pulmonary function tests before and after surgery were performed. CT scans were analyzed by prototype software: automated segmentation and volumetry of lung lobes was performed with minimal user interaction. Determined volumes of different lung lobes were used to predict postoperative FEV1 as percentage of the preoperative values. Predicted FEV1 values were compared to the observed postoperative values as standard of reference. Patients underwent lobectomy in twelve cases (6 upper lobes; 1 middle lobe; 5 lower lobes; 6 right side; 6 left side) and pneumonectomy in three cases. Automated calculation of predicted postoperative lung function was successful in all cases. Predicted FEV1 ranged from 54% to 95% (mean 75% +/- 11%) of the preoperative values. Two cases with obviously erroneous LFT were excluded from analysis. Mean error of predicted FEV1 was 20 +/- 160 ml, indicating absence of systematic error; mean absolute error was 7.4 +/- 3.3% respective 137 +/- 77 ml/s. The 200 ml reproducibility criterion for FEV1 was met in 11 of 13 cases (85%). In conclusion, software-assisted prediction of postoperative lung function yielded a clinically acceptable agreement with the observed postoperative values. This method might add useful information for evaluation of functional operability of patients with lung cancer.

  6. The LIM homeobox protein mLIM3/Lhx3 induces expression of the prolactin gene by a Pit-1/GHF-1-independent pathway in corticotroph AtT20 cells.

    PubMed

    Girardin, S E; Benjannet, S; Barale, J C; Chrétien, M; Seidah, N G

    1998-07-24

    mLIM3, a member of the LIM homeobox family, was recently demonstrated to be critical for proliferation and differentiation of the pituitary cell lineage. Using a pool of degenerate oligonucleotides we determined the DNA sequence ANNAGGAAA(T/C)GA(CIG)AA as the set preferentially recognized by mLIM3. A nearly identical sequence is found in the prolactin (PRL) promoter, within a 15-mer stretch from nucleotides (nts) -218 to -204 which is highly conserved between human, rat, and bovine. In order to test the hypothesis of a transcriptional effect of mLIM3 on the prolactin promoter, stable transfectants of mLIM3 cDNA in AtT20 tumor cells revealed that PRL mRNA expression was induced in 3 separate stable clones. Gel retardation experiments performed using nuclear extracts isolated from one of the AtT20/mLIM3 stable transfectants revealed affinity towards the 15-mer element of the PRL promoter. From these results, we propose that the PRL promoter element (nts -218 to -204) could be functional in vivo. Finally, we demonstrate that in AtT20 cells prolactin mRNA expression is not induced by the Pit-1/GHF-1 pathway and that growth hormone mRNA is not detected concomitantly with prolactin. We conclude that mLIM3 may play a key role in inducing PRL gene expression in lactotrophs by binding to a conserved motif close to a Pit-1/GHF-1 site within the proximal PRL promoter.

  7. Correlated regions of cerebral blood flow with clinical parameters in Parkinson's disease; comparison using 'Anatomy' and 'Talairach Daemon' software.

    PubMed

    Yoon, Hyun Jin; Cheon, Sang Myung; Jeong, Young Jin; Kang, Do-Young

    2012-02-01

    We assign the anatomical names of functional activation regions in the brain, based on the probabilistic cyto-architectonic atlas by Anatomy 1.7 from an analysis of correlations between regional cerebral blood flow (rCBF) and clinical parameters of the non-demented Parkinson's disease (PD) patients by SPM8. We evaluated Anatomy 1.7 of SPM toolbox compared to 'Talairach Daemon' (TD) Client 2.4.2 software. One hundred and thirty-six patients (mean age 60.0 ± 9.09 years; 73 women and 63 men) with non-demented PD were selected. Tc-99m-HMPAO brain single-photon emission computed tomography (SPECT) scans were performed on the patients using a two-head gamma-camera. We analyzed the brain image of PD patients by SPM8 and found the anatomical names of correlated regions of rCBF perfusion with the clinical parameters using TD Client 2.4.2 and Anatomy 1.7. The SPM8 provided a correlation coefficient between clinical parameters and cerebral hypoperfusion by a simple regression method. To the clinical parameters were added age, duration of disease, education period, Hoehn and Yahr (H&Y) stage and Korean mini-mental state examination (K-MMSE) score. Age was correlated with cerebral perfusion in the Brodmann area (BA) 6 and BA 3b assigned by Anatomy 1.7 and BA 6 and pyramis in gray matter by TD Client 2.4.2 with p < 0.001 uncorrected. Also, assigned significant correlated regions were found in the left and right lobules VI (Hem) with duration of disease, in left and right lobules VIIa crus I (Hem) with education, in left insula (Ig2), left and right lobules VI (Hem) with H&Y, and in BA 4a and 6 with K-MMSE score with p < 0.05 uncorrected by Anatomy 1.7, respectively. Most areas of correlation were overlapped by two different anatomical labeling methods, but some correlation areas were found with different names. Age was the most significantly correlated clinical parameter with rCBF. TD Client found the exact anatomical name by the peak intensity position of the cluster while

  8. The intelligent clinical laboratory as a tool to increase cancer care management productivity.

    PubMed

    Mohammadzadeh, Niloofar; Safdari, Reza

    2014-01-01

    Studies of the causes of cancer, early detection, prevention or treatment need accurate, comprehensive, and timely cancer data. The clinical laboratory provides important cancer information needed for physicians which influence clinical decisions regarding treatment, diagnosis and patient monitoring. Poor communication between health care providers and clinical laboratory personnel can lead to medical errors and wrong decisions in providing cancer care. Because of the key impact of laboratory information on cancer diagnosis and treatment the quality of the tests, lab reports, and appropriate lab management are very important. A laboratory information management system (LIMS) can have an important role in diagnosis, fast and effective access to cancer data, decrease redundancy and costs, and facilitate the integration and collection of data from different types of instruments and systems. In spite of significant advantages LIMS is limited by factors such as problems in adaption to new instruments that may change existing work processes. Applications of intelligent software simultaneously with existing information systems, in addition to remove these restrictions, have important benefits including adding additional non-laboratory-generated information to the reports, facilitating decision making, and improving quality and productivity of cancer care services. Laboratory systems must have flexibility to change and have the capability to develop and benefit from intelligent devices. Intelligent laboratory information management systems need to benefit from informatics tools and latest technologies like open sources. The aim of this commentary is to survey application, opportunities and necessity of intelligent clinical laboratory as a tool to increase cancer care management productivity.

  9. Role of the New South Wales Department of Primary Industries' Laboratory Information Management System (LIMS) in the 2007 equine influenza emergency animal disease response.

    PubMed

    Croft, M G; Fraser, G C; Gaul, W N

    2011-07-01

    A Laboratory Information Management System (LIMS) was used to manage the laboratory data and support planning and field activities as part of the response to the equine influenza outbreak in Australia in 2007. The database structure of the LIMS and the system configurations that were made to best handle the laboratory implications of the disease response are discussed. The operational aspects of the LIMS and the related procedures used at the laboratory to process the increased sample throughput are reviewed, as is the interaction of the LIMS with other corporate systems used in the management of the response. Outcomes from this tailored configuration and operation of the LIMS resulted in effective provision and control of the laboratory and laboratory information aspects of the response. The extent and immediate availability of the information provided from the LIMS was critical to some of the activities of key operatives involved in controlling the response. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

  10. Frame rate required for speckle tracking echocardiography: A quantitative clinical study with open-source, vendor-independent software.

    PubMed

    Negoita, Madalina; Zolgharni, Massoud; Dadkho, Elham; Pernigo, Matteo; Mielewczik, Michael; Cole, Graham D; Dhutia, Niti M; Francis, Darrel P

    2016-09-01

    To determine the optimal frame rate at which reliable heart walls velocities can be assessed by speckle tracking. Assessing left ventricular function with speckle tracking is useful in patient diagnosis but requires a temporal resolution that can follow myocardial motion. In this study we investigated the effect of different frame rates on the accuracy of speckle tracking results, highlighting the temporal resolution where reliable results can be obtained. 27 patients were scanned at two different frame rates at their resting heart rate. From all acquired loops, lower temporal resolution image sequences were generated by dropping frames, decreasing the frame rate by up to 10-fold. Tissue velocities were estimated by automated speckle tracking. Above 40 frames/s the peak velocity was reliably measured. When frame rate was lower, the inter-frame interval containing the instant of highest velocity also contained lower velocities, and therefore the average velocity in that interval was an underestimate of the clinically desired instantaneous maximum velocity. The higher the frame rate, the more accurately maximum velocities are identified by speckle tracking, until the frame rate drops below 40 frames/s, beyond which there is little increase in peak velocity. We provide in an online supplement the vendor-independent software we used for automatic speckle-tracked velocity assessment to help others working in this field. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. Accuracy of two digital implant impression systems based on confocal microscopy with variations in customized software and clinical parameters.

    PubMed

    Giménez, Beatriz; Pradíes, Guillermo; Martínez-Rus, Francisco; Özcan, Mutlu

    2015-01-01

    To evaluate the accuracy of two digital impression systems based on the same technology but different postprocessing correction modes of customized software, with consideration of several clinical parameters. A maxillary master model with six implants located in the second molar, second premolar, and lateral incisor positions was fitted with six cylindrical scan bodies. Scan bodies were placed at different angulations or depths apical to the gingiva. Two experienced and two inexperienced operators performed scans with either 3D Progress (MHT) or ZFX Intrascan (Zimmer Dental). Five different distances between implants (scan bodies) were measured, yielding five data points per impression and 100 per impression system. Measurements made with a high-accuracy three-dimensional coordinate measuring machine (CMM) of the master model acted as the true values. The values obtained from the digital impressions were subtracted from the CMM values to identify the deviations. The differences between experienced and inexperienced operators and implant angulation and depth were compared statistically. Experience of the operator, implant angulation, and implant depth were not associated with significant differences in deviation from the true values with both 3D Progress and ZFX Intrascan. Accuracy in the first scanned quadrant was significantly better with 3D Progress, but ZFX Intrascan presented better accuracy in the full arch. Neither of the two systems tested would be suitable for digital impression of multiple-implant prostheses. Because of the errors, further development of both systems is required.

  12. On the Quality of the Nimbus 7 LIMS Version 6 Ozone for Studies of the Middle Atmosphere

    NASA Technical Reports Server (NTRS)

    Remsberg, Ellis; Lingenfelser, Gretchen; Natarajan, Murali; Gordley, Larry; Thompson, Earl

    2006-01-01

    The Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS) radiance profile dataset of 1978/79 was reconditioned and reprocessed to Version 6 (V6) profiles of temperature and species that are improved significantly over those from Version 5 (V5). The LIMS V6 dataset was archived for public use in 2002. Improvements for its ozone include: (1) a more accurate accounting for instrument and spacecraft motion effects in the radiances, (2) the use of better spectroscopic line parameters for its ozone forward model, (3) retrievals of all its scans, (4) more accurate and compatible temperature versus pressure profiles (or T(p)), which are needed for the registration of the ozone radiances and for the removal of temperature effects from them, and (5) a better accounting for interfering species in the lower stratosphere. The retrieved V6 ozone profiles extend from near cloud top altitudes to about 80 km and from 64S to 84N latitude with better sampling along the orbit than for the V5 dataset. Calculated estimates of the single-profile precision and accuracy are provided for the V6 ozone from this study. Precision estimates based on the data themselves are of order 3% or better from 1 to 30 hPa. Estimates of total systematic error for a single profile are hard to generalize because the separate sources of error may not all be of the same sign and they depend somewhat on the atmospheric state. It is estimated that the V6 zonal mean ozone distributions are accurate to within 9% to 7% from 50 hPa to 3 hPa, respectively. Effects of a temperature bias can be significant and may be present at 1 to 2 hPa though. There may be ozone biases of order 10% at those levels due to possible biases of up to +2 K, but there is no indication of a similar problem elsewhere in the stratosphere. Simulation studies show that the LIMS retrievals are also underestimating slightly the small amplitudes of the atmospheric temperature tides, which affect its retrieved day/night ozone differences

  13. Interaction of subway LIM vehicle with ballasted track in polygonal wheel wear development

    NASA Astrophysics Data System (ADS)

    Li, Ling; Xiao, Xin-Biao; Jin, Xue-Song

    2011-04-01

    This paper develops a coupled dynamics model for a linear induction motor (LIM) vehicle and a subway track to investigate the influence of polygonal wheels of the vehicle on the dynamic behavior of the system. In the model, the vehicle is modeled as a multi-body system with 35 degrees of freedom. A Timoshenko beam is used to model the rails which are discretely supported by sleepers. The sleepers are modeled as rigid bodies with their vertical, lateral, and rolling motions being considered. In order to simulate the vehicle running along the track, a moving sleeper support model is introduced to simulate the excitation by the discrete sleeper supporters, in which the sleepers are assumed to move backward at a constant speed that is the same as the train speed. The Hertzian contact theory and the Shen-Hedrick-Elkins' model are utilized to deal with the normal dynamic forces and the tangential forces between wheels and rails, respectively. In order to better characterize the linear metro system (LMS), Euler beam theory based on modal superposition method is used to model LIM and RP. The vertical electric magnetic force and the lateral restoring force between the LIM and RP are also taken into consideration. The former has gap-varying nonlinear characteristics, whilst the latter is considered as a constant restoring force of 1 kN. The numerical analysis considers the effect of the excitation due to polygonal wheels on the dynamic behavior of the system at different wear stages, in which the used data regarding the polygonal wear on the wheel tread are directly measured at the subway site.

  14. Effects of polar stratospheric clouds in the Nimbus 7 LIMS Version 6 data set

    NASA Astrophysics Data System (ADS)

    Remsberg, Ellis; Harvey, V. Lynn

    2016-07-01

    The historic Limb Infrared Monitor of the Stratosphere (LIMS) measurements of 1978-1979 from the Nimbus 7 satellite were re-processed with Version 6 (V6) algorithms and archived in 2002. The V6 data set employs updated radiance registration methods, improved spectroscopic line parameters, and a common vertical resolution for all retrieved parameters. Retrieved profiles are spaced about every 1.6° of latitude along orbits and include the additional parameter of geopotential height. Profiles of O3 are sensitive to perturbations from emissions of polar stratospheric clouds (PSCs). This work presents results of implementing a first-order screening for effects of PSCs using simple algorithms based on vertical gradients of the O3 mixing ratio. Their occurrences are compared with the co-located, retrieved temperatures and related to the temperature thresholds needed for saturation of H2O and/or HNO3 vapor onto PSC particles. Observed daily locations where the major PSC screening criteria are satisfied are validated against PSCs observed with the Stratospheric Aerosol Monitor (SAM) II experiment also on Nimbus 7. Remnants of emissions from PSCs are characterized for O3 and HNO3 following the screening. PSCs may also impart a warm bias in the co-located LIMS temperatures, but by no more than 1-2 K at the altitudes of where effects of PSCs are a maximum in the ozone; thus, no PSC screening was applied to the V6 temperatures. Minimum temperatures vary between 187 and 194 K and often occur 1 to 2 km above where PSC effects are first identified in the ozone (most often between about 21 and 28 hPa). Those temperature-pressure values are consistent with conditions for the existence of nitric acid trihydrate (NAT) mixtures and to a lesser extent of super-cooled ternary solution (STS) droplets. A local, temporary uptake of HNO3 vapor of order 1-3 ppbv is indicated during mid-January for the 550 K surface. Seven-month time series of the distributions of LIMS O3 and HNO3 are shown

  15. ROCK1 and LIM kinase modulate retrovirus particle release and cell-cell transmission events.

    PubMed

    Wen, Xiaoyun; Ding, Lingmei; Wang, Jaang-Jiun; Qi, Mingli; Hammonds, Jason; Chu, Hin; Chen, Xuemin; Hunter, Eric; Spearman, Paul

    2014-06-01

    The assembly and release of retroviruses from the host cells require dynamic interactions between viral structural proteins and a variety of cellular factors. It has been long speculated that the actin cytoskeleton is involved in retrovirus production, and actin and actin-related proteins are enriched in HIV-1 virions. However, the specific role of actin in retrovirus assembly and release remains unknown. Here we identified LIM kinase 1 (LIMK1) as a cellular factor regulating HIV-1 and Mason-Pfizer monkey virus (M-PMV) particle release. Depletion of LIMK1 reduced not only particle output but also virus cell-cell transmission and was rescued by LIMK1 replenishment. Depletion of the upstream LIMK1 regulator ROCK1 inhibited particle release, as did a competitive peptide inhibitor of LIMK1 activity that prevented cofilin phosphorylation. Disruption of either ROCK1 or LIMK1 led to enhanced particle accumulation on the plasma membrane as revealed by total internal reflection fluorescence microscopy (TIRFM). Electron microscopy demonstrated a block to particle release, with clusters of fully mature particles on the surface of the cells. Our studies support a model in which ROCK1- and LIMK1-regulated phosphorylation of cofilin and subsequent local disruption of dynamic actin turnover play a role in retrovirus release from host cells and in cell-cell transmission events. Viruses often interact with the cellular cytoskeletal machinery in order to deliver their components to the site of assembly and budding. This study indicates that a key regulator of actin dynamics at the plasma membrane, LIM kinase, is important for the release of viral particles for HIV as well as for particle release by a distantly related retrovirus, Mason-Pfizer monkey virus. Moreover, disruption of LIM kinase greatly diminished the spread of HIV from cell to cell. These findings suggest that LIM kinase and its dynamic modulation of the actin cytoskeleton in the cell may be an important host factor for

  16. Description of data on the Nimbus 7 LIMS map archive tape: Water vapor and nitrogen dioxide

    NASA Technical Reports Server (NTRS)

    Haggard, Kenneth V.; Marshall, B. T.; Kurzeja, Robert J.; Remsberg, Ellis E.; Russell, James M., III

    1988-01-01

    Described is the process by which the analysis of the Limb Infrared Monitor of the Stratosphere (LIMS) experiment data were used to produce estimates of synoptic maps of water vapor and nitrogen dioxide. In addition to a detailed description of the analysis procedure, also discussed are several interesting features in the data which are used to demonstrate how the analysis procedure produced the final maps and how one can estimate the uncertainties in the maps. In addition, features in the analysis are noted that would influence how one might use, or interpret, the results. These include subjects such as smoothing and the interpretation of wave components.

  17. LIM domain protein TES changes its conformational states in different cellular compartments.

    PubMed

    Zhong, Yingli; Zhu, Jiaolian; Wang, Yan; Zhou, Jianlin; Ren, Kaiqun; Ding, Xiaofeng; Zhang, Jian

    2009-01-01

    The human TESTIN (TES) is a putative tumor suppressor and localizes to the cytoplasm as a component of focal adhesions and cell contacts. TES contains a PET domain in the NH(2)-terminus and three tandem LIM domains in the COOH-terminus. It has been hypothesized that interactions between two termini of TES might lead to a "closed" conformational state of the protein. Here, we provide evidence for different conformational states of TES. We confirmed that the NH(2)-terminus of TES can interact with its third LIM domain in the COOH-terminus by GST pull-down assays. In addition, antisera against the full-length or two truncations of TES were prepared to examine the relationship between the conformation and cellular distribution of the protein. We found that these antisera recognize different regions of TES and showed that TES is co-localised with the marker protein B23 in nucleolus, in addition to its localization in endoplasmic reticulum (ER). Furthermore, our co-immunoprecipitation (co-IP) analysis of TES and B23 demonstrated their co-existence in the same complex. Taken together, our results suggest that TES has different conformational states in different cellular compartments, and a "closed" conformational state of TES may be involved in nucleolar localization.

  18. Description of data on the Nimbus 7 LIMS map archive tape: Ozone and nitric acid

    NASA Technical Reports Server (NTRS)

    Remsberg, E. E.; Kurzeja, R. J.; Haggard, K. V.; Russell, J. M., III; Gordley, L. L.

    1986-01-01

    The Nimbus 7 Limb Infrared Monitor of the Stratosphere (LIMS) data set has been processed into a Fourier coefficient representation with a Kalman filter algorithm applied to profile data at individual latitudes and pressure levels. The algorithm produces synoptic data at noon Greenwich Mean Time (GMT) from the asynoptic orbital profiles. This form of the data set is easy to use and is appropriate for time series analysis and further data manipulation and display. Ozone and nitric acid results are grouped together in this report because the LIMS vertical field of views (FOV's) and analysis characteristics for these species are similar. A comparison of the orbital input data with mixing ratios derived from Kalman filter coefficients indicates errors in mixing ratio of generally less than 5 percent, with 15 percent being a maximum error. The high quality of the mapped data was indicated by coherence of both the phases and the amplitudes of waves with latitude and pressure. Examples of the mapped fields are presented, and details are given concerning the importance of diurnal variations, the removal of polar stratospheric cloud signatures, and the interpretation of bias effects in the data near the tops of profiles.

  19. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data

    PubMed Central

    Wang, Norman; Sherwood, Alison R; Kurihara, Akira; Conklin, Kimberly Y; Sauvage, Thomas; Presting, Gernot G

    2009-01-01

    Background Organization and presentation of biodiversity data is greatly facilitated by databases that are specially designed to allow easy data entry and organized data display. Such databases also have the capacity to serve as Laboratory Information Management Systems (LIMS). The Hawaiian Algal Database was designed to showcase specimens collected from the Hawaiian Archipelago, enabling users around the world to compare their specimens with our photographs and DNA sequence data, and to provide lab personnel with an organizational tool for storing various biodiversity data types. Description We describe the Hawaiian Algal Database, a comprehensive and searchable database containing photographs and micrographs, geo-referenced collecting information, taxonomic checklists and standardized DNA sequence data. All data for individual samples are linked through unique accession numbers. Users can search online for sample information by accession number, numerous levels of taxonomy, or collection site. At the present time the database contains data representing over 2,000 samples of marine, freshwater and terrestrial algae from the Hawaiian Archipelago. These samples are primarily red algae, although other taxa are being added. Conclusion The Hawaiian Algal Database is a digital repository for Hawaiian algal samples and acts as a LIMS for the laboratory. Users can make use of the online search tool to view and download specimen photographs and micrographs, DNA sequences and relevant habitat data, including georeferenced collecting locations. It is publicly available at . PMID:19728892

  20. Visually directed vs. software-based targeted biopsy compared to transperineal template mapping biopsy in the detection of clinically significant prostate cancer.

    PubMed

    Valerio, Massimo; McCartan, Neil; Freeman, Alex; Punwani, Shonit; Emberton, Mark; Ahmed, Hashim U

    2015-10-01

    Targeted biopsy based on cognitive or software magnetic resonance imaging (MRI) to transrectal ultrasound registration seems to increase the detection rate of clinically significant prostate cancer as compared with standard biopsy. However, these strategies have not been directly compared against an accurate test yet. The aim of this study was to obtain pilot data on the diagnostic ability of visually directed targeted biopsy vs. software-based targeted biopsy, considering transperineal template mapping (TPM) biopsy as the reference test. Prospective paired cohort study included 50 consecutive men undergoing TPM with one or more visible targets detected on preoperative multiparametric MRI. Targets were contoured on the Biojet software. Patients initially underwent software-based targeted biopsies, then visually directed targeted biopsies, and finally systematic TPM. The detection rate of clinically significant disease (Gleason score ≥3+4 and/or maximum cancer core length ≥4mm) of one strategy against another was compared by 3×3 contingency tables. Secondary analyses were performed using a less stringent threshold of significance (Gleason score ≥4+3 and/or maximum cancer core length ≥6mm). Median age was 68 (interquartile range: 63-73); median prostate-specific antigen level was 7.9ng/mL (6.4-10.2). A total of 79 targets were detected with a mean of 1.6 targets per patient. Of these, 27 (34%), 28 (35%), and 24 (31%) were scored 3, 4, and 5, respectively. At a patient level, the detection rate was 32 (64%), 34 (68%), and 38 (76%) for visually directed targeted, software-based biopsy, and TPM, respectively. Combining the 2 targeted strategies would have led to detection rate of 39 (78%). At a patient level and at a target level, software-based targeted biopsy found more clinically significant diseases than did visually directed targeted biopsy, although this was not statistically significant (22% vs. 14%, P = 0.48; 51.9% vs. 44.3%, P = 0.24). Secondary

  1. A prospective development study of software-guided radio-frequency ablation of primary and secondary liver tumors: Clinical intervention modelling, planning and proof for ablation cancer treatment (ClinicIMPPACT).

    PubMed

    Reinhardt, Martin; Brandmaier, Philipp; Seider, Daniel; Kolesnik, Marina; Jenniskens, Sjoerd; Sequeiros, Roberto Blanco; Eibisberger, Martin; Voglreiter, Philip; Flanagan, Ronan; Mariappan, Panchatcharam; Busse, Harald; Moche, Michael

    2017-12-01

    Radio-frequency ablation (RFA) is a promising minimal-invasive treatment option for early liver cancer, however monitoring or predicting the size of the resulting tissue necrosis during the RFA-procedure is a challenging task, potentially resulting in a significant rate of under- or over treatments. Currently there is no reliable lesion size prediction method commercially available. ClinicIMPPACT is designed as multicenter-, prospective-, non-randomized clinical trial to evaluate the accuracy and efficiency of innovative planning and simulation software. 60 patients with early liver cancer will be included at four European clinical institutions and treated with the same RFA system. The preinterventional imaging datasets will be used for computational planning of the RFA treatment. All ablations will be simulated simultaneously to the actual RFA procedure, using the software environment developed in this project. The primary outcome measure is the comparison of the simulated ablation zones with the true lesions shown in follow-up imaging after one month, to assess accuracy of the lesion prediction. This unique multicenter clinical trial aims at the clinical integration of a dedicated software solution to accurately predict lesion size and shape after radiofrequency ablation of liver tumors. Accelerated and optimized workflow integration, and real-time intraoperative image processing, as well as inclusion of patient specific information, e.g. organ perfusion and registration of the real RFA needle position might make the introduced software a powerful tool for interventional radiologists to optimize patient outcomes.

  2. LIMS Instrument Package (LIP) balloon experiment: Nimbus 7 satellite correlative temperature, ozone, water vapor, and nitric acid measurements

    NASA Technical Reports Server (NTRS)

    Lee, R. B., III; Gandrud, B. W.; Robbins, D. E.; Rossi, L. C.; Swann, N. R. W.

    1982-01-01

    The Limb Infrared Monitor of the Stratosphere (LIMS) LIP balloon experiment was used to obtain correlative temperature, ozone, water vapor, and nitric acid data at altitudes between 10 and 36 kilometers. The performance of the LIMS sensor flown on the Nimbus 7 Satellite was assessed. The LIP consists of the modified electrochemical concentration cell ozonesonde, the ultraviolet absorption photometric of ozone, the water vapor infrared radiometer sonde, the chemical absorption filter instrument for nitric acid vapor, and the infrared radiometer for nitric acid vapor. The limb instrument package (LIP), its correlative sensors, and the resulting data obtained from an engineering and four correlative flights are described.

  3. Characterisation of Four LIM Protein-Encoding Genes Involved in Infection-Related Development and Pathogenicity by the Rice Blast Fungus Magnaporthe oryzae

    PubMed Central

    Li, Ya; Yue, Xiaofeng; Que, Yawei; Yan, Xia; Ma, Zhonghua; Talbot, Nicholas J.; Wang, Zhengyi

    2014-01-01

    LIM domain proteins contain contiguous double-zinc finger domains and play important roles in cytoskeletal re-organisation and organ development in multi-cellular eukaryotes. Here, we report the characterization of four genes encoding LIM proteins in the rice blast fungus Magnaporthe oryzae. Targeted gene replacement of either the paxillin-encoding gene, PAX1, or LRG1 resulted in a significant reduction in hyphal growth and loss of pathogenicity, while deletion of RGA1 caused defects in conidiogenesis and appressorium development. A fourth LIM domain gene, LDP1, was not required for infection-associated development by M. oryzae. Live cell imaging revealed that Lrg1-GFP and Rga1-GFP both localize to septal pores, while Pax1-GFP is present in the cytoplasm. To explore the function of individual LIM domains, we carried out systematic deletion of each LIM domain, which revealed the importance of the Lrg1-LIM2 and Lrg1-RhoGAP domains for Lrg1 function and overlapping functions of the three LIM domains of Pax1. Interestingly, deletion of either PAX1 or LRG1 led to decreased sensitivity to cell wall-perturbing agents, such as Congo Red and SDS (sodium dodecyl sulfate). qRT-PCR analysis demonstrated the importance of both Lrg1 and Pax1 to regulation of genes associated with cell wall biogenesis. When considered together, our results indicate that LIM domain proteins are key regulators of infection-associated morphogenesis by the rice blast fungus. PMID:24505448

  4. Targeting nitrative stress for attenuating cisplatin-induced downregulation of cochlear LIM domain only 4 and ototoxicity.

    PubMed

    Jamesdaniel, Samson; Rathinam, Rajamani; Neumann, William L

    2016-12-01

    Cisplatin-induced ototoxicity remains a primary dose-limiting adverse effect of this highly effective anticancer drug. The clinical utility of cisplatin could be enhanced if the signaling pathways that regulate the toxic side-effects are delineated. In previous studies, we reported cisplatin-induced nitration of cochlear proteins and provided the first evidence for nitration and downregulation of cochlear LIM domain only 4 (LMO4) in cisplatin ototoxicity. Here, we extend these findings to define the critical role of nitrative stress in cisplatin-induced downregulation of LMO4 and its consequent ototoxic effects in UBOC1 cell cultures derived from sensory epithelial cells of the inner ear and in CBA/J mice. Cisplatin treatment increased the levels of nitrotyrosine and active caspase 3 in UBOC1 cells, which was detected by immunocytochemical and flow cytometry analysis, respectively. The cisplatin-induced nitrative stress and apoptosis were attenuated by co-treatment with SRI110, a peroxynitrite decomposition catalyst (PNDC), which also attenuated the cisplatin-induced downregulation of LMO4 in a dose-dependent manner. Furthermore, transient overexpression of LMO4 in UBOC1 cells prevented cisplatin-induced cytotoxicity while repression of LMO4 exacerbated cisplatin-induced cell death, indicating a direct link between LMO4 protein levels and cisplatin ototoxicity. Finally, auditory brainstem responses (ABR) recorded from CBA/J mice indicated that co-treatment with SRI110 mitigated cisplatin-induced hearing loss. Together, these results suggest that cisplatin-induced nitrative stress leads to a decrease in the levels of LMO4, downregulation of LMO4 is a critical determinant in cisplatin-induced ototoxicity, and targeting peroxynitrite could be a promising strategy for mitigating cisplatin-induced hearing loss. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Comparative study of Arctic sea ice response from NEMO-LIM3 to two different atmospheric forcings

    NASA Astrophysics Data System (ADS)

    Massonnet, Francois; Fichefet, Thierry; Goosse, Hugues; Mathiot, Pierre; König Beatty, Christof; Vancoppenolle, Martin

    2010-05-01

    Sea ice plays a key role within the climate system as it is, e.g., an efficient barrier to transfers of heat, mass and momentum between atmosphere and ocean. In order to simulate the observed sea ice state, global Ocean General Circulation Models (OGCMs) must benefit from good quality atmospheric forcings. NEMO-LIM3 is one of those OGCMs. This model results from the coupling of the sea ice model LIM3 with the ocean model OPA. So far, the NCEP/NCAR reanalysis dataset (2-m atmospheric temperatures and 10-m wind speeds) has been used jointly with monthly climatologies of relative humidity, cloudiness and precipitation to set up and calibrate NEMO-LIM3. Clear biases in model outputs have been tentatively attributed to this forcing. Here, we investigate the consequences of using the ERA-40-based DFS4 forcing on an ORCA1 configuration (1° resolution), with focus on the Arctic sea ice. Using an adequate metric, we measure the discrepancies between the simulations resulting from the respective forcings. A particular attention is paid to the sea ice features along Siberia at the beginning of the 80s, as previous NEMO-LIM3 runs with the NCEP/NCAR forcing exhibit a significant overestimation of ice extent in this area during this time period.

  6. Development of quantitative laser ionization mass spectrometry (LIMS). Final report, 1 Aug 87-1 Jan 90

    SciTech Connect

    Odom, R.W.

    1991-06-04

    The objective of the research was to develop quantitative microanalysis methods for dielectric thin films using the laser ionization mass spectrometry (LIMS) technique. The research involved preparation of thin (5,000 A) films of SiO2, Al2O3, MgF2, TiO2, Cr2O3, Ta2O5, Si3N4, and ZrO2, and doping these films with ion implant impurities of 11B, 40Ca, 56Fe, 68Zn, 81Br, and 121Sb. Laser ionization mass spectrometry (LIMS), secondary ion mass spectrometry (SIMS) and Rutherford backscattering spectrometry (RBS) were performed on these films. The research demonstrated quantitative LIMS analysis down to detection levels of 10-100 ppm, and led to the development of (1) a compoundmore » thin film standards product line for the performing organization, (2) routine LIMS analytical methods, and (3) the manufacture of high speed preamplifiers for time-of-flight mass spectrometry (TOF-MS) techniques.« less

  7. A Lagrangian analysis of a sudden stratospheric warming - Comparison of a model simulation and LIMS observations

    NASA Technical Reports Server (NTRS)

    Pierce, R. B.; Remsberg, Ellis E.; Fairlie, T. D.; Blackshear, W. T.; Grose, William L.; Turner, Richard E.

    1992-01-01

    Lagrangian area diagnostics and trajectory techniques are used to investigate the radiative and dynamical characteristics of a spontaneous sudden warming which occurred during a 2-yr Langley Research Center model simulation. The ability of the Langley Research Center GCM to simulate the major features of the stratospheric circulation during such highly disturbed periods is illustrated by comparison of the simulated warming to the observed circulation during the LIMS observation period. The apparent sink of vortex area associated with Rossby wave-breaking accounts for the majority of the reduction of the size of the vortex and also acts to offset the radiatively driven increase in the area occupied by the 'surf zone'. Trajectory analysis of selected material lines substantiates the conclusions from the area diagnostics.

  8. Description of data on the Nimbus 7 LIMS map archive tape: Temperature and geopotential height

    NASA Technical Reports Server (NTRS)

    Haggard, K. V.; Remsberg, E. E.; Grose, W. L.; Russell, J. M., III; Marshall, B. T.; Lingenfelser, G.

    1986-01-01

    The process by which the analysis of the Limb Infared Monitor of the Stratosphere (LIMS) experiment data were used to produce estimates of synoptic maps of temperature and geopotential height is described. In addition to a detailed description of the analysis procedure, several interesting features in the data are discussed and these features are used to demonstrate how the analysis procedure produced the final maps and how one can estimate the uncertainties in the maps. In addition, features in the analysis are noted that would influence how one might use, or interpret, the results. These include subjects such as smoothing and the interpretation of wave components. While some suggestions are made for an improved analysis of the data, it is shown that, in general, the maps are an excellent estimation of the synoptic fields.

  9. Preliminary clinical evaluation of automated analysis of the sublingual microcirculation in the assessment of patients with septic shock: Comparison of automated versus semi-automated software.

    PubMed

    Sharawy, Nivin; Mukhtar, Ahmed; Islam, Sufia; Mahrous, Reham; Mohamed, Hassan; Ali, Mohamed; Hakeem, Amr A; Hossny, Osama; Refaa, Amera; Saka, Ahmed; Cerny, Vladimir; Whynot, Sara; George, Ronald B; Lehmann, Christian

    2017-01-01

    The outcome of patients in septic shock has been shown to be related to changes within the microcirculation. Modern imaging technologies are available to generate high resolution video recordings of the microcirculation in humans. However, evaluation of the microcirculation is not yet implemented in the routine clinical monitoring of critically ill patients. This is mainly due to large amount of time and user interaction required by the current video analysis software. The aim of this study was to validate a newly developed automated method (CCTools®) for microcirculatory analysis of sublingual capillary perfusion in septic patients in comparison to standard semi-automated software (AVA3®). 204 videos from 47 patients were recorded using incident dark field (IDF) imaging. Total vessel density (TVD), proportion of perfused vessels (PPV), perfused vessel density (PVD), microvascular flow index (MFI) and heterogeneity index (HI) were measured using AVA3® and CCTools®. Significant differences between the numeric results obtained by the two different software packages were observed. The values for TVD, PVD and MFI were statistically related though. The automated software technique successes to show septic shock induced microcirculation alterations in near real time. However, we found wide degrees of agreement between AVA3® and CCTools® values due to several technical factors that should be considered in the future studies.

  10. LIM Kinase, a Newly Identified Regulator of Presynaptic Remodeling by Rod Photoreceptors After Injury

    PubMed Central

    Wang, Weiwei; Townes-Anderson, Ellen

    2015-01-01

    Purpose Rod photoreceptors retract their axon terminals and develop neuritic sprouts in response to retinal detachment and reattachment, respectively. This study examines the role of LIM kinase (LIMK), a component of RhoA and Rac pathways, in the presynaptic structural remodeling of rod photoreceptors. Methods Phosphorylated LIMK (p-LIMK), the active form of LIMK, was examined in salamander retina with Western blot and confocal microscopy. Axon length within the first 7 hours and process growth after 3 days of culture were assessed in isolated rod photoreceptors treated with inhibitors of upstream regulators ROCK and p21-activated kinase (Pak) (Y27632 and IPA-3) and a direct LIMK inhibitor (BMS-5). Porcine retinal explants were also treated with BMS-5 and analyzed 24 hours after detachment. Because Ca2+ influx contributes to axonal retraction, L-type channels were blocked in some experiments with nicardipine. Results Phosphorylated LIMK is present in rod terminals during retraction and in newly formed processes. Axonal retraction over 7 hours was significantly reduced by inhibition of LIMK or its regulators, ROCK and Pak. Process growth was reduced by LIMK or Pak inhibition especially at the basal (axon-bearing) region of the rod cells. Combining Ca2+ channel and LIMK inhibition had no additional effect on retraction but did further inhibit sprouting after 3 days. In detached porcine retina, LIMK inhibition reduced rod axonal retraction and improved retinal morphology. Conclusions Thus structural remodeling, in the form of either axonal retraction or neuritic growth, requires LIMK activity. LIM kinase inhibition may have therapeutic potential for reducing pathologic rod terminal plasticity after retinal injury. PMID:26658506

  11. Nuclear accumulation of myocyte muscle LIM protein is regulated by heme oxygenase 1 and correlates with cardiac function in the transition to failure

    PubMed Central

    Paudyal, Anju; Dewan, Sukriti; Ikie, Cindy; Whalley, Benjamin J; de Tombe, Pieter P.

    2016-01-01

    Key points The present study investigated the mechanism associated with impaired cardiac mechanosensing that leads to heart failure by examining the factors regulating muscle LIM protein subcellular distribution in myocytes.In myocytes, muscle LIM protein subcellular distribution is regulated by cell contractility rather than passive stretch via heme oxygenase‐1 and histone deacetylase signalling. The result of the present study provide new insights into mechanotransduction in cardiac myocytes.Myocyte mechanosensitivity, as indicated by the muscle LIM protein ratio, is also correlated with cardiac function in the transition to failure in a guinea‐pig model of disease. This shows that the loss mechanosensitivity plays an important role during the transition to failure in the heart.The present study provides the first indication that mechanosensing could be modified pharmacologically during the transition to heart failure. Abstract Impaired mechanosensing leads to heart failure and a decreased ratio of cytoplasmic to nuclear CSRP3/muscle LIM protein (MLP ratio) is associated with a loss of mechanosensitivity. In the present study, we tested whether passive or active stress/strain was important in modulating the MLP ratio and determined whether this correlated with heart function during the transition to failure. We exposed cultured neonatal rat myocytes to a 10% cyclic mechanical stretch at 1 Hz, or electrically paced myocytes at 6.8 V (1 Hz) for 48 h. The MLP ratio decreased by 50% (P < 0.05, n = 4) only in response to electrical pacing, suggesting impaired mechanosensitivity. Inhibition of contractility with 10 μm blebbistatin resulted in an ∼3‐fold increase in the MLP ratio (n = 8, P < 0.05), indicating that myocyte contractility regulates nuclear MLP. Inhibition of histone deacetylase (HDAC) signalling with trichostatin A increased nuclear MLP following passive stretch, suggesting that HDACs block MLP nuclear accumulation. Inhibition of heme

  12. From the SAIN,LIM system to the SENS algorithm: a review of a French approach of nutrient profiling.

    PubMed

    Tharrey, Marion; Maillot, Matthieu; Azaïs-Braesco, Véronique; Darmon, Nicole

    2017-08-01

    Nutrient profiling aims to classify or rank foods according to their nutritional composition to assist policies aimed at improving the nutritional quality of foods and diets. The present paper reviews a French approach of nutrient profiling by describing the SAIN,LIM system and its evolution from its early draft to the simplified nutrition labelling system (SENS) algorithm. Considered in 2010 by WHO as the 'French model' of nutrient profiling, SAIN,LIM classifies foods into four classes based on two scores: a nutrient density score (NDS) called SAIN and a score of nutrients to limit called LIM, and one threshold on each score. The system was first developed by the French Food Standard Agency in 2008 in response to the European regulation on nutrition and health claims (European Commission (EC) 1924/2006) to determine foods that may be eligible for bearing claims. Recently, the European regulation (EC 1169/2011) on the provision of food information to consumers allowed simplified nutrition labelling to facilitate consumer information and help them make fully informed choices. In that context, the SAIN,LIM was adapted to obtain the SENS algorithm, a system able to rank foods for simplified nutrition labelling. The implementation of the algorithm followed a step-by-step, systematic, transparent and logical process where shortcomings of the SAIN,LIM were addressed by integrating specificities of food categories in the SENS, reducing the number of nutrients, ordering the four classes and introducing European reference intakes. Through the French example, this review shows how an existing nutrient profiling system can be specifically adapted to support public health nutrition policies.

  13. EpHLA software: a timesaving and accurate tool for improving identification of acceptable mismatches for clinical purposes.

    PubMed

    Filho, Herton Luiz Alves Sales; da Mata Sousa, Luiz Claudio Demes; von Glehn, Cristina de Queiroz Carrascosa; da Silva, Adalberto Socorro; dos Santos Neto, Pedro de Alcântara; do Nascimento, Ferraz; de Castro, Adail Fonseca; do Nascimento, Liliane Machado; Kneib, Carolina; Bianchi Cazarote, Helena; Mayumi Kitamura, Daniele; Torres, Juliane Roberta Dias; da Cruz Lopes, Laiane; Barros, Aryela Loureiro; da Silva Edlin, Evelin Nildiane; de Moura, Fernanda Sá Leal; Watanabe, Janine Midori Figueiredo; do Monte, Semiramis Jamil Hadad

    2012-06-01

    The HLAMatchmaker algorithm, which allows the identification of “safe” acceptable mismatches (AMMs) for recipients of solid organ and cell allografts, is rarely used in part due to the difficulty in using it in the current Excel format. The automation of this algorithm may universalize its use to benefit the allocation of allografts. Recently, we have developed a new software called EpHLA, which is the first computer program automating the use of the HLAMatchmaker algorithm. Herein, we present the experimental validation of the EpHLA program by showing the time efficiency and the quality of operation. The same results, obtained by a single antigen bead assay with sera from 10 sensitized patients waiting for kidney transplants, were analyzed either by conventional HLAMatchmaker or by automated EpHLA method. Users testing these two methods were asked to record: (i) time required for completion of the analysis (in minutes); (ii) number of eplets obtained for class I and class II HLA molecules; (iii) categorization of eplets as reactive or non-reactive based on the MFI cutoff value; and (iv) determination of AMMs based on eplets' reactivities. We showed that although both methods had similar accuracy, the automated EpHLA method was over 8 times faster in comparison to the conventional HLAMatchmaker method. In particular the EpHLA software was faster and more reliable but equally accurate as the conventional method to define AMMs for allografts. The EpHLA software is an accurate and quick method for the identification of AMMs and thus it may be a very useful tool in the decision-making process of organ allocation for highly sensitized patients as well as in many other applications.

  14. Software Epistemology

    DTIC Science & Technology

    2016-03-01

    in-vitro decision to incubate a startup, Lexumo [7], which is developing a commercial Software as a Service ( SaaS ) vulnerability assessment...LTS Label Transition System MUSE Mining and Understanding Software Enclaves RTEMS Real-Time Executive for Multi-processor Systems SaaS Software ...as a Service SSA Static Single Assignment SWE Software Epistemology UD/DU Def-Use/Use-Def Chains (Dataflow Graph)

  15. Software Program: Software Management Guidebook

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The purpose of this NASA Software Management Guidebook is twofold. First, this document defines the core products and activities required of NASA software projects. It defines life-cycle models and activity-related methods but acknowledges that no single life-cycle model is appropriate for all NASA software projects. It also acknowledges that the appropriate method for accomplishing a required activity depends on characteristics of the software project. Second, this guidebook provides specific guidance to software project managers and team leaders in selecting appropriate life cycles and methods to develop a tailored plan for a software engineering project.

  16. Proprietary software

    NASA Technical Reports Server (NTRS)

    Marnock, M. J.

    1971-01-01

    The protection of intellectual property by a patent, a copyright, or trade secrets is reviewed. The present and future use of computers and software are discussed, along with the governmental uses of software. The popularity of contractual agreements for sale or lease of computer programs and software services is also summarized.

  17. Numerical Simulations of the 1991 Limón Tsunami, Costa Rica Caribbean Coast

    NASA Astrophysics Data System (ADS)

    Chacón-Barrantes, Silvia; Zamora, Natalia

    2017-08-01

    The second largest recorded tsunami along the Caribbean margin of Central America occurred 25 years ago. On April 22nd, 1991, an earthquake with magnitude Mw 7.6 ruptured along the thrust faults that form the North Panamá Deformed Belt (NPDB). The earthquake triggered a tsunami that affected the Caribbean coast of Costa Rica and Panamá within few minutes, generating two casualties. These are the only deaths caused by a tsunami in Costa Rica. Coseismic uplift up to 1.6 m and runup values larger than 2 m were measured along some coastal sites. Here, we consider three solutions for the seismic source as initial conditions to model the tsunami, each considering a single rupture plane. We performed numerical modeling of the tsunami propagation and runup using NEOWAVE numerical model (Yamazaki et al. in Int J Numer Methods Fluids 67:2081-2107, 2010, doi: 10.1002/fld.2485 ) on a system of nested grids from the entire Caribbean Sea to Limón city. The modeled surface deformation and tsunami runup agreed with the measured data along most of the coastal sites with one preferred model that fits the field data. The model results are useful to determine how the 1991 tsunami could have affected regions where tsunami records were not preserved and to simulate the effects of the coastal surface deformations as buffer to tsunami. We also performed tsunami modeling to simulate the consequences if a similar event with larger magnitude Mw 7.9 occurs offshore the southern Costa Rican Caribbean coast. Such event would generate maximum wave heights of more than 5 m showing that Limón and northwestern Panamá coastal areas are exposed to moderate-to-large tsunamis. These simulations considering historical events and maximum credible scenarios can be useful for hazard assessment and also as part of studies leading to tsunami evacuation maps and mitigation plans, even when that is not the scope of this paper.

  18. Clinical experience with Mobius FX software for 3D dose verification for prostate VMAT plans and comparison with physical measurements

    NASA Astrophysics Data System (ADS)

    Vazquez-Quino, L. A.; Huerta-Hernandez, C. I.; Rangaraj, D.

    2017-05-01

    MobiusFX, an add-on software module from Mobius Medical Systems for IMRT and VMAT QA, uses measurements in linac treatment logs to calculate and verify the 3D dose delivered to patients. In this study, 10 volumetric-modulated arc therapy (VMAT) prostate plans were planned and delivered in a Varian TrueBeam linac. The plans consisted of beams with 6 and 10 MV energy and 2 to 3 arcs per plan. The average gamma value with criterion of 3% and 3mm MobiusFX and TPS: 99.96%, 2% and 2mm MobiusFX and TPS: 98.70 %. Further comparison with ArcCheck measurements was conducted.

  19. [Development of multi-channels cardiac electrophysiological polygraph with LabVIEW as software platform and its clinical application].

    PubMed

    Fan, Shounian; Jiang, Yi; Jiang, Chenxi; Yang, Tianhe; Zhang, Chengyun; Liu, Junshi; Wu, Qiang; Zheng, Yaxi; Liu, Xiaoqiao

    2004-10-01

    Polygraph has become a necessary instrument in interventional cardiology and fundamental research of medicine up to the present. In this study, a LabView development system (DS) (developed by NI in U.S.) used as software platform, a DAQ data acquisition module and universal computer used as hardware platform, were creatively coupled with our self-made low noise multi-channels preamplifier to develop Multi-channels electrocardiograph. The device possessed the functions such as real time display of physiological process, digit highpass and lowpass, 50Hz filtered and gain adjustment, instant storing, random playback and printing, and process control stimulation. Besides, it was small-sized, economically practical and easy to operate. It could advance the spread of cardiac intervention treatment in hospitals.

  20. SU-F-P-54: Guidelines to Check Image Registration QA of a Clinical Deformation Registration Software: A Single Institution Preliminary Study

    SciTech Connect

    Gill, G; Souri, S; Rea, A

    Purpose: The objective of this study is to verify and analyze the accuracy of a clinical deformable image registration (DIR) software. Methods: To test clinical DIR software qualitatively and quantitatively, we focused on lung radiotherapy and analyzed a single (Lung) patient CT scan. Artificial anatomical changes were applied to account for daily variations during the course of treatment including the planning target volume (PTV) and organs at risk (OAR). The primary CT (pCT) and the structure set (pST) was deformed with commercial tool (ImSimQA-Oncology Systems Limited) and after artificial deformation (dCT and dST) sent to another commercial tool (VelocityAI-Varian Medicalmore » Systems). In Velocity, the deformed CT and structures (dCT and dST) were inversely deformed back to original primary CT (dbpCT and dbpST). We compared the dbpST and pST structure sets using similarity metrics. Furthermore, a binary deformation field vector (BDF) was created and sent to ImSimQA software for comparison with known “ground truth” deformation vector fields (DVF). Results: An image similarity comparison was made by using “ground truth” DVF and “deformed output” BDF with an output of normalized “cross correlation (CC)” and “mutual information (MI)” in ImSimQA software. Results for the lung case were MI=0.66 and CC=0.99. The artificial structure deformation in both pST and dbpST was analyzed using DICE coefficient, mean distance to conformity (MDC) and deformation field error volume histogram (DFEVH) by comparing them before and after inverse deformation. We have noticed inadequate structure match for CTV, ITV and PTV due to close proximity of heart and overall affected by lung expansion. Conclusion: We have seen similarity between pCT and dbpCT but not so well between pST and dbpST, because of inadequate structure deformation in clinical DIR system. This system based quality assurance test will prepare us for adopting the guidelines of upcoming AAPM task

  1. Computer software.

    PubMed

    Rosenthal, L E

    1986-10-01

    Software is the component in a computer system that permits the hardware to perform the various functions that a computer system is capable of doing. The history of software and its development can be traced to the early nineteenth century. All computer systems are designed to utilize the "stored program concept" as first developed by Charles Babbage in the 1850s. The concept was lost until the mid-1940s, when modern computers made their appearance. Today, because of the complex and myriad tasks that a computer system can perform, there has been a differentiation of types of software. There is software designed to perform specific business applications. There is software that controls the overall operation of a computer system. And there is software that is designed to carry out specialized tasks. Regardless of types, software is the most critical component of any computer system. Without it, all one has is a collection of circuits, transistors, and silicone chips.

  2. Islamic Education Philosophy Development (Study Analysis on Ta'lim Al-Kitab Al-Zarnuji Muta'allim Works)

    ERIC Educational Resources Information Center

    Asrori, H. Achmad

    2016-01-01

    "Ta'lim Muta'allim" is one of the monumental works of Shaykh Tajuddin Nu'man ibn Ibrahim ibn al-Khalil al-Zarnuji, who lived in the 6th century H/13-14 M. The reason for writing this study ie: (1) it is very rich with the basic values of Islamic education, (2) the values are already widely practiced in the world of education, especially…

  3. LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing

    PubMed Central

    James, Victoria; Zhang, Yining; Foxler, Daniel E.; de Moor, Cornelia H.; Kong, Yi Wen; Webb, Thomas M.; Self, Tim J.; Feng, Yungfeng; Lagos, Dimitrios; Chu, Chia-Ying; Rana, Tariq M.; Morley, Simon J.; Longmore, Gregory D.; Bushell, Martin; Sharp, Tyson V.

    2010-01-01

    In recent years there have been major advances with respect to the identification of the protein components and mechanisms of microRNA (miRNA) mediated silencing. However, the complete and precise repertoire of components and mechanism(s) of action remain to be fully elucidated. Herein we reveal the identification of a family of three LIM domain-containing proteins, LIMD1, Ajuba and WTIP (Ajuba LIM proteins) as novel mammalian processing body (P-body) components, which highlight a novel mechanism of miRNA-mediated gene silencing. Furthermore, we reveal that LIMD1, Ajuba, and WTIP bind to Ago1/2, RCK, Dcp2, and eIF4E in vivo, that they are required for miRNA-mediated, but not siRNA-mediated gene silencing and that all three proteins bind to the mRNA 5′ m7GTP cap–protein complex. Mechanistically, we propose the Ajuba LIM proteins interact with the m7GTP cap structure via a specific interaction with eIF4E that prevents 4EBP1 and eIF4G interaction. In addition, these LIM-domain proteins facilitate miRNA-mediated gene silencing by acting as an essential molecular link between the translationally inhibited eIF4E-m7GTP-5′cap and Ago1/2 within the miRISC complex attached to the 3′-UTR of mRNA, creating an inhibitory closed-loop complex. PMID:20616046

  4. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action.

    PubMed

    Wallner, Jürgen; Hochegger, Kerstin; Chen, Xiaojun; Mischak, Irene; Reinbacher, Knut; Pau, Mauro; Zrnc, Tomislav; Schwenzer-Zimmerer, Katja; Zemann, Wolfgang; Schmalstieg, Dieter; Egger, Jan

    2018-01-01

    Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However-due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score and the Hausdorff distance. Overall semi-automatic GrowCut segmentation times were about one minute. Mean Dice Score values of over 85% and Hausdorff Distances below 33.5 voxel could be achieved between the algorithmic GrowCut-based segmentations and the manual generated ground truth schemes. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the two groups. Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Due to an open-source basis the used method could be further developed by other groups or specialists

  5. An update on the LIM and SH3 domain protein 1 (LASP1): a versatile structural, signaling, and biomarker protein

    PubMed Central

    Orth, Martin F.; Cazes, Alex; Butt, Elke; Grunewald, Thomas G. P.

    2015-01-01

    The gene encoding the LIM and SH3 domain protein (LASP1) was cloned two decades ago from a cDNA library of breast cancer metastases. As the first protein of a class comprising one N-terminal LIM and one C-terminal SH3 domain, LASP1 founded a new LIM-protein subfamily of the nebulin group. Since its discovery LASP1 proved to be an extremely versatile protein because of its exceptional structure allowing interaction with various binding partners, its ubiquitous expression in normal tissues, albeit with distinct expression patterns, and its ability to transmit signals from the cytoplasm into the nucleus. As a result, LASP1 plays key roles in cell structure, physiological processes, and cell signaling. Furthermore, LASP1 overexpression contributes to cancer aggressiveness hinting to a potential value of LASP1 as a cancer biomarker. In this review we summarize published data on structure, regulation, function, and expression pattern of LASP1, with a focus on its role in human cancer and as a biomarker protein. In addition, we provide a comprehensive transcriptome analysis of published microarrays (n=2,780) that illustrates the expression profile of LASP1 in normal tissues and its overexpression in a broad range of human cancer entities. PMID:25622104

  6. Characterization of a unique motif in LIM mineralization protein-1 that interacts with jun activation-domain-binding protein 1.

    PubMed

    Sangadala, Sreedhara; Yoshioka, Katsuhito; Enyo, Yoshio; Liu, Yunshan; Titus, Louisa; Boden, Scott D

    2014-01-01

    Development and repair of the skeletal system and other organs are highly dependent on precise regulation of the bone morphogenetic protein (BMP) pathway. The use of BMPs clinically to induce bone formation has been limited in part by the requirement of much higher doses of recombinant proteins in primates than were needed in cell culture or rodents. Therefore, increasing cellular responsiveness to BMPs has become our focus. We determined that an osteogenic LIM mineralization protein, LMP-1 interacts with Smurf1 (Smad ubiquitin regulatory factor 1) and prevents ubiquitination of Smads resulting in potentiation of BMP activity. In the region of LMP-1 responsible for bone formation, there is a motif that directly interacts with the Smurf1 WW2 domain and thus effectively competes for binding with Smad1 and Smad5, key signaling proteins in the BMP pathway. Here we show that the same region also contains a motif that interacts with Jun activation-domain-binding protein 1 (Jab1) which targets a common Smad, Smad4, shared by both the BMP and transforming growth factor-β (TGF-β) pathways, for proteasomal degradation. Jab1 was first identified as a coactivator of the transcription factor c-Jun. Jab1 binds to Smad4, Smad5, and Smad7, key intracellular signaling molecules of the TGF-β superfamily, and causes ubiquitination and/or degradation of these Smads. We confirmed a direct interaction of Jab1 with LMP-1 using recombinantly expressed wild-type and mutant proteins in slot-blot-binding assays. We hypothesized that LMP-1 binding to Jab1 prevents the binding and subsequent degradation of these Smads causing increased accumulation of osteogenic Smads in cells. We identified a sequence motif in LMP-1 that was predicted to interact with Jab1 based on the MAME/MAST sequence analysis of several cellular signaling molecules that are known to interact with Jab-1. We further mutated the potential key interacting residues in LMP-1 and showed loss of binding to Jab1 in binding

  7. Tissue specific characterisation of Lim-kinase 1 expression during mouse embryogenesis

    PubMed Central

    Lindström, Nils O.; Neves, Carlos; McIntosh, Rebecca; Miedzybrodzka, Zosia; Vargesson, Neil; Collinson, J. Martin

    2012-01-01

    The Lim-kinase (LIMK) proteins are important for the regulation of the actin cytoskeleton, in particular the control of actin nucleation and depolymerisation via regulation of cofilin, and hence may control a large number of processes during development, including cell tensegrity, migration, cell cycling, and axon guidance. LIMK1/LIMK2 knockouts disrupt spinal cord morphogenesis and synapse formation but other tissues and developmental processes that require LIMK are yet to be fully determined. To identify tissues and cell-types that may require LIMK, we characterised the pattern of LIMK1 protein during mouse embryogenesis. We showed that LIMK1 displays an expression pattern that is temporally dynamic and tissue-specific. In several tissues LIMK1 is detected in cell-types that also express Wilms’ tumour protein 1 and that undergo transitions between epithelial and mesenchymal states, including the pleura, epicardium, kidney nephrons, and gonads. LIMK1 was also found in a subset of cells in the dorsal retina, and in mesenchymal cells surrounding the peripheral nerves. This detailed study of the spatial and temporal expression of LIMK1 shows that LIMK1 expression is more dynamic than previously reported, in particular at sites of tissue–tissue interactions guiding multiple developmental processes. PMID:21167960

  8. Palmitoylation of LIM Kinase-1 ensures spine-specific actin polymerization and morphological plasticity

    PubMed Central

    George, Joju; Soares, Cary; Montersino, Audrey; Beique, Jean-Claude; Thomas, Gareth M

    2015-01-01

    Precise regulation of the dendritic spine actin cytoskeleton is critical for neurodevelopment and neuronal plasticity, but how neurons spatially control actin dynamics is not well defined. Here, we identify direct palmitoylation of the actin regulator LIM kinase-1 (LIMK1) as a novel mechanism to control spine-specific actin dynamics. A conserved palmitoyl-motif is necessary and sufficient to target LIMK1 to spines and to anchor LIMK1 in spines. ShRNA knockdown/rescue experiments reveal that LIMK1 palmitoylation is essential for normal spine actin polymerization, for spine-specific structural plasticity and for long-term spine stability. Palmitoylation is critical for LIMK1 function because this modification not only controls LIMK1 targeting, but is also essential for LIMK1 activation by its membrane-localized upstream activator PAK. These novel roles for palmitoylation in the spatial control of actin dynamics and kinase signaling provide new insights into structural plasticity mechanisms and strengthen links between dendritic spine impairments and neuropathological conditions. DOI: http://dx.doi.org/10.7554/eLife.06327.001 PMID:25884247

  9. From LIMS to OMPS-LP: limb ozone observations for future reanalyses

    NASA Astrophysics Data System (ADS)

    Wargan, K.; Kramarova, N. A.; Remsberg, E. E.; Coy, L.; Harvey, L.; Livesey, N. J.; Pawson, S.

    2017-12-01

    High vertical resolution and accuracy of ozone data from satellite-borne limb sounders have made them an invaluable tool in scientific studies of the middle and upper atmosphere. However, it was not until recently that these measurements were successfully incorporated in atmospheric reanalyses: of the major multidecadal reanalyses only ECMWF's ERA-Interim/ERA5 and NASA's MERRA-2 use limb ozone data. Validation and comparison studies have demonstrated that the addition of observations from the Microwave Limb Sounder (MLS) on EOS Aura greatly improved the quality of ozone fields in MERRA-2 making these assimilated data sets useful for scientific research. In this presentation, we will show the results of test experiments assimilating retrieved ozone from the Limb Infrared Monitor of the Stratosphere (LIMS, 1978/1979) and Ozone Mapping Profiler Suite Limb Profiler (OMPS-LP, 2012 to present). Our approach builds on the established assimilation methodology used for MLS in MERRA-2 and, in the case of OMPS-LP, extends the excellent record of MLS ozone assimilation into the post-EOS era in Earth observations. We will show case studies, discuss comparisons of the new experiments with MERRA-2, strategies for bias correction and the potential for combined assimilation of multiple limb ozone data types in future reanalyses for studies of multidecadal stratospheric ozone changes including trends.

  10. From LIMS to OMPS-LP: Limb Ozone Observations for Future Reanalyses

    NASA Technical Reports Server (NTRS)

    Wargan, K.; Kramarova, N.; Remsberg, E.; Coy, L.; Harvey, L.; Livesey, N.; Pawson, S.

    2017-01-01

    High vertical resolution and accuracy of ozone data from satellite-borne limb sounders has made them an invaluable tool in scientific studies of the middle and upper atmosphere. However, it was not until recently that these measurements were successfully incorporated in atmospheric reanalyses: of the major multidecadal reanalyses only ECMWF's (European Centre for Medium-Range Weather Forecasts') ERA (ECMWF Re-Analysis)-Interim/ERA5 and NASA's MERRA-2 (Modern-Era Retrospective Analysis for Research and Applications-2) use limb ozone data. Validation and comparison studies have demonstrated that the addition of observations from the Microwave Limb Sounder (MLS) on EOS (Earth Observing System) Aura greatly improved the quality of ozone fields in MERRA-2 making these assimilated data sets useful for scientific research. In this presentation, we will show the results of test experiments assimilating retrieved ozone from the Limb Infrared Monitor of the Stratosphere (LIMS, 1978/1979) and Ozone Mapping Profiler Suite Limb Profiler (OMPS-LP, 2012 to present). Our approach builds on the established assimilation methodology used for MLS in MERRA-2 and, in the case of OMPS-LP, extends the excellent record of MLS ozone assimilation into the post-EOS era in Earth observations. We will show case studies, discuss comparisons of the new experiments with MERRA-2, strategies for bias correction and the potential for combined assimilation of multiple limb ozone data types in future reanalyses for studies of multidecadal stratospheric ozone changes including trends.

  11. Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities

    PubMed Central

    2010-01-01

    Background Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. Results We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. Conclusions The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities. PMID:20482787

  12. LIM kinase inhibitors disrupt mitotic microtubule organization and impair tumor cell proliferation

    PubMed Central

    Mardilovich, Katerina; Baugh, Mark; Crighton, Diane; Kowalczyk, Dominika; Gabrielsen, Mads; Munro, June; Croft, Daniel R.; Lourenco, Filipe; James, Daniel; Kalna, Gabriella; McGarry, Lynn; Rath, Oliver; Shanks, Emma; Garnett, Mathew J.; McDermott, Ultan; Brookfield, Joanna; Charles, Mark; Hammonds, Tim; Olson, Michael F.

    2015-01-01

    The actin and microtubule cytoskeletons are critically important for cancer cell proliferation, and drugs that target microtubules are widely-used cancer therapies. However, their utility is compromised by toxicities due to dose and exposure. To overcome these issues, we characterized how inhibition of the actin and microtubule cytoskeleton regulatory LIM kinases could be used in drug combinations to increase efficacy. A previously-described LIMK inhibitor (LIMKi) induced dose-dependent microtubule alterations that resulted in significant mitotic defects, and increased the cytotoxic potency of microtubule polymerization inhibitors. By combining LIMKi with 366 compounds from the GSK Published Kinase Inhibitor Set, effective combinations were identified with kinase inhibitors including EGFR, p38 and Raf. These findings encouraged a drug discovery effort that led to development of CRT0105446 and CRT0105950, which potently block LIMK1 and LIMK2 activity in vitro, and inhibit cofilin phosphorylation and increase αTubulin acetylation in cells. CRT0105446 and CRT0105950 were screened against 656 cancer cell lines, and rhabdomyosarcoma, neuroblastoma and kidney cancer cells were identified as significantly sensitive to both LIMK inhibitors. These large-scale screens have identified effective LIMK inhibitor drug combinations and sensitive cancer types. In addition, the LIMK inhibitory compounds CRT0105446 and CRT0105950 will enable further development of LIMK-targeted cancer therapy. PMID:26540348

  13. Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

    PubMed

    Tolopko, Andrew N; Sullivan, John P; Erickson, Sean D; Wrobel, David; Chiang, Su L; Rudnicki, Katrina; Rudnicki, Stewart; Nale, Jennifer; Selfors, Laura M; Greenhouse, Dara; Muhlich, Jeremy L; Shamu, Caroline E

    2010-05-18

    Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. These shared facilities require a unique informatics infrastructure that must not only provide access to and analysis of screening data, but must also manage the administrative and technical challenges associated with conducting numerous, interleaved screening efforts run by multiple independent research groups. We have developed Screensaver, a free, open source, web-based lab information management system (LIMS), to address the informatics needs of our small molecule and RNAi screening facility. Screensaver supports the storage and comparison of screening data sets, as well as the management of information about screens, screeners, libraries, and laboratory work requests. To our knowledge, Screensaver is one of the first applications to support the storage and analysis of data from both genome-scale RNAi screening projects and small molecule screening projects. The informatics and administrative needs of an HTS facility may be best managed by a single, integrated, web-accessible application such as Screensaver. Screensaver has proven useful in meeting the requirements of the ICCB-Longwood/NSRB Screening Facility at Harvard Medical School, and has provided similar benefits to other HTS facilities.

  14. Patient-specific IMRT verification using independent fluence-based dose calculation software: experimental benchmarking and initial clinical experience.

    PubMed

    Georg, Dietmar; Stock, Markus; Kroupa, Bernhard; Olofsson, Jörgen; Nyholm, Tufve; Ahnesjö, Anders; Karlsson, Mikael

    2007-08-21

    Experimental methods are commonly used for patient-specific intensity-modulated radiotherapy (IMRT) verification. The purpose of this study was to investigate the accuracy and performance of independent dose calculation software (denoted as 'MUV' (monitor unit verification)) for patient-specific quality assurance (QA). 52 patients receiving step-and-shoot IMRT were considered. IMRT plans were recalculated by the treatment planning systems (TPS) in a dedicated QA phantom, in which an experimental 1D and 2D verification (0.3 cm(3) ionization chamber; films) was performed. Additionally, an independent dose calculation was performed. The fluence-based algorithm of MUV accounts for collimator transmission, rounded leaf ends, tongue-and-groove effect, backscatter to the monitor chamber and scatter from the flattening filter. The dose calculation utilizes a pencil beam model based on a beam quality index. DICOM RT files from patient plans, exported from the TPS, were directly used as patient-specific input data in MUV. For composite IMRT plans, average deviations in the high dose region between ionization chamber measurements and point dose calculations performed with the TPS and MUV were 1.6 +/- 1.2% and 0.5 +/- 1.1% (1 S.D.). The dose deviations between MUV and TPS slightly depended on the distance from the isocentre position. For individual intensity-modulated beams (total 367), an average deviation of 1.1 +/- 2.9% was determined between calculations performed with the TPS and with MUV, with maximum deviations up to 14%. However, absolute dose deviations were mostly less than 3 cGy. Based on the current results, we aim to apply a confidence limit of 3% (with respect to the prescribed dose) or 6 cGy for routine IMRT verification. For off-axis points at distances larger than 5 cm and for low dose regions, we consider 5% dose deviation or 10 cGy acceptable. The time needed for an independent calculation compares very favourably with the net time for an experimental

  15. Software safety

    NASA Technical Reports Server (NTRS)

    Leveson, Nancy

    1987-01-01

    Software safety and its relationship to other qualities are discussed. It is shown that standard reliability and fault tolerance techniques will not solve the safety problem for the present. A new attitude requires: looking at what you do NOT want software to do along with what you want it to do; and assuming things will go wrong. New procedures and changes to entire software development process are necessary: special software safety analysis techniques are needed; and design techniques, especially eliminating complexity, can be very helpful.

  16. Frequency and analysis of non-clinical errors made in radiology reports using the National Integrated Medical Imaging System voice recognition dictation software.

    PubMed

    Motyer, R E; Liddy, S; Torreggiani, W C; Buckley, O

    2016-11-01

    Voice recognition (VR) dictation of radiology reports has become the mainstay of reporting in many institutions worldwide. Despite benefit, such software is not without limitations, and transcription errors have been widely reported. Evaluate the frequency and nature of non-clinical transcription error using VR dictation software. Retrospective audit of 378 finalised radiology reports. Errors were counted and categorised by significance, error type and sub-type. Data regarding imaging modality, report length and dictation time was collected. 67 (17.72 %) reports contained ≥1 errors, with 7 (1.85 %) containing 'significant' and 9 (2.38 %) containing 'very significant' errors. A total of 90 errors were identified from the 378 reports analysed, with 74 (82.22 %) classified as 'insignificant', 7 (7.78 %) as 'significant', 9 (10 %) as 'very significant'. 68 (75.56 %) errors were 'spelling and grammar', 20 (22.22 %) 'missense' and 2 (2.22 %) 'nonsense'. 'Punctuation' error was most common sub-type, accounting for 27 errors (30 %). Complex imaging modalities had higher error rates per report and sentence. Computed tomography contained 0.040 errors per sentence compared to plain film with 0.030. Longer reports had a higher error rate, with reports >25 sentences containing an average of 1.23 errors per report compared to 0-5 sentences containing 0.09. These findings highlight the limitations of VR dictation software. While most error was deemed insignificant, there were occurrences of error with potential to alter report interpretation and patient management. Longer reports and reports on more complex imaging had higher error rates and this should be taken into account by the reporting radiologist.

  17. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen

    1988-01-01

    Presents reviews of six computer software programs for teaching science. Provides the publisher, grade level, cost, and descriptions of software, including: (1) "Recycling Logic"; (2) "Introduction to Biochemistry"; (3) "Food for Thought"; (4) "Watts in a Home"; (5) "Geology in Action"; and (6)…

  18. Software Repository

    NASA Technical Reports Server (NTRS)

    Merwarth, P., D.

    1983-01-01

    The Common Software Module Repository (CSMR) is computerized library system with high product and service visibility to potential users. Online capabilities of system allow both librarian and user to interact with library. Librarian is responsible for maintaining information in CSMR library. User searches library to locate software modules that meet his or her current needs.

  19. Expression of the LIM-Homeodomain Protein Isl1 in the Developing and Mature Mouse Retina

    PubMed Central

    Elshatory, Yasser; Deng, Min; Xie, Xiaoling; Gan, Lin

    2010-01-01

    The mammalian retina is comprised of six major neuronal cell types and is subdivided into more morphological and physiological subtypes. The transcriptional machinery underlying these subtype fate choices is largely unknown. The LIM-homeodomain protein, Isl1, plays an essential role in central nervous system (CNS) differentiation but its relationship to retinal neurogenesis remains unknown. We report here its dynamic spatiotemporal expression in the mouse retina. Among bipolar interneurons, Isl1 expression commences at postnatal day (P)5 and is later restricted to ON-bipolar cells. The intensity of Isl1 expression is found to segregate the pool of ON-bipolar cells into rod and ON-cone bipolar cells with higher expression in rod bipolar cells. As bipolar cell development proceeds from P5–10 the colocalization of Isl1 and the pan-bipolar cell marker Chx10 reveals the organization of ON-center bipolar cell nuclei to the upper portion of the inner nuclear layer. Further, whereas Isl1 is predominantly a ganglion cell marker prior to embryonic day (E)15.5, at E15.5 and later its expression in nonganglion cells expands. We demonstrate that these Isl1-positive, nonganglion cells acquire the expression of amacrine cell markers embryonically, likely representing nascent cholinergic amacrine cells. Taken together, Isl1 is expressed during the maturation of and is later maintained in retinal ganglion cells and subtypes of amacrine and bipolar cells where it may function in the maintenance of these cells into adulthood. J. Comp. Neurol. 503: 182–197, 2007. PMID:17480014

  20. FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data

    PubMed Central

    2015-01-01

    Background Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical. These assays may be used as an alternative to animal experimentation and are becoming increasingly important in modern laboratories. However, the execution of these assays in large scale and different laboratories requires, among other things, the management of protocols, reagents, cell lines used as well as the data produced, which can be a challenge. The management of all this information is greatly improved by the utilization of computational tools to save time and guarantee quality. However, a tool that performs this task designed specifically for cytotoxicity assays is not yet available. Results In this work, we have used a workflow based LIMS -- the Flux system -- and the Together Workflow Editor as a framework to develop FluxCTTX, a tool for management of data from cytotoxicity assays performed at different laboratories. The main work is the development of a workflow, which represents all stages of the assay and has been developed and uploaded in Flux. This workflow models the activities of cytotoxicity assays performed as described in the OECD 129 Guidance Document. Conclusions FluxCTTX presents a solution for the management of the data produced by cytotoxicity assays performed at Interlaboratory comparisons. Its adoption will contribute to guarantee the quality of activities in the process of cytotoxicity tests and enforce the use of Good Laboratory Practices (GLP). Furthermore, the workflow developed is complete and can be adapted to other contexts and different tests for management of other types of data. PMID:26696462

  1. LIM-domain protein AJUBA suppresses malignant mesothelioma cell proliferation via Hippo signaling cascade.

    PubMed

    Tanaka, I; Osada, H; Fujii, M; Fukatsu, A; Hida, T; Horio, Y; Kondo, Y; Sato, A; Hasegawa, Y; Tsujimura, T; Sekido, Y

    2015-01-02

    Malignant mesothelioma (MM) is one of the most aggressive neoplasms usually associated with asbestos exposure and is highly refractory to current therapeutic modalities. MMs show frequent activation of a transcriptional coactivator Yes-associated protein (YAP), which is attributed to the neurofibromatosis type 2 (NF2)-Hippo pathway dysfunction, leading to deregulated cell proliferation and acquisition of a malignant phenotype. However, the whole mechanism of disordered YAP activation in MMs has not yet been well clarified. In the present study, we investigated various components of the NF2-Hippo pathway, and eventually found that MM cells frequently showed downregulation of LIM-domain protein AJUBA, a binding partner of large tumor suppressor type 2 (LATS2), which is one of the last-step kinases of the NF2-Hippo pathway. Although loss of AJUBA expression was independent of the alteration status of other Hippo pathway components, MM cell lines with AJUBA inactivation showed a more dephosphorylated (activated) level of YAP. Immunohistochemical analysis showed frequent downregulation of AJUBA in primary MMs, which was associated with YAP constitutive activation. We found that AJUBA transduction into MM cells significantly suppressed promoter activities of YAP-target genes, and the suppression of YAP activity by AJUBA was remarkably canceled by knockdown of LATS2. In connection with these results, transduction of AJUBA-expressing lentivirus significantly inhibited the proliferation and anchorage-independent growth of the MM cells that harbored ordinary LATS family expression. Taken together, our findings indicate that AJUBA negatively regulates YAP activity through the LATS family, and inactivation of AJUBA is a novel key mechanism in MM cell proliferation.

  2. The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource

    PubMed Central

    2012-01-01

    Background Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species. Description The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers (“Isolate Accession”), the first five of which correspond to the collection site (“Environmental Accession”). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages. Conclusions HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and

  3. LIM homeobox transcription factor Isl1 is required for melatonin synthesis in the pig pineal gland.

    PubMed

    Zhang, Jinglin; Qiu, Jingtao; Zhou, Yewen; Wang, Yue; Li, Hongjiao; Zhang, Taojie; Jiang, Ying; Gou, Kemian; Cui, Sheng

    2018-02-26

    Melatonin is a key hormone that regulates circadian rhythms, metabolism, and reproduction. However, the mechanisms of melatonin synthesis and secretion have not been fully defined. The purpose of this study was to investigate the functions of the LIM homeobox transcription factor Isl1 in regulating melatonin synthesis and secretion in porcine pineal gland. We found that Isl1 is highly expressed in the melatonin-producing cells in the porcine pineal gland. Further functional studies demonstrate that Isl1 knockdown in cultured primary porcine pinealocytes results in the decline of melatonin and arylalkylamine N-acetyltransferase (AANAT) mRNA levels by 29.2% and 72.2%, respectively, whereas Isl1 overexpression raised by 1.3-fold and 2.7-fold. In addition, the enhancing effect of norepinephrine (NE) on melatonin synthesis was abolished by Isl1 knockdown. The in vivo intracerebroventricular NE injections upregulate Isl1 mRNA and protein levels by about threefold and 4.5-fold in the porcine pineal gland. We then examined the changes in Isl1 expression in the pineal gland and global melatonin levels throughout the day. The results show that Isl1 protein level at 24:00 is 2.5-fold higher than that at 12:00, which is parallel to melatonin levels. We further found that Isl1 increases the activity of AANAT promoter, and the effect of NE on Isl1 expression was blocked by an ERK inhibitor. Collectively, the results presented here demonstrate that Isl1 positively modulates melatonin synthesis by targeting AANAT, via the ERK signaling pathway of NE. These suggest that Isl1 plays important roles in maintaining the daily circadian rhythm. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. LIM Domain Only 2 Regulates Endothelial Proliferation, Angiogenesis, and Tissue Regeneration.

    PubMed

    Meng, Shu; Matrone, Gianfranco; Lv, Jie; Chen, Kaifu; Wong, Wing Tak; Cooke, John P

    2016-10-06

    LIM domain only 2 (LMO2, human gene) is a key transcription factor that regulates hematopoiesis and vascular development. However, its role in adult endothelial function has been incompletely characterized. In vitro loss- and gain-of-function studies on LMO2 were performed in human umbilical vein endothelial cells with lentiviral overexpression or short hairpin RNA knockdown (KD) of LMO2, respectively. LMO2 KD significantly impaired endothelial proliferation. LMO2 controls endothelial G1/S transition through transcriptional regulation of cyclin-dependent kinase 2 and 4 as determined by reverse transcription polymerase chain reaction (PCR), western blot, and chromatin immunoprecipitation, and also influences the expression of Cyclin D1 and Cyclin A1. LMO2 KD also impaired angiogenesis by reducing transforming growth factor-β (TGF-β) expression, whereas supplementation of exogenous TGF-β restored defective network formation in LMO2 KD human umbilical vein endothelial cells. In a zebrafish model of caudal fin regeneration, RT-PCR revealed that the lmo2 (zebrafish gene) gene was upregulated at day 5 postresection. The KD of lmo2 by vivo-morpholino injections in adult Tg(fli1:egfp) y1 zebrafish reduced 5-bromo-2'-deoxyuridine incorporation in endothelial cells, impaired neoangiogenesis in the resected caudal fin, and substantially delayed fin regeneration. The transcriptional factor LMO2 regulates endothelial proliferation and angiogenesis in vitro. Furthermore, LMO2 is required for angiogenesis and tissue healing in vivo. Thus, LMO2 is a critical determinant of vascular and tissue regeneration. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

  5. SU-E-J-04: Integration of Interstitial High Intensity Therapeutic Ultrasound Applicators On a Clinical MRI-Guided High Intensity Focused Ultrasound Treatment Planning Software Platform

    SciTech Connect

    Ellens, N; Partanen, A; Ghoshal, G

    Purpose: Interstitial high intensity therapeutic ultrasound (HITU) applicators can be used to ablate tissue percutaneously, allowing for minimally-invasive treatment without ionizing radiation [1,2]. The purpose of this study was to evaluate the feasibility and usability of combining multielement interstitial HITU applicators with a clinical magnetic resonance imaging (MRI)-guided focused ultrasound software platform. Methods: The Sonalleve software platform (Philips Healthcare, Vantaa, Finland) combines anatomical MRI for target selection and multi-planar MRI thermometry to provide real-time temperature information. The MRI-compatible interstitial US applicators (Acoustic MedSystems, Savoy, IL, USA) had 1–4 cylindrical US elements, each 1 cm long with either 180° or 360°more » of active surface. Each applicator (4 Fr diameter, enclosed within a 13 Fr flexible catheter) was inserted into a tissue-mimicking agar-silica phantom. Degassed water was circulated around the transducers for cooling and coupling. Based on the location of the applicator, a virtual transducer overlay was added to the software to assist targeting and to allow automatic thermometry slice placement. The phantom was sonicated at 7 MHz for 5 minutes with 6–8 W of acoustic power for each element. MR thermometry data were collected during and after sonication. Results: Preliminary testing indicated that the applicator location could be identified in the planning images and the transducer locations predicted within 1 mm accuracy using the overlay. Ablation zones (thermal dose ≥ 240 CEM43) for 2 active, adjacent US elements ranged from 18 mm × 24 mm (width × length) to 25 mm × 25 mm for the 6 W and 8 W sonications, respectively. Conclusion: The combination of interstitial HITU applicators and this software platform holds promise for novel approaches in minimally-invasive MRI-guided therapy, especially when bony structures or air-filled cavities may preclude extracorporeal HIFU.[1

  6. Radiological assessment of breast density by visual classification (BI-RADS) compared to automated volumetric digital software (Quantra): implications for clinical practice.

    PubMed

    Regini, Elisa; Mariscotti, Giovanna; Durando, Manuela; Ghione, Gianluca; Luparia, Andrea; Campanino, Pier Paolo; Bianchi, Caterina Chiara; Bergamasco, Laura; Fonio, Paolo; Gandini, Giovanni

    2014-10-01

    This study was done to assess breast density on digital mammography and digital breast tomosynthesis according to the visual Breast Imaging Reporting and Data System (BI-RADS) classification, to compare visual assessment with Quantra software for automated density measurement, and to establish the role of the software in clinical practice. We analysed 200 digital mammograms performed in 2D and 3D modality, 100 of which positive for breast cancer and 100 negative. Radiological density was assessed with the BI-RADS classification; a Quantra density cut-off value was sought on the 2D images only to discriminate between BI-RADS categories 1-2 and BI-RADS 3-4. Breast density was correlated with age, use of hormone therapy, and increased risk of disease. The agreement between the 2D and 3D assessments of BI-RADS density was high (K 0.96). A cut-off value of 21% is that which allows us to best discriminate between BI-RADS categories 1-2 and 3-4. Breast density was negatively correlated to age (r = -0.44) and positively to use of hormone therapy (p = 0.0004). Quantra density was higher in breasts with cancer than in healthy breasts. There is no clear difference between the visual assessments of density on 2D and 3D images. Use of the automated system requires the adoption of a cut-off value (set at 21%) to effectively discriminate BI-RADS 1-2 and 3-4, and could be useful in clinical practice.

  7. LIM mineralization protein-1 potentiates bone morphogenetic protein responsiveness via a novel interaction with Smurf1 resulting in decreased ubiquitination of Smads.

    PubMed

    Sangadala, Sreedhara; Boden, Scott D; Viggeswarapu, Manjula; Liu, Yunshan; Titus, Louisa

    2006-06-23

    Development and repair of the skeletal system and other organs is highly dependent on precise regulation of bone morphogenetic proteins (BMPs), their receptors, and their intracellular signaling proteins known as Smads. The use of BMPs clinically to induce bone formation has been limited in part by the requirement of much higher doses of recombinant proteins in primates than were needed in cell culture or rodents. Therefore, control of cellular responsiveness to BMPs is now a critical area that is poorly understood. We determined that LMP-1, a LIM domain protein capable of inducing de novo bone formation, interacts with Smurf1 (Smad ubiquitin regulatory factor 1) and prevents ubiquitination of Smads. In the region of LMP responsible for bone formation, there is a motif that directly interacts with the Smurf1 WW2 domain and can effectively compete with Smad1 and Smad5 for binding. We have shown that small peptides containing this motif can mimic the ability to block Smurf1 from binding Smads. This novel interaction of LMP-1 with the WW2 domain of Smurf1 to block Smad binding results in increased cellular responsiveness to exogenous BMP and demonstrates a novel regulatory mechanism for the BMP signaling pathway.

  8. Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action

    PubMed Central

    Wallner, Jürgen; Hochegger, Kerstin; Chen, Xiaojun; Mischak, Irene; Reinbacher, Knut; Pau, Mauro; Zrnc, Tomislav; Schwenzer-Zimmerer, Katja; Zemann, Wolfgang; Schmalstieg, Dieter

    2018-01-01

    Introduction Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However—due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. Material and methods In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score and the Hausdorff distance. Results Overall semi-automatic GrowCut segmentation times were about one minute. Mean Dice Score values of over 85% and Hausdorff Distances below 33.5 voxel could be achieved between the algorithmic GrowCut-based segmentations and the manual generated ground truth schemes. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the two groups. Discussion Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Due to an open-source basis the used method could be

  9. Software testing

    NASA Astrophysics Data System (ADS)

    Price-Whelan, Adrian M.

    2016-01-01

    Now more than ever, scientific results are dependent on sophisticated software and analysis. Why should we trust code written by others? How do you ensure your own code produces sensible results? How do you make sure it continues to do so as you update, modify, and add functionality? Software testing is an integral part of code validation and writing tests should be a requirement for any software project. I will talk about Python-based tools that make managing and running tests much easier and explore some statistics for projects hosted on GitHub that contain tests.

  10. Software Smarts

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Under an SBIR (Small Business Innovative Research) contract with Johnson Space Center, Knowledge Based Systems Inc. (KBSI) developed an intelligent software environment for modeling and analyzing mission planning activities, simulating behavior, and, using a unique constraint propagation mechanism, updating plans with each change in mission planning activities. KBSI developed this technology into a commercial product, PROJECTLINK, a two-way bridge between PROSIm, KBSI's process modeling and simulation software and leading project management software like Microsoft Project and Primavera's SureTrak Project Manager.

  11. Software Metrics

    DTIC Science & Technology

    1988-12-01

    software development scene is often charac- c. SPQR Model-Jones terized by: * schedule and cost estimates that are gross-d. COPMO-Thebaut ly inaccurate, SEI...time c. SPQR Model-Jones (in seconds) is simply derived from E by dividing T. Capers Jones has developed a software cost by the Stroud number, S...estimation model called the Software Produc- T=E/S tivity, Quality, and Reliability ( SPQR ) model. The basic approach is similar to that of Boehm’s The value

  12. Software Reviews.

    ERIC Educational Resources Information Center

    Mathematics and Computer Education, 1988

    1988-01-01

    Presents reviews of six software packages. Includes (1) "Plain Vanilla Statistics"; (2) "MathCAD 2.0"; (3) "GrFx"; (4) "Trigonometry"; (5) "Algebra II"; (6) "Algebra Drill and Practice I, II, and III." (PK)

  13. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1987-01-01

    Provides a review of four science software programs. Includes topics such as plate tectonics, laboratory experiment simulations, the human body, and light and temperature. Contains information on ordering and reviewers' comments. (ML)

  14. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Eugene T., Ed.

    1988-01-01

    Presents reviews by classroom teachers of software for teaching science. Includes material on the work of geologists, genetics, earth science, classification of living things, astronomy, endangered species, skeleton, drugs, and heartbeat. Provides information on availability and equipment needed. (RT)

  15. Software Reviews.

    ERIC Educational Resources Information Center

    Davis, Shelly J., Ed.; Knaupp, Jon, Ed.

    1984-01-01

    Reviewed is computer software on: (1) classification of living things, a tutorial program for grades 5-10; and (2) polynomial practice using tiles, a drill-and-practice program for algebra students. (MNS)

  16. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1987-01-01

    Reviews seven computer software programs that can be used in science education programs. Describes courseware which deals with muscles and bones, terminology, classifying animals without backbones, molecular structures, drugs, genetics, and shaping the earth's surface. (TW)

  17. Software Reviews.

    ERIC Educational Resources Information Center

    Kimball, Jeffrey P.; And Others

    1987-01-01

    Describes a variety of computer software. The packages reviewed include a variety of simulations, a spread sheet, a printer driver and an alternative operating system for DBM.PCs and compatible programs. (BSR)

  18. Software Reviews.

    ERIC Educational Resources Information Center

    Classroom Computer Learning, 1988

    1988-01-01

    Provides reviews of three software packages including "MusicShapes,""For Comment," and "Colortrope," which were developed for music, writing, and science, respectively. Includes information on grade levels, publishers, hardware needed, and cost. (TW)

  19. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1990-01-01

    Reviewed are six computer software packages including "Lunar Greenhouse,""Dyno-Quest,""How Weather Works,""Animal Trackers,""Personal Science Laboratory," and "The Skeletal and Muscular Systems." Availability, functional, and hardware requirements are discussed. (CW)

  20. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1987-01-01

    Provides reviews of six computer software programs designed for use in elementary science education programs. Provides the title, publisher, grade level, and descriptions of courseware on ant farms, drugs, genetics, beachcombing, matter, and test generation. (TW)

  1. Software Reviews.

    ERIC Educational Resources Information Center

    Dwyer, Donna; And Others

    1989-01-01

    Reviewed are seven software packages for Apple and IBM computers. Included are: "Toxicology"; "Science Corner: Space Probe"; "Alcohol and Pregnancy"; "Science Tool Kit Plus"; Computer Investigations: Plant Growth"; "Climatrolls"; and "Animal Watch: Whales." (CW)

  2. Software Reviews.

    ERIC Educational Resources Information Center

    Miller, Anne, Ed.; Radziemski, Cathy, Ed.

    1988-01-01

    Three pieces of computer software are described and reviewed: HyperCard, to build and use varied applications; Iggy's Gnees, for problem solving with shapes in grades kindergarten-two; and Algebra Shop, for practicing skills and problem solving. (MNS)

  3. Software Reviews.

    ERIC Educational Resources Information Center

    Classroom Computer Learning, 1990

    1990-01-01

    Reviewed are three computer software packages including "Martin Luther King, Jr.: Instant Replay of History,""Weeds to Trees," and "The New Print Shop, School Edition." Discussed are hardware requirements, costs, grade levels, availability, emphasis, strengths, and weaknesses. (CW)

  4. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1988-01-01

    Reviews seven instructional software packages covering a variety of topics. Includes: "Science Square-Off"; "The Desert"; "Science Courseware: Physical Science"; "Odell Lake"; "Safety First"; "An Experience in Artificial Intelligence"; and "Master Mapper." (TW)

  5. LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.

    PubMed

    Cañada, Andres; Capella-Gutierrez, Salvador; Rabal, Obdulia; Oyarzabal, Julen; Valencia, Alfonso; Krallinger, Martin

    2017-07-03

    A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions. It integrates a range of text mining, named entity recognition and information extraction components. LimTox relies on machine-learning, rule-based, pattern-based and term lookup strategies. This system processes scientific abstracts, a set of full text articles and medical agency assessment reports. Although the main focus of LimTox is on adverse liver events, it enables also basic searches for other organ level toxicity associations (nephrotoxicity, cardiotoxicity, thyrotoxicity and phospholipidosis). This tool supports specialized search queries for: chemical compounds/drugs, genes (with additional emphasis on key enzymes in drug metabolism, namely P450 cytochromes-CYPs) and biochemical liver markers. The LimTox website is free and open to all users and there is no login requirement. LimTox can be accessed at: http://limtox.bioinfo.cnio.es. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

    PubMed Central

    Cañada, Andres; Rabal, Obdulia; Oyarzabal, Julen; Valencia, Alfonso

    2017-01-01

    Abstract A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions. It integrates a range of text mining, named entity recognition and information extraction components. LimTox relies on machine-learning, rule-based, pattern-based and term lookup strategies. This system processes scientific abstracts, a set of full text articles and medical agency assessment reports. Although the main focus of LimTox is on adverse liver events, it enables also basic searches for other organ level toxicity associations (nephrotoxicity, cardiotoxicity, thyrotoxicity and phospholipidosis). This tool supports specialized search queries for: chemical compounds/drugs, genes (with additional emphasis on key enzymes in drug metabolism, namely P450 cytochromes—CYPs) and biochemical liver markers. The LimTox website is free and open to all users and there is no login requirement. LimTox can be accessed at: http://limtox.bioinfo.cnio.es PMID:28531339

  7. Astronomy Software

    NASA Technical Reports Server (NTRS)

    1995-01-01

    Software Bisque's TheSky, SkyPro and Remote Astronomy Software incorporate technology developed for the Hubble Space Telescope. TheSky and SkyPro work together to orchestrate locating, identifying and acquiring images of deep sky objects. With all three systems, the user can directly control computer-driven telescopes and charge coupled device (CCD) cameras through serial ports. Through the systems, astronomers and students can remotely operate a telescope at the Mount Wilson Observatory Institute.

  8. Validation in daily clinical situations of Diascope®, a software developed to help healthcare professionals individualize antidiabetic treatment in type 2 diabetes.

    PubMed

    Ampudia-Blasco, Francisco Javier; García-Soidán, Francisco Javier; Rubio Sánchez, Manuela; Phan, Tra-Mi

    2017-03-01

    DiaScope ® is a software to help in individualized prescription of antidiabetic treatment in type 2 diabetes. This study assessed its value and acceptability by different professionals. DiaScope ® was developed based on the ADA-EASD 2012 algorithm and on the recommendation of 12 international diabetes experts using the RAND/UCLA appropriateness method. The current study was performed at a single session. In the first phase, 5 clinical scenarios were evaluated, selecting the most appropriated therapeutic option among 4 possibilities (initial test). In a second phase, the same clinical cases were evaluated with DiaScope ® (final test).Opinion surveys on DiaScope ® were also performed (questionnaire). DiaScope ® changed the selected option 1 or more times in 70.5% of cases. Among 275 evaluated questionnaires, 54.0% strongly agree that DiaScope ® allowed finding easily a similar therapeutic scenario to the corresponding patient, and 52.5 among the obtained answers were clinically plausible. Up to 58.3% will recommend it to a colleague. In particular, primary care physicians with >20 years of professional dedication found with DiaScope ® the most appropriate option for a particular situation against specialists or those with less professional dedication (p<.05). DiaScope ® is an easy to use tool for antidiabetic drug prescription that provides plausible solutions and is especially useful for primary care physicians with more years of professional practice. Copyright © 2017 SEEN. Publicado por Elsevier España, S.L.U. All rights reserved.

  9. [Final clinical indications and etiology in 1,023 enucleations. Descriptive databank evaluation with SPSS software in variable response mode with dummy variables].

    PubMed

    Becker, H; Bialasiewicz, A A; Schaudig, U; Schäfer, H; von Domarus, D

    2002-05-01

    A new data bank developed for ophthalmopathology using a computer-generated, multidigital data code is expected to be able to accomplish complex clinicopathologic correlations of diagnoses and signs, as provided by (multiple) clinical events and histopathologically proven etiologies, and to facilitate the documentation of new data. In the ophthalmopathology laboratory 2890 eyes were examined between January 20, 1975 and December 12, 1996. The main diagnoses and patient data from this 22-year period were recorded. To facilitate the presentation of data, a 10-year period with eyes of 976 patients enucleated from December, 1986 to December, 1996 was chosen. Principal and secondary diagnoses served for establishing the data bank. The frequencies of successive histologic and clinical diagnoses were evaluated by a descriptive computing program using an SPSS-multi-response mode with dummy variables and a categorical variable listing of the software (SPSS version 10.0) classified as (a) non-filtered random, (b) filtered by multiple etiologies, and (c) filtered by multiple events. The principal groups (e.g., histologic diagnoses concerning etiology) and subgroups (e.g., trauma, neoplasia, surgery, systemic diseases, and inflammations) were defined and correlated with 798 separate diagnoses. From 11 diagnoses/events ascribed to the clinical cases, 11,198 namings resulted. Thus, a comparative study of complex etiologies and events leading to enucleation in different hospitals of a specific area may be performed using this electronic ophthalmopathologic data bank system. The complexity of rare disease and integration into a superimposed structure can be managed with this custom-made data bank. A chronologically and demographically oriented consideration of reasons for enucleation is thus feasible.

  10. Software reengineering

    NASA Technical Reports Server (NTRS)

    Fridge, Ernest M., III

    1991-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

  11. Software engineering

    NASA Technical Reports Server (NTRS)

    Fridge, Ernest M., III; Hiott, Jim; Golej, Jim; Plumb, Allan

    1993-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. The Johnson Space Center (JSC) created a significant set of tools to develop and maintain FORTRAN and C code during development of the space shuttle. This tool set forms the basis for an integrated environment to reengineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. The latest release of the environment was in Feb. 1992.

  12. Architecture of a high-performance surgical guidance system based on C-arm cone-beam CT: software platform for technical integration and clinical translation

    NASA Astrophysics Data System (ADS)

    Uneri, Ali; Schafer, Sebastian; Mirota, Daniel; Nithiananthan, Sajendra; Otake, Yoshito; Reaungamornrat, Sureerat; Yoo, Jongheun; Stayman, J. Webster; Reh, Douglas; Gallia, Gary L.; Khanna, A. Jay; Hager, Gregory; Taylor, Russell H.; Kleinszig, Gerhard; Siewerdsen, Jeffrey H.

    2011-03-01

    Intraoperative imaging modalities are becoming more prevalent in recent years, and the need for integration of these modalities with surgical guidance is rising, creating new possibilities as well as challenges. In the context of such emerging technologies and new clinical applications, a software architecture for cone-beam CT (CBCT) guided surgery has been developed with emphasis on binding open-source surgical navigation libraries and integrating intraoperative CBCT with novel, application-specific registration and guidance technologies. The architecture design is focused on accelerating translation of task-specific technical development in a wide range of applications, including orthopaedic, head-and-neck, and thoracic surgeries. The surgical guidance system is interfaced with a prototype mobile C-arm for high-quality CBCT and through a modular software architecture, integration of different tools and devices consistent with surgical workflow in each of these applications is realized. Specific modules are developed according to the surgical task, such as: 3D-3D rigid or deformable registration of preoperative images, surgical planning data, and up-to-date CBCT images; 3D-2D registration of planning and image data in real-time fluoroscopy and/or digitally reconstructed radiographs (DRRs); compatibility with infrared, electromagnetic, and video-based trackers used individually or in hybrid arrangements; augmented overlay of image and planning data in endoscopic or in-room video; real-time "virtual fluoroscopy" computed from GPU-accelerated DRRs; and multi-modality image display. The platform aims to minimize offline data processing by exposing quantitative tools that analyze and communicate factors of geometric precision. The system was translated to preclinical phantom and cadaver studies for assessment of fiducial (FRE) and target registration error (TRE) showing sub-mm accuracy in targeting and video overlay within intraoperative CBCT. The work culminates in

  13. The LIM protein complex establishes a retinal circuitry of visual adaptation by regulating Pax6 α-enhancer activity

    PubMed Central

    Kim, Yeha; Lim, Soyeon; Ha, Taejeong; Song, You-Hyang; Sohn, Young-In; Park, Dae-Jin; Paik, Sun-Sook; Kim-Kaneyama, Joo-ri; Song, Mi-Ryoung; Leung, Amanda; Levine, Edward M; Kim, In-Beom; Goo, Yong Sook; Lee, Seung-Hee; Kang, Kyung Hwa; Kim, Jin Woo

    2017-01-01

    The visual responses of vertebrates are sensitive to the overall composition of retinal interneurons including amacrine cells, which tune the activity of the retinal circuitry. The expression of Paired-homeobox 6 (PAX6) is regulated by multiple cis-DNA elements including the intronic α-enhancer, which is active in GABAergic amacrine cell subsets. Here, we report that the transforming growth factor ß1-induced transcript 1 protein (Tgfb1i1) interacts with the LIM domain transcription factors Lhx3 and Isl1 to inhibit the α-enhancer in the post-natal mouse retina. Tgfb1i1-/- mice show elevated α-enhancer activity leading to overproduction of Pax6ΔPD isoform that supports the GABAergic amacrine cell fate maintenance. Consequently, the Tgfb1i1-/- mouse retinas show a sustained light response, which becomes more transient in mice with the auto-stimulation-defective Pax6ΔPBS/ΔPBS mutation. Together, we show the antagonistic regulation of the α-enhancer activity by Pax6 and the LIM protein complex is necessary for the establishment of an inner retinal circuitry, which controls visual adaptation. DOI: http://dx.doi.org/10.7554/eLife.21303.001 PMID:28139974

  14. The Drosophila muscle LIM protein, Mlp84B, cooperates with D-titin to maintain muscle structural integrity.

    PubMed

    Clark, Kathleen A; Bland, Jennifer M; Beckerle, Mary C

    2007-06-15

    Muscle LIM protein (MLP) is a cytoskeletal LIM-only protein expressed in striated muscle. Mutations in human MLP are associated with cardiomyopathy; however, the molecular mechanism by which MLP functions is not established. A Drosophila MLP homolog, mlp84B, displays many of the same features as the vertebrate protein, illustrating the utility of the fly for the study of MLP function. Animals lacking Mlp84B develop into larvae with a morphologically intact musculature, but the mutants arrest during pupation with impaired muscle function. Mlp84B displays muscle-specific expression and is a component of the Z-disc and nucleus. Preventing nuclear retention of Mlp84B does not affect its function, indicating that Mlp84B site of action is likely to be at the Z-disc. Within the Z-disc, Mlp84B is colocalized with the N-terminus of D-titin, a protein crucial for sarcomere organization and stretch mechanics. The mlp84B mutants phenotypically resemble weak D-titin mutants. Furthermore, reducing D-titin activity in the mlp84B background leads to pronounced enhancement of the mlp84B muscle defects and loss of muscle structural integrity. The genetic interactions between mlp84B and D-titin reveal a role for Mlp84B in maintaining muscle structural integrity that was not obvious from analysis of the mlp84B mutants themselves, and suggest Mlp84B and D-titin cooperate to stabilize muscle sarcomeres.

  15. Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer.

    PubMed

    Davila, Monica; Jhala, Darshana; Ghosh, Debashis; Grizzle, William E; Chakrabarti, Ratna

    2007-06-08

    LIM kinase 1 (LIMK1), a LIM domain containing serine/threonine kinase, modulates actin dynamics through inactivation of the actin depolymerizing protein cofilin. Recent studies have indicated an important role of LIMK1 in growth and invasion of prostate and breast cancer cells; however, the molecular mechanism whereby LIMK1 induces tumor progression is unknown. In this study, we investigated the effects of ectopic expression of LIMK1 on cellular morphology, cell cycle progression and expression profile of LIMK1 in prostate tumors. Ectopic expression of LIMK1 in benign prostatic hyperplasia cells (BPH), which naturally express low levels of LIMK1, resulted in appearance of abnormal mitotic spindles, multiple centrosomes and smaller chromosomal masses. Furthermore, a transient G1/S phase arrest and delayed G2/M progression was observed in BPH cells expressing LIMK1. When treated with chemotherapeutic agent Taxol, no metaphase arrest was noted in these cells. We have also noted increased nuclear staining of LIMK1 in tumors with higher Gleason Scores and incidence of metastasis. Our results show that increased expression of LIMK1 results in chromosomal abnormalities, aberrant cell cycle progression and alteration of normal cellular response to microtubule stabilizing agent Taxol; and that LIMK1 expression may be associated with cancerous phenotype of the prostate.

  16. Antiterrorist Software

    NASA Technical Reports Server (NTRS)

    Clark, David A.

    1998-01-01

    In light of the escalation of terrorism, the Department of Defense spearheaded the development of new antiterrorist software for all Government agencies by issuing a Broad Agency Announcement to solicit proposals. This Government-wide competition resulted in a team that includes NASA Lewis Research Center's Computer Services Division, who will develop the graphical user interface (GUI) and test it in their usability lab. The team launched a program entitled Joint Sphere of Security (JSOS), crafted a design architecture (see the following figure), and is testing the interface. This software system has a state-ofthe- art, object-oriented architecture, with a main kernel composed of the Dynamic Information Architecture System (DIAS) developed by Argonne National Laboratory. DIAS will be used as the software "breadboard" for assembling the components of explosions, such as blast and collapse simulations.

  17. Control Software

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Real-Time Innovations, Inc. (RTI) collaborated with Ames Research Center, the Jet Propulsion Laboratory and Stanford University to leverage NASA research to produce ControlShell software. RTI is the first "graduate" of Ames Research Center's Technology Commercialization Center. The ControlShell system was used extensively on a cooperative project to enhance the capabilities of a Russian-built Marsokhod rover being evaluated for eventual flight to Mars. RTI's ControlShell is complex, real-time command and control software, capable of processing information and controlling mechanical devices. One ControlShell tool is StethoScope. As a real-time data collection and display tool, StethoScope allows a user to see how a program is running without changing its execution. RTI has successfully applied its software savvy in other arenas, such as telecommunications, networking, video editing, semiconductor manufacturing, automobile systems, and medical imaging.

  18. Reviews, Software.

    ERIC Educational Resources Information Center

    Science Teacher, 1988

    1988-01-01

    Reviews two software programs for Apple series computers. Includes "Orbital Mech," a basic planetary orbital simulation for the Macintosh, and "START: Stimulus and Response Tools for Experiments in Memory, Learning, Cognition, and Perception," a program that demonstrates basic psychological principles and experiments. (CW)

  19. Software Reviews.

    ERIC Educational Resources Information Center

    Science and Children, 1988

    1988-01-01

    Reviews six software packages for use with school age children ranging from grade 3 to grade 12. Includes "The Microcomputer Based Lab Project: Motion, Sound"; "Genetics"; "Geologic History"; "The Microscope Simulator"; and "Wiz Works" all for Apple II and "Reading for Information: Level…

  20. Software Review.

    ERIC Educational Resources Information Center

    McGrath, Diane, Ed.

    1989-01-01

    Reviewed is a computer software package entitled "Audubon Wildlife Adventures: Grizzly Bears" for Apple II and IBM microcomputers. Included are availability, hardware requirements, cost, and a description of the program. The murder-mystery flavor of the program is stressed in this program that focuses on illegal hunting and game…

  1. Software Reviews.

    ERIC Educational Resources Information Center

    Science and Children, 1990

    1990-01-01

    Reviewed are seven computer software packages for IBM and/or Apple Computers. Included are "Windows on Science: Volume 1--Physical Science"; "Science Probe--Physical Science"; "Wildlife Adventures--Grizzly Bears"; "Science Skills--Development Programs"; "The Clean Machine"; "Rock Doctor";…

  2. Software Reviews.

    ERIC Educational Resources Information Center

    Science Software Quarterly, 1984

    1984-01-01

    Provides extensive reviews of computer software, examining documentation, ease of use, performance, error handling, special features, and system requirements. Includes statistics, problem-solving (TK Solver), label printing, database management, experimental psychology, Encyclopedia Britannica biology, and DNA-sequencing programs. A program for…

  3. Software reengineering

    NASA Technical Reports Server (NTRS)

    Fridge, Ernest M., III

    1991-01-01

    Programs in use today generally have all of the function and information processing capabilities required to do their specified job. However, older programs usually use obsolete technology, are not integrated properly with other programs, and are difficult to maintain. Reengineering is becoming a prominent discipline as organizations try to move their systems to more modern and maintainable technologies. The Johnson Space Center (JSC) Software Technology Branch (STB) is researching and developing a system to support reengineering older FORTRAN programs into more maintainable forms that can also be more readily translated to a modern languages such as FORTRAN 8x, Ada, or C. This activity has led to the development of maintenance strategies for design recovery and reengineering. These strategies include a set of standards, methodologies, and the concepts for a software environment to support design recovery and reengineering. A brief description of the problem being addressed and the approach that is being taken by the STB toward providing an economic solution to the problem is provided. A statement of the maintenance problems, the benefits and drawbacks of three alternative solutions, and a brief history of the STB experience in software reengineering are followed by the STB new FORTRAN standards, methodology, and the concepts for a software environment.

  4. Software Reviews.

    ERIC Educational Resources Information Center

    Science and Children, 1988

    1988-01-01

    Reviews five software packages for use with school age children. Includes "Science Toolkit Module 2: Earthquake Lab"; "Adaptations and Identification"; "Geoworld"; "Body Systems II Series: The Blood System: A Liquid of Life," all for Apple II, and "Science Courseware: Life Science/Biology" for…

  5. Reviews, Software.

    ERIC Educational Resources Information Center

    Science Teacher, 1988

    1988-01-01

    Reviews two computer software packages for use in physical science, physics, and chemistry classes. Includes "Physics of Model Rocketry" for Apple II, and "Black Box" for Apple II and IBM compatible computers. "Black Box" is designed to help students understand the concept of indirect evidence. (CW)

  6. Software Reviews.

    ERIC Educational Resources Information Center

    Kinnaman, Daniel E.; And Others

    1988-01-01

    Reviews four educational software packages for Apple, IBM, and Tandy computers. Includes "How the West was One + Three x Four,""Mavis Beacon Teaches Typing,""Math and Me," and "Write On." Reviews list hardware requirements, emphasis, levels, publisher, purchase agreements, and price. Discusses the strengths…

  7. Software Reviews.

    ERIC Educational Resources Information Center

    Wulfson, Stephen, Ed.

    1990-01-01

    Reviewed are six software packages for Apple and/or IBM computers. Included are "Autograph,""The New Game Show,""Science Probe-Earth Science,""Pollution Patrol,""Investigating Plant Growth," and "AIDS: The Investigation." Discussed are the grade level, function, availability, cost, and hardware requirements of each. (CW)

  8. Software Reviews.

    ERIC Educational Resources Information Center

    Bitter, Gary G., Ed.

    1989-01-01

    Reviews three software packages: (1) "Physics," tutorial, grades 11-12, Macintosh; (2) "Hands On Math: Volume I," interactive math exploration/simulation of manipulatives use, grades K-7, Apple II; and (3) "A.I.: An Experience with Artificial Intelligence," simulation, grades 5-12, Apple II. (MVL)

  9. Software Reviews.

    ERIC Educational Resources Information Center

    Science and Children, 1989

    1989-01-01

    Reviews of seven software packages are presented including "The Environment I: Habitats and EcoSystems; II Cycles and Interactions"; "Super Sign Maker"; "The Great Knowledge Race: Substance Abuse"; "Exploring Science: Temperature"; "Fast Food Calculator and RD Aide"; "The Human Body:…

  10. Software Patents.

    ERIC Educational Resources Information Center

    Burke, Edmund B.

    1994-01-01

    Outlines basic patent law information that pertains to computer software programs. Topics addressed include protection in other countries; how to obtain patents; kinds of patents; duration; classes of patentable subject matter, including machines and processes; patentability searches; experimental use prior to obtaining a patent; and patent…

  11. Software Reviews.

    ERIC Educational Resources Information Center

    Bitter, Gary G., Ed.

    1989-01-01

    Describes three software packages: (1) "MacMendeleev"--database/graphic display for chemistry, grades 10-12, Macintosh; (2) "Geometry One: Foundations"--geometry tutorial, grades 7-12, IBM; (3) "Mathematics Exploration Toolkit"--algebra and calculus tutorial, grades 8-12, IBM. (MVL)

  12. Software Reviews.

    ERIC Educational Resources Information Center

    Mathematics and Computer Education, 1987

    1987-01-01

    Presented are reviews of several microcomputer software programs. Included are reviews of: (1) Microstat (Zenith); (2) MathCAD (MathSoft); (3) Discrete Mathematics (True Basic); (4) CALCULUS (True Basic); (5) Linear-Kit (John Wiley); and (6) Geometry Sensei (Broderbund). (RH)

  13. Software Reviews.

    ERIC Educational Resources Information Center

    Teles, Elizabeth, Ed.; And Others

    1990-01-01

    Reviewed are two computer software packages for Macintosh microcomputers including "Phase Portraits," an exploratory graphics tool for studying first-order planar systems; and "MacMath," a set of programs for exploring differential equations, linear algebra, and other mathematical topics. Features, ease of use, cost, availability, and hardware…

  14. Software Reviews.

    ERIC Educational Resources Information Center

    McGrath, Diane, Ed.

    1989-01-01

    Reviewed are two computer software programs for Apple II computers on weather for upper elementary and middle school grades. "Weather" introduces the major factors (temperature, humidity, wind, and air pressure) affecting weather. "How Weather Works" uses simulation and auto-tutorial formats on sun, wind, fronts, clouds, and…

  15. Software Update.

    ERIC Educational Resources Information Center

    Currents, 2000

    2000-01-01

    A chart of 40 alumni-development database systems provides information on vendor/Web site, address, contact/phone, software name, price range, minimum suggested workstation/suggested server, standard reports/reporting tools, minimum/maximum record capacity, and number of installed sites/client type. (DB)

  16. Reviews: Software.

    ERIC Educational Resources Information Center

    Mackenzie, Norma N.; And Others

    1988-01-01

    Reviews four computer software packages including: "The Physical Science Series: Sound" which demonstrates making waves, speed of sound, doppler effect, and human hearing; "Andromeda" depicting celestial motions in any direction; "Biology Quiz: Humans" covering chemistry, cells, viruses, and human biology; and…

  17. Calculation Software

    NASA Technical Reports Server (NTRS)

    1994-01-01

    MathSoft Plus 5.0 is a calculation software package for electrical engineers and computer scientists who need advanced math functionality. It incorporates SmartMath, an expert system that determines a strategy for solving difficult mathematical problems. SmartMath was the result of the integration into Mathcad of CLIPS, a NASA-developed shell for creating expert systems. By using CLIPS, MathSoft, Inc. was able to save the time and money involved in writing the original program.

  18. Survivable Software

    DTIC Science & Technology

    2013-04-01

    machine transitions. 2. We developed the TraceContract API for trace analysis in the Scala programming language. TraceContract combines a high-level...DATE (DD-MM-YYYY) 2. REPORT TYPE 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...awarded within the Software and Systems program . The original Pro- gram Manager was David Luginbuhl. Bob Bonneau took over as PM in March 2011. The award

  19. Comparative study of sea ice dynamics simulations with a Maxwell elasto-brittle rheology and the elastic-viscous-plastic rheology in NEMO-LIM3

    NASA Astrophysics Data System (ADS)

    Raulier, Jonathan; Dansereau, Véronique; Fichefet, Thierry; Legat, Vincent; Weiss, Jérôme

    2017-04-01

    Sea ice is a highly dynamical environment characterized by a dense mesh of fractures or leads, constantly opening and closing over short time scales. This characteristic geomorphology is linked to the existence of linear kinematic features, which consist of quasi-linear patterns emerging from the observed strain rate field of sea ice. Standard rheologies used in most state-of-the-art sea ice models, like the well-known elastic-viscous-plastic rheology, are thought to misrepresent those linear kinematic features and the observed statistical distribution of deformation rates. Dedicated rheologies built to catch the processes known to be at the origin of the formation of leads are developed but still need evaluations on the global scale. One of them, based on a Maxwell elasto-brittle formulation, is being integrated in the NEMO-LIM3 global ocean-sea ice model (www.nemo-ocean.eu; www.elic.ucl.ac.be/lim). In the present study, we compare the results of the sea ice model LIM3 obtained with two different rheologies: the elastic-viscous-plastic rheology commonly used in LIM3 and a Maxwell elasto-brittle rheology. This comparison is focused on the statistical characteristics of the simulated deformation rate and on the ability of the model to reproduce the existence of leads within the ice pack. The impact of the lead representation on fluxes between ice, atmosphere and ocean is also assessed.

  20. Space Station Software Issues

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor); Beskenis, S. (Editor)

    1985-01-01

    Issues in the development of software for the Space Station are discussed. Software acquisition and management, software development environment, standards, information system support for software developers, and a future software advisory board are addressed.

  1. Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies.

    PubMed

    Milisavljevic, Marko; Hearty, Taryn; Wong, Tony Y T; Portales-Casamar, Elodie; Simpson, Elizabeth M; Wasserman, Wyeth W

    2010-06-01

    Laboratory Animal Management Assistant (LAMA) is an internet-based system for tracking large laboratory mouse colonies. It has a user-friendly interface with powerful search capabilities that ease day-to-day tasks such as tracking breeding cages and weaning litters. LAMA was originally developed to manage hundreds of new mouse strains generated by a large functional genomics program, the Pleiades Promoter Project ( http://www.pleiades.org ). The software system has proven to be highly flexible, suitable for diverse management approaches to mouse colonies. It allows custom tagging and grouping of animals, simplifying project-specific handling and access to data. Finally, LAMA was developed in close collaboration with mouse technicians to ease the transition from paper- or Excel-based management systems to computerized tracking, allowing data export in a popular spreadsheet format and automatic printing of cage cards. LAMA is an open-access software tool, freely available to the research community at http://launchpad.net/mousedb .

  2. LIM Protein Ajuba associates with the RPA complex through direct cell cycle-dependent interaction with the RPA70 subunit.

    PubMed

    Fowler, Sandy; Maguin, Pascal; Kalan, Sampada; Loayza, Diego

    2018-06-22

    DNA damage response pathways are essential for genome stability and cell survival. Specifically, the ATR kinase is activated by DNA replication stress. An early event in this activation is the recruitment and phosphorylation of RPA, a single stranded DNA binding complex composed of three subunits, RPA70, RPA32 and RPA14. We have previously shown that the LIM protein Ajuba associates with RPA, and that depletion of Ajuba leads to potent activation of ATR. In this study, we provide evidence that the Ajuba-RPA interaction occurs through direct protein contact with RPA70, and that their association is cell cycle-regulated and is reduced upon DNA replication stress. We propose a model in which Ajuba negatively regulates the ATR pathway by directly interacting with RPA70, thereby preventing inappropriate ATR activation. Our results provide a framework to further our understanding of the mechanism of ATR regulation in human cells in the context of cellular transformation.

  3. SU-G-JeP2-06: Dosimetric and Workflow Evaluation of First Commercial Synthetic CT Software for Clinical Use in Pelvis

    SciTech Connect

    Tyagi, N; Zhang, J; Happersett, L

    2016-06-15

    Purpose: evaluate a commercial synthetic CT (syn-CT) software for use in prostate radiotherapy Methods: Twenty prostate patients underwent CT and MR simulation scans in treatment position on a 3T Philips scanner. The MR protocol consisted of a T2w turbo spin-echo for soft tissue contrast, a 2D balanced-fast field echo (b-FFE) for fiducial identification, a dual-echo 3D FFE B0 map for distortion analysis and a 3D mDIXON FFE sequence to generate syn-CT. Two echoes are acquired during mDIXON scan, allowing water, fat, and in-phase images to be derived using the frequency shift of the fat and water protons. Tissues were classifiedmore » as: air, adipose, water, trabecular/spongy bone and compact/cortical bone and assigned specific bulk HU values. Bone structures are segmented based on a pelvis bone atlas. Accuracy of syn-CT for patient treatment planning was analyzed by transferring the original plan and structures from the CT to syn-CT via rigid registration and recalculating dose. In addition, new IMRT plans were generated on the syn-CT using structures contoured on MR and transferred to the syn-CT. Accuracy of fiducial-based localization at the treatment machine performed using syn-CT or DRRs generated from syn-CT was assessed by comparing to orthogonal kV radiographs or CBCT. Results: Dosimetric comparison between CT and syn-CT was within 0.5% for all structures. The de-novo optimized plans generated on the syn-CT met our institutional clinical objectives for target and normal structures. Patient-induced susceptibility distortion based on B0 maps was within 1mm and 0.4 mm in the body and prostate. The rectal and bladder outlines on the syn-CT were deemed sufficient for assessing rectal and bladder filling on the CBCT at the time of treatment. CBCT localization showed a median error of < ±1 mm in LR, AP and SI direction. Conclusion: MRI derived syn-CT can be used clinically in MR-alone planning and treatment process for prostate. Drs. Deasy, Hunt and Tyagi have

  4. Software Prototyping

    PubMed Central

    Del Fiol, Guilherme; Hanseler, Haley; Crouch, Barbara Insley; Cummins, Mollie R.

    2016-01-01

    Summary Background Health information exchange (HIE) between Poison Control Centers (PCCs) and Emergency Departments (EDs) could improve care of poisoned patients. However, PCC information systems are not designed to facilitate HIE with EDs; therefore, we are developing specialized software to support HIE within the normal workflow of the PCC using user-centered design and rapid prototyping. Objective To describe the design of an HIE dashboard and the refinement of user requirements through rapid prototyping. Methods Using previously elicited user requirements, we designed low-fidelity sketches of designs on paper with iterative refinement. Next, we designed an interactive high-fidelity prototype and conducted scenario-based usability tests with end users. Users were asked to think aloud while accomplishing tasks related to a case vignette. After testing, the users provided feedback and evaluated the prototype using the System Usability Scale (SUS). Results Survey results from three users provided useful feedback that was then incorporated into the design. After achieving a stable design, we used the prototype itself as the specification for development of the actual software. Benefits of prototyping included having 1) subject-matter experts heavily involved with the design; 2) flexibility to make rapid changes, 3) the ability to minimize software development efforts early in the design stage; 4) rapid finalization of requirements; 5) early visualization of designs; 6) and a powerful vehicle for communication of the design to the programmers. Challenges included 1) time and effort to develop the prototypes and case scenarios; 2) no simulation of system performance; 3) not having all proposed functionality available in the final product; and 4) missing needed data elements in the PCC information system. PMID:27081404

  5. Simulation Software

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Various NASA Small Business Innovation Research grants from Marshall Space Flight Center, Langley Research Center and Ames Research Center were used to develop the 'kernel' of COMCO's modeling and simulation software, the PHLEX finite element code. NASA needed it to model designs of flight vehicles; one of many customized commercial applications is UNISIM, a PHLEX-based code for analyzing underground flows in oil reservoirs for Texaco, Inc. COMCO's products simulate a computational mechanics problem, estimate the solution's error and produce the optimal hp-adapted mesh for the accuracy the user chooses. The system is also used as a research or training tool in universities and in mechanical design in industrial corporations.

  6. Analysis Software

    NASA Technical Reports Server (NTRS)

    1994-01-01

    General Purpose Boundary Element Solution Technology (GPBEST) software employs the boundary element method of mechanical engineering analysis, as opposed to finite element. It is, according to one of its developers, 10 times faster in data preparation and more accurate than other methods. Its use results in less expensive products because the time between design and manufacturing is shortened. A commercial derivative of a NASA-developed computer code, it is marketed by Best Corporation to solve problems in stress analysis, heat transfer, fluid analysis and yielding and cracking of solids. Other applications include designing tractor and auto parts, household appliances and acoustic analysis.

  7. Software system safety

    NASA Technical Reports Server (NTRS)

    Uber, James G.

    1988-01-01

    Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

  8. The terminal basal mitosis of chicken retinal Lim1 horizontal cells is not sensitive to cisplatin-induced cell cycle arrest.

    PubMed

    Shirazi Fard, Shahrzad; Thyselius, Malin; All-Ericsson, Charlotta; Hallböök, Finn

    2014-01-01

    For proper development, cells need to coordinate proliferation and cell cycle-exit. This is mediated by a cascade of proteins making sure that each phase of the cell cycle is controlled before the initiation of the next. Retinal progenitor cells divide during the process of interkinetic nuclear migration, where they undergo S-phase on the basal side, followed by mitoses on the apical side of the neuroepithelium. The final cell cycle of chicken retinal horizontal cells (HCs) is an exception to this general cell cycle behavior. Lim1 expressing (+) horizontal progenitor cells (HPCs) have a heterogenic final cell cycle, with some cells undergoing a terminal mitosis on the basal side of the retina. The results in this study show that this terminal basal mitosis of Lim1+ HPCs is not dependent on Chk1/2 for its regulation compared to retinal cells undergoing interkinetic nuclear migration. Neither activating nor blocking Chk1 had an effect on the basal mitosis of Lim1+ HPCs. Furthermore, the Lim1+ HPCs were not sensitive to cisplatin-induced DNA damage and were able to continue into mitosis in the presence of γ-H2AX without activation of caspase-3. However, Nutlin3a-induced expression of p21 did reduce the mitoses, suggesting the presence of a functional p53/p21 response in HPCs. In contrast, the apical mitoses were blocked upon activation of either Chk1/2 or p21, indicating the importance of these proteins during the process of interkinetic nuclear migration. Inhibiting Cdk1 blocked M-phase transition both for apical and basal mitoses. This confirmed that the cyclin B1-Cdk1 complex was active and functional during the basal mitosis of Lim1+ HPCs. The regulation of the final cell cycle of Lim1+ HPCs is of particular interest since it has been shown that the HCs are able to sustain persistent DNA damage, remain in the cell cycle for an extended period of time and, consequently, survive for months.

  9. Avoidable Software Procurements

    DTIC Science & Technology

    2012-09-01

    software license, software usage, ELA, Software as a Service , SaaS , Software Asset...PaaS Platform as a Service SaaS Software as a Service SAM Software Asset Management SMS System Management Server SEWP Solutions for Enterprise Wide...delivery of full Cloud Services , we will see the transition of the Cloud Computing service model from Iaas to SaaS , or Software as a Service . Software

  10. Evaluation of the Vitek Card GPS105 and VTK-RO7.01 Software for Detection of Oxacillin Resistance in Clinically Relevant Coagulase-Negative Staphylococci

    PubMed Central

    Martinez, Fernando; Chandler, Laura J.; Reisner, Barbara S.; Woods, Gail L.

    2001-01-01

    The performance of Vitek cards GPS105 with software version VTK-R07.01 for detection of oxacillin resistance in coagulase-negative staphylococci (CoNS) was compared to disk diffusion and PCR detection for mecA. The sensitivity and specificity of the Vitek GPS105 method were 97.6 and 85.5%, respectively. PMID:11574604

  11. Desktop software to identify patients eligible for recruitment into a clinical trial: using SARMA to recruit to the ROAD feasibility trial.

    PubMed

    Treweek, Shaun; Pearson, Ewan; Smith, Natalie; Neville, Ron; Sargeant, Paul; Boswell, Brian; Sullivan, Frank

    2010-01-01

    Recruitment to trials in primary care is often difficult, particularly when practice staff need to identify study participants with acute conditions during consultations. The Scottish Acute Recruitment Management Application (SARMA) system is linked to general practice electronic medical record (EMR) systems and is designed to provide recruitment support to multi-centre trials by screening patients against trial inclusion criteria and alerting practice staff if the patient appears eligible. For patients willing to learn more about the trial, the software allows practice staff to send the patient's contact details to the research team by text message. To evaluate the ability of the software to support trial recruitment. Software evaluation embedded in a randomised controlled trial. Five general practices in Tayside and Fife, Scotland. SARMA was used to support recruitment to a feasibility trial (the Response to Oral Agents in Diabetes, or ROAD trial) looking at users of oral therapy in diabetes. The technical performance of the software and its utility as a recruitment tool were evaluated. The software was successfully installed at four of the five general practices and recruited 11 of the 29 participants for ROAD (other methods were letter and direct invitation by a practice nurse) and had a recruitment return of 35% (11 of 31 texts sent led to a recruitment). Screen failures were relatively low (7 of 31 referred). Practice staff members were positive about the system. An automated recruitment tool can support primary care trials in Scotland and has the potential to support recruitment in other jurisdictions. It offers a low-cost supplement to other trial recruitment methods and is likely to have a much lower screen failure rate than blanket approaches such as mailshots and newspaper campaigns.

  12. Office Computer Software: A Comprehensive Review of Software Programs.

    ERIC Educational Resources Information Center

    Secretary, 1992

    1992-01-01

    Describes types of software including system software, application software, spreadsheets, accounting software, graphics packages, desktop publishing software, database, desktop and personal information management software, project and records management software, groupware, and shareware. (JOW)

  13. The pH sensibility of actin-bundling LIM proteins is governed by the acidic properties of their C-terminal domain.

    PubMed

    Moes, Danièle; Hoffmann, Céline; Dieterle, Monika; Moreau, Flora; Neumann, Katrin; Papuga, Jessica; Furtado, Angela Tavares; Steinmetz, André; Thomas, Clément

    2015-08-19

    Actin-bundling Arabidopsis LIM proteins are subdivided into two subfamilies differing in their pH sensitivity. Widely-expressed WLIMs are active under low and high physiologically-relevant pH conditions, whereas pollen-enriched PLIMs are inactivated by pH values above 6.8. By a domain swapping approach we identified the C-terminal (Ct) domain of PLIMs as the domain responsible for pH responsiveness. Remarkably, this domain conferred pH sensitivity to LIM proteins, when provided "in trans" (i.e., as a single, independent, peptide), indicating that it operates through the interaction with another domain. An acidic 6xc-Myc peptide functionally mimicked the Ct domain of PLIMs and efficiently inhibited LIM actin bundling activity under high pH conditions. Together, our data suggest a model where PLIMs are regulated by an intermolecular interaction between their acidic Ct domain and another, yet unidentified, domain. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  14. Cytoskeleton-interacting LIM-domain protein CRP1 suppresses cell proliferation and protects from stress-induced cell death

    SciTech Connect

    Latonen, Leena; Jaervinen, Paeivi M.; Haartman Institute, University of Helsinki, FIN-00014 Helsinki

    2008-02-15

    Members of the cysteine-rich protein (CRP) family are actin cytoskeleton-interacting LIM-domain proteins known to act in muscle cell differentiation. We have earlier found that CRP1, a founding member of this family, is transcriptionally induced by UV radiation in human diploid fibroblasts [M. Gentile, L. Latonen, M. Laiho, Cell cycle arrest and apoptosis provoked by UV radiation-induced DNA damage are transcriptionally highly divergent responses, Nucleic Acids Res. 31 (2003) 4779-4790]. Here we show that CRP1 is induced by growth-inhibitory signals, such as increased cellular density, and cytotoxic stress induced by UV radiation or staurosporine. We found that high levels of CRP1more » correlate with differentiation-associated morphology towards the myofibroblast lineage and that expression of ectopic CRP1 suppresses cell proliferation. Following UV- and staurosporine-induced stresses, expression of CRP1 provides a survival advantage evidenced by decreased cellular death and increased cellular metabolic activity and attachment. Our studies identify that CRP1 is a novel stress response factor, and provide evidence for its growth-inhibitory and cytoprotective functions.« less

  15. Modeling and analysis of molecularinteraction between Smurf1-WW2 domain and various isoforms of LIM mineralization protein.

    PubMed

    Sangadala, Sreedhara; Boden, Scott D; Metpally, Raghu Prasad Rao; Reddy, Boojala Vijay B

    2007-08-15

    LIM Mineralization Protein-1 (LMP-1) has been cloned and shown to be osteoinductive. Our efforts to understand the mode of action of LMP-1 led to the determination that LMP-1 interacts with Smad Ubiquitin Regulatory Factor-1 (Smurf1). Smurf1 targets osteogenic Smads, Smad1/5, for ubiquitin-mediated proteasomal degradation. Smurf1 interaction with LMP-1 or Smads is based on the presence of unique WW-domain interacting motif in these target molecules. By performing site-directed mutagenesis and binding studies in vitro on purified recombinant proteins, we identified a specific motif within the osteogenic region of several LMP isoforms that is necessary for Smurf1 interaction. Similarly, we have identified that the WW2 domain of Smurf1 is necessary for target protein interaction. Here, we present a homology-based modeling of the Smurf1 WW2 domain and its interacting motif of LMP-1. We performed computational docking of the interacting domains in Smurf1 and LMPs to identify the key amino acid residues involved in their binding regions. In support of the computational predictions, we also present biochemical evidence supporting the hypothesis that the physical interaction of Smurf1 and osteoinductive forms of LMP may prevent Smurf1 from targeting osteogenic Smads by ubiquitin-mediated proteasomal degradation.

  16. Interactions between Arctic sea ice drift, concentration and thickness modeled by NEMO-LIM3 at different resolutions

    NASA Astrophysics Data System (ADS)

    Docquier, David; Massonnet, François; Raulier, Jonathan; Lecomte, Olivier; Fichefet, Thierry

    2016-04-01

    Sea ice concentration and thickness have substantially decreased in the Arctic since the beginning of the satellite era. As a result, mechanical strength has decreased allowing more fracturing and leading to increased sea ice drift. However, recent studies have highlighted that the interplay between sea ice thermodynamics and dynamics is poorly represented in contemporary global climate model (GCM) simulations. Thus, the considerable inter-model spread in terms of future sea ice extent projections could be reduced by better understanding the interactions between drift, concentration and thickness. This study focuses on the results coming from the global coupled ocean-sea ice model NEMO-LIM3 between 1979 and 2012. Three different simulations are forced by the Drakkar Forcing Set (DFS) 5.2 and run on the global tripolar ORCA grid at spatial resolutions of 0.25, 1° and 2°. The relation between modeled sea ice drift, concentration and thickness is further analyzed, compared to observations and discussed in the framework of the above-mentioned poor representation. It is proposed as a process-based metric for evaluating model performance. This study forms part of the EU Horizon 2020 PRIMAVERA project aiming at developing a new generation of advanced and well-evaluated high-resolution GCMs.

  17. Implications of the stratospheric water vapor distribution as determined from the Nimbus 7 LIMS experiment. [Limb Infrared Monitor of Stratosphere

    NASA Technical Reports Server (NTRS)

    Remsberg, E. E.; Russell, J. M., III; Gordley, L. L.; Gille, J. C.; Bailey, P. L.

    1984-01-01

    The LIMS experiment on Nimbus 7 has provided new results on the stratospheric water vapor distribution. The data show (1) a latitudinal gradient with mixing ratios that increase by a factor of 2 from equator to + or - 60 degrees at 50 mb, (2) most of the time there is a fairly uniform mixing ratio of 5 ppmv at high latitudes, but more variation exists during winter, (3) a well-developed hygropause at low to midlatitudes of the lower stratosphere, (4) a source region of water vapor in the upper stratospehere to lower mesosphere that is consistent with methane oxidation chemistry, at least within the uncertainties of the data, (5) an apparent zonal mean H2O distribution that is consistent with the circulation proposed by Brewer in 1949, and (6) a zonal mean distribution in the lower stratosphere that is consistent with the idea of quasi-isentropic transport by eddies in the meridional direction. Limits to the use of the data in the refinement of our understanding of the stratospheric water vapor budget are noted.

  18. Software Assurance Competency Model

    DTIC Science & Technology

    2013-03-01

    COTS) software , and software as a service ( SaaS ). L2: Define and analyze risks in the acquisition of contracted software , COTS software , and SaaS ...2010a]: Application of technologies and processes to achieve a required level of confidence that software systems and services function in the...

  19. PASSIM--an open source software system for managing information in biomedical studies.

    PubMed

    Viksna, Juris; Celms, Edgars; Opmanis, Martins; Podnieks, Karlis; Rucevskis, Peteris; Zarins, Andris; Barrett, Amy; Neogi, Sudeshna Guha; Krestyaninova, Maria; McCarthy, Mark I; Brazma, Alvis; Sarkans, Ugis

    2007-02-09

    One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management. We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project. The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.

  20. Software Library: A Reusable Software Issue.

    DTIC Science & Technology

    1984-06-01

    On reverse aide it neceeary aid Identify by block number) Software Library; Program Library; Reusability; Generator 20 ABSTRACT (Cmlnue on revere... Software Library. A particular example of the Software Library, the Program Library, is described as a prototype of a reusable library. A hierarchical... programming libraries are described. Finally, non code products in the Software Library are discussed. Accesson Fo NTIS R~jS DrrC TA Availability Codes 0

  1. Software attribute visualization for high integrity software

    SciTech Connect

    Pollock, G.M.

    1998-03-01

    This report documents a prototype tool developed to investigate the use of visualization and virtual reality technologies for improving software surety confidence. The tool is utilized within the execution phase of the software life cycle. It provides a capability to monitor an executing program against prespecified requirements constraints provided in a program written in the requirements specification language SAGE. The resulting Software Attribute Visual Analysis Tool (SAVAnT) also provides a technique to assess the completeness of a software specification.

  2. Selecting Software for Libraries.

    ERIC Educational Resources Information Center

    Beiser, Karl

    1993-01-01

    Discusses resources and strategies that libraries can use to evaluate competing database management software for purchase. Needs assessments, types of software available, features of good software, evaluation aids, shareware, and marketing and product trends are covered. (KRN)

  3. Report: Scientific Software.

    ERIC Educational Resources Information Center

    Borman, Stuart A.

    1985-01-01

    Discusses various aspects of scientific software, including evaluation and selection of commercial software products; program exchanges, catalogs, and other information sources; major data analysis packages; statistics and chemometrics software; and artificial intelligence. (JN)

  4. Space Flight Software Development Software for Intelligent System Health Management

    NASA Technical Reports Server (NTRS)

    Trevino, Luis C.; Crumbley, Tim

    2004-01-01

    The slide presentation examines the Marshall Space Flight Center Flight Software Branch, including software development projects, mission critical space flight software development, software technical insight, advanced software development technologies, and continuous improvement in the software development processes and methods.

  5. The LIM-homeodomain transcription factor LMX1B regulates expression of NF-kappa B target genes

    SciTech Connect

    Rascle, Anne; Neumann, Tanja; Raschta, Anne-Sarah

    2009-01-01

    LMX1B is a LIM-homeodomain transcription factor essential for development. Putative LMX1B target genes have been identified through mouse gene targeting studies, but their identity as direct LMX1B targets remains hypothetical. We describe here the first molecular characterization of LMX1B target gene regulation. Microarray analysis using a tetracycline-inducible LMX1B expression system in HeLa cells revealed that a subset of NF-{kappa}B target genes, including IL-6 and IL-8, are upregulated in LMX1B-expressing cells. Inhibition of NF-{kappa}B activity by short interfering RNA-mediated knock-down of p65 impairs, while activation of NF-{kappa}B activity by TNF-{alpha} synergizes induction of NF-{kappa}B target genes by LMX1B. Chromatin immunoprecipitation demonstratedmore » that LMX1B binds to the proximal promoter of IL-6 and IL-8 in vivo, in the vicinity of the characterized {kappa}B site, and that LMX1B recruitment correlates with increased NF-{kappa}B DNA association. IL-6 promoter-reporter assays showed that the {kappa}B site and an adjacent putative LMX1B binding motif are both involved in LMX1B-mediated transcription. Expression of NF-{kappa}B target genes is affected in the kidney of Lmx1b{sup -/-} knock-out mice, thus supporting the biological relevance of our findings. Together, these data demonstrate for the first time that LMX1B directly regulates transcription of a subset of NF-{kappa}B target genes in cooperation with nuclear p50/p65 NF-{kappa}B.« less

  6. Effects of different agricultural systems on soil quality in Northern Limón province, Costa Rica.

    PubMed

    Cornwell, Emma

    2014-09-01

    Conversion of native rainforest ecosystems in Limón Province of Costa Rica to banana and pineapple monoculture has led to reductions in biodiversity and soil quality. Agroforestry management of cacao (Theobroma cacao) is an alternative system that may maintain the agricultural livelihood of the region while more closely mimicking native ecosystems. This study compared physical, biological and chemical soil quality indicators of a cacao plantation under organic agroforestry management with banana, pineapple, and pasture systems; a native forest nearby served as a control. For bulk density and earthworm analysis, 18 samples were collected between March and April 2012 from each ecosystem paired with 18 samples from the cacao. Cacao had a lower bulk density than banana and pineapple monocultures, but greater than the forest (p < 0.05). Cacao also hosted a greater number and mass of earthworms than banana and pineapple (p < 0.05), but similar to forest and pasture. For soil chemical characteristics, three composite samples were collected in March 2012 from each agroecosystem paired with three samples from the cacao plantation. Forest and pineapple ecosystems had the lowest pH, cation exchange capacity, and exchangeable nutrient cations, while cacao had the greatest (p < 0.05). Total nutrient levels of P and N were slightly greater in banana, pineapple and pasture than in cacao; probably related to addition of chemical fertilizer and manure from cattle grazing. Forest and cacao also had greater %C, than other ecosystems, which is directly related to soil organic matter content (p < 0.0001). Overall, cacao had more favorable physical, biological and chemical soil characteristics than banana and pineapple monocultures, while trends were less conclusive compared to the pastureland. While organic cacao was inferior to native forest in some soil characteristics such as bulk density and organic carbon, its soil quality did best mimic that of the native forest. This supports

  7. Lmcd1/Dyxin, a novel Z-disc associated LIM protein, mediates cardiac hypertrophy in vitro and in vivo.

    PubMed

    Frank, Derk; Frauen, Robert; Hanselmann, Christiane; Kuhn, Christian; Will, Rainer; Gantenberg, Johanne; Füzesi, Laszlo; Katus, Hugo A; Frey, Norbert

    2010-10-01

    To identify new mediators of cardiac hypertrophy, we performed a genome-wide mRNA screen of stretched neonatal rat cardiomyocytes (NRCMs). In addition to known members of the hypertrophic gene program, we found the novel sarcomeric Z-disc LIM protein Lmcd1/Dyxin markedly upregulated. Consistently, Lmcd1 was also induced in several mouse models of myocardial hypertrophy suggesting a causal role in cardiac hypertrophy. We overexpressed Lmcd1 in NRCM, which led to cardiomyocyte hypertrophy and induction of the hypertrophic gene program. Likewise, the calcineurin-responsive gene RCAN1-4 was found significantly upregulated. Conversely, knockdown of Lmcd1 blunted the response to hypertrophic stimuli such as stretch and phenylephrine (PE), suggesting that Lmcd1 is required for the hypertrophic response. Furthermore, PE-mediated activation of calcineurin was completely blocked by knockdown of Lmcd1. To confirm these results in vivo, we generated transgenic mice with cardiac-restricted overexpression of Lmcd1. Despite normal cardiac function, adult transgenic mice displayed significant cardiac hypertrophy, again accompanied by induction of hypertrophic marker genes such as ANF and alpha-skeletal actin. Likewise, Rcan1-4 was found upregulated. Moreover, when crossed with transgenic mice overexpressing constitutionally active calcineurin, Lmcd1 transgenic mice revealed an exacerbated cardiomyopathic phenotype with depressed contractile function and further increased cardiomyocyte hypertrophy. We show that the novel z-disc protein Lmcd1/Dyxin is significantly upregulated in several models of cardiac hypertrophy. Lmcd1/Dyxin potently induces cardiomyocyte hypertrophy both in vitro and in vivo, while knockdown of this molecule prevents hypertrophy. Mechanistically, Lmcd1/Dyxin appears to signal through the calcineurin pathway. Lmcd1/Dyxin may thus represent an attractive target for novel antihypertrophic strategies. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. Quantitative DNA methylation analysis of paired box gene 1 and LIM homeobox transcription factor 1 α genes in cervical cancer

    PubMed Central

    Xu, Ling; Xu, Jun; Hu, Zheng; Yang, Baohua; Wang, Lifeng; Lin, Xiao; Xia, Ziyin; Zhang, Zhiling; Zhu, Yunheng

    2018-01-01

    DNA methylation is associated with tumorigenesis and may act as a potential biomarker for detecting cervical cancer. The aim of the present study was to explore the methylation status of the paired box gene 1 (PAX1) and the LIM homeobox transcription factor 1 α (LMX1A) gene in a spectrum of cervical lesions in an Eastern Chinese population. This single-center study involved 121 patients who were divided into normal cervix (NC; n=28), low-grade squamous intraepithelial lesion (LSIL; n=32), high-grade squamous intraepithelial lesion (HSIL; n=34) and cervical squamous cell carcinoma (CSCC; n=27) groups, according to biopsy results. Following extraction and modification of the DNA, quantitative assessment of the PAX1 and LMX1A genes in exfoliated cells was performed using pyrosequencing analysis. Receiver operating characteristic (ROC) curves were generated to calculate the sensitivity and specificity of each parameter and cut-off values of the percentage of methylation reference (PMR) for differentiation diagnosis. Analysis of variance was used to identify differences among groups. The PMR of the two genes was significantly higher in the HSIL and CSCC groups compared with that in the NC and LSIL groups (P<0.001). ROC curve analysis demonstrated that the sensitivity, specificity and accuracy for detection of CSCC were 0.790, 0.837 and 0.809, respectively, using PAX1; and 0.633, 0.357 and 0.893, respectively, using LMX1A. These results indicated that quantitative PAX1 methylation demonstrates potential for cervical cancer screening, while further investigation is required to determine the potential of LMX1A methylation. PMID:29541217

  9. Context-specific function of the LIM homeobox 1 transcription factor in head formation of the mouse embryo.

    PubMed

    Fossat, Nicolas; Ip, Chi Kin; Jones, Vanessa J; Studdert, Joshua B; Khoo, Poh-Lynn; Lewis, Samara L; Power, Melinda; Tourle, Karin; Loebel, David A F; Kwan, Kin Ming; Behringer, Richard R; Tam, Patrick P L

    2015-06-01

    Lhx1 encodes a LIM homeobox transcription factor that is expressed in the primitive streak, mesoderm and anterior mesendoderm of the mouse embryo. Using a conditional Lhx1 flox mutation and three different Cre deleters, we demonstrated that LHX1 is required in the anterior mesendoderm, but not in the mesoderm, for formation of the head. LHX1 enables the morphogenetic movement of cells that accompanies the formation of the anterior mesendoderm, in part through regulation of Pcdh7 expression. LHX1 also regulates, in the anterior mesendoderm, the transcription of genes encoding negative regulators of WNT signalling, such as Dkk1, Hesx1, Cer1 and Gsc. Embryos carrying mutations in Pcdh7, generated using CRISPR-Cas9 technology, and embryos without Lhx1 function specifically in the anterior mesendoderm displayed head defects that partially phenocopied the truncation defects of Lhx1-null mutants. Therefore, disruption of Lhx1-dependent movement of the anterior mesendoderm cells and failure to modulate WNT signalling both resulted in the truncation of head structures. Compound mutants of Lhx1, Dkk1 and Ctnnb1 show an enhanced head truncation phenotype, pointing to a functional link between LHX1 transcriptional activity and the regulation of WNT signalling. Collectively, these results provide comprehensive insight into the context-specific function of LHX1 in head formation: LHX1 enables the formation of the anterior mesendoderm that is instrumental for mediating the inductive interaction with the anterior neuroectoderm and LHX1 also regulates the expression of factors in the signalling cascade that modulate the level of WNT activity. © 2015. Published by The Company of Biologists Ltd.

  10. Alternative splicing for members of human mosaic domain superfamilies. I. The CH and LIM domains containing group of proteins.

    PubMed

    Friedberg, Felix

    2009-05-01

    In this paper we examine (restricted to homo sapiens) the products resulting from gene duplication and the subsequent alternative splicing for the members of a multidomain group of proteins which possess the evolutionary conserved calponin homology CH domain, i.e. an "actin binding domain", as a singlet and which, in addition, contain the conserved cysteine rich double Zn finger possessing Lim domain, also as a singlet. Seven genes, resulting from gene duplications, were identified that code for seven group members for which pre-mRNAs appear to have undergone multiple alternative splicing: Mical 1, 2 and 3 are located on chromosomes 6q21, 11p15 and 22q11, respectively. The LMO7 gene is present on chromosome 13q22 and the LIMCH1 gene on chromosome 4p13. Micall1 is mapped to chromosome 22q13 and Micall2 to chromosome 7p22. Translated Gen/Bank ESTs suggest the existence of multiple products alternatively spliced from the pre-mRNAs encoded by these genes. Characteristic indicators of such splicing among the proteins derived from one gene must include containment of some common extensive 100% identical regions. In some instances only one exon might be partly or completely eliminated. Sometimes alternative splicing is also associated with an increased frequency of creation of an exon or part of an exon from an intron. Not only coding regions for the body of the protein but also for its N- or -C ends could be affected by the splicing. If created forms are merely beginning at different starting points but remain identical in sequence thereafter, their existence as products of alternate splicing must be questioned. In the splicings, described in this paper, multiple isoforms rather than a single isoform appear as products during the gene expression.

  11. Software Engineering Guidebook

    NASA Technical Reports Server (NTRS)

    Connell, John; Wenneson, Greg

    1993-01-01

    The Software Engineering Guidebook describes SEPG (Software Engineering Process Group) supported processes and techniques for engineering quality software in NASA environments. Three process models are supported: structured, object-oriented, and evolutionary rapid-prototyping. The guidebook covers software life-cycles, engineering, assurance, and configuration management. The guidebook is written for managers and engineers who manage, develop, enhance, and/or maintain software under the Computer Software Services Contract.

  12. Creating a Clinical Video-Conferencing Facility in a Security-Constrained Environment Using Open-Source AccessGrid Software and Consumer Hardware

    PubMed Central

    Terrazas, Enrique; Hamill, Timothy R.; Wang, Ye; Channing Rodgers, R. P.

    2007-01-01

    The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components. PMID:18693930

  13. Creating a clinical video-conferencing facility in a security-constrained environment using open-source AccessGrid software and consumer hardware.

    PubMed

    Terrazas, Enrique; Hamill, Timothy R; Wang, Ye; Channing Rodgers, R P

    2007-10-11

    The Department of Laboratory Medicine at the University of California, San Francisco (UCSF) has been split into widely separated facilities, leading to much time being spent traveling between facilities for meetings. We installed an open-source AccessGrid multi-media-conferencing system using (largely) consumer-grade equipment, connecting 6 sites at 5 separate facilities. The system was accepted rapidly and enthusiastically, and was inexpensive compared to alternative approaches. Security was addressed by aspects of the AG software and by local network administrative practices. The chief obstacles to deployment arose from security restrictions imposed by multiple independent network administration regimes, requiring a drastically reduced list of network ports employed by AG components.

  14. Software Configuration Management Guidebook

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The growth in cost and importance of software to NASA has caused NASA to address the improvement of software development across the agency. One of the products of this program is a series of guidebooks that define a NASA concept of the assurance processes which are used in software development. The Software Assurance Guidebook, SMAP-GB-A201, issued in September, 1989, provides an overall picture of the concepts and practices of NASA in software assurance. Lower level guidebooks focus on specific activities that fall within the software assurance discipline, and provide more detailed information for the manager and/or practitioner. This is the Software Configuration Management Guidebook which describes software configuration management in a way that is compatible with practices in industry and at NASA Centers. Software configuration management is a key software development process, and is essential for doing software assurance.

  15. Metal artifact reduction software used with abdominopelvic dual-energy CT of patients with metal hip prostheses: assessment of image quality and clinical feasibility.

    PubMed

    Han, Seung Chol; Chung, Yong Eun; Lee, Young Han; Park, Kwan Kyu; Kim, Myeong Jin; Kim, Ki Whang

    2014-10-01

    The objective of our study was to determine the feasibility of using Metal Artifact Reduction (MAR) software for abdominopelvic dual-energy CT in patients with metal hip prostheses. This retrospective study included 33 patients (male-female ratio, 19:14; mean age, 63.7 years) who received total hip replacements and 20 patients who did not have metal prostheses as the control group. All of the patients underwent dual-energy CT. The quality of the images reconstructed using the MAR algorithm and of those reconstructed using the standard reconstruction was evaluated in terms of the visibility of the bladder wall, pelvic sidewall, rectal shelf, and bone-prosthesis interface and the overall diagnostic image quality with a 4-point scale. The mean and SD attenuation values in Hounsfield units were measured in the bladder, pelvic sidewall, and rectal shelf. For validation of the MAR interpolation algorithm, pelvis phantoms with small bladder "lesions" and metal hip prostheses were made, and images of the phantoms both with and without MAR reconstruction were evaluated. Image quality was significantly better with MAR reconstruction than without at all sites except the rectal shelf, where the image quality either had not changed or had worsened after MAR reconstruction. The mean attenuation value was changed after MAR reconstruction to its original expected value at the pelvic sidewall (p < 0.001) and inside the bladder (p < 0.001). The SD attenuation value was significantly decreased after MAR reconstruction at the pelvic sidewall (p = 0.019) but did not show significant differences at the bladder (p = 0.173) or rectal shelf (p = 0.478). In the phantom study, all lesions obscured by metal artifacts on the standard reconstruction images were visualized after MAR reconstruction; however, new artifacts had developed in other parts of the MAR reconstruction images. The use of MAR software with dual-energy CT decreases metal artifacts and increases diagnostic confidence in the

  16. The Ras suppressor Rsu-1 binds to the LIM 5 domain of the adaptor protein PINCH1 and participates in adhesion-related functions

    SciTech Connect

    Dougherty, Gerard W.; Section on Structural Cell Biology, National Institute on Deafness and Communication Disorders; Chopp, Treasa

    2005-05-15

    Rsu-1 is a highly conserved leucine rich repeat (LRR) protein that is expressed ubiquitously in mammalian cells. Rsu-1 was identified based on its ability to inhibit transformation by Ras, and previous studies demonstrated that ectopic expression of Rsu-1 inhibited anchorage-independent growth of Ras-transformed cells and human tumor cell lines. Using GAL4-based yeast two-hybrid screening, the LIM domain protein, PINCH1, was identified as the binding partner of Rsu-1. PINCH1 is an adaptor protein that localizes to focal adhesions and it has been implicated in the regulation of adhesion functions. Subdomain mapping in yeast revealed that Rsu-1 binds to the LIM 5more » domain of PINCH1, a region not previously identified as a specific binding domain for any other protein. Additional testing demonstrated that PINCH2, which is highly homologous to PINCH1, except in the LIM 5 domain, does not interact with Rsu-1. Glutathione transferase fusion protein binding studies determined that the LRR region of Rsu-1 interacts with PINCH1. Transient expression studies using epitope-tagged Rsu-1 and PINCH1 revealed that Rsu-1 co-immunoprecipitated with PINCH1 and colocalized with vinculin at sites of focal adhesions in mammalian cells. In addition, endogenous P33 Rsu-1 from 293T cells co-immunoprecipitated with transiently expressed myc-tagged PINCH1. Furthermore, RNAi-induced reduction in Rsu-1 RNA and protein inhibited cell attachment, and while previous studies demonstrated that ectopic expression of Rsu-1 inhibited Jun kinase activation, the depletion of Rsu-1 resulted in activation of Jun and p38 stress kinases. These studies demonstrate that Rsu-1 interacts with PINCH1 in mammalian cells and functions, in part, by altering cell adhesion.« less

  17. Statistical Software Engineering

    DTIC Science & Technology

    1998-04-13

    multiversion software subject to coincident errors. IEEE Trans. Software Eng. SE-11:1511-1517. Eckhardt, D.E., A.K Caglayan, J.C. Knight, L.D. Lee, D.F...J.C. and N.G. Leveson. 1986. Experimental evaluation of the assumption of independence in multiversion software. IEEE Trans. Software

  18. Finding Helpful Software Reviews.

    ERIC Educational Resources Information Center

    Kruse, Ted, Comp.

    1987-01-01

    Provides a list of evaluation services currently producing critical reviews of educational software. Includes information about The Apple K-12 Curriculum Software Reference, The Educational Software Preview, The Educational Software Selector, MicroSIFT, and Only The Best: The Discriminating Guide for Preschool-Grade 12. (TW)

  19. Agile Software Development

    ERIC Educational Resources Information Center

    Biju, Soly Mathew

    2008-01-01

    Many software development firms are now adopting the agile software development method. This method involves the customer at every level of software development, thus reducing the impact of change in the requirement at a later stage. In this article, the principles of the agile method for software development are explored and there is a focus on…

  20. Software Engineering Education Directory

    DTIC Science & Technology

    1990-04-01

    and Engineering (CMSC 735) Codes: GPEV2 * Textiooks: IEEE Tutoria on Models and Metrics for Software Management and Engameeing by Basi, Victor R...Software Engineering (Comp 227) Codes: GPRY5 Textbooks: IEEE Tutoria on Software Design Techniques by Freeman, Peter and Wasserman, Anthony 1. Software

  1. Commercial Literacy Software.

    ERIC Educational Resources Information Center

    Balajthy, Ernest

    1997-01-01

    Presents the first year's results of a continuing project to monitor the availability of software of relevance for literacy education purposes. Concludes there is an enormous amount of software available for use by teachers of reading and literacy--whereas drill-and-practice software is the largest category of software available, large numbers of…

  2. Software Formal Inspections Standard

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This Software Formal Inspections Standard (hereinafter referred to as Standard) is applicable to NASA software. This Standard defines the requirements that shall be fulfilled by the software formal inspections process whenever this process is specified for NASA software. The objective of this Standard is to define the requirements for a process that inspects software products to detect and eliminate defects as early as possible in the software life cycle. The process also provides for the collection and analysis of inspection data to improve the inspection process as well as the quality of the software.

  3. Software For Computing Reliability Of Other Software

    NASA Technical Reports Server (NTRS)

    Nikora, Allen; Antczak, Thomas M.; Lyu, Michael

    1995-01-01

    Computer Aided Software Reliability Estimation (CASRE) computer program developed for use in measuring reliability of other software. Easier for non-specialists in reliability to use than many other currently available programs developed for same purpose. CASRE incorporates mathematical modeling capabilities of public-domain Statistical Modeling and Estimation of Reliability Functions for Software (SMERFS) computer program and runs in Windows software environment. Provides menu-driven command interface; enabling and disabling of menu options guides user through (1) selection of set of failure data, (2) execution of mathematical model, and (3) analysis of results from model. Written in C language.

  4. Neotectonics and paleoseismology of the Limón and pedro miguel faults in Panamá: earthquake hazard to the Panamá canal

    USGS Publications Warehouse

    Rockwell, Thomas; Gath, Edon; Gonzalez, Tania; Madden, Chris; Verdugo, Danielle; Lippincott, Caitlin; Dawson, Tim; Owen, Lewis A.; Fuchs, Markus; Cadena, Ana; Williams, Pat; Weldon, Elise; Franceschi, Pastora

    2010-01-01

    We present new geologic, tectonic geomorphic, and geochronologic data on the slip rate, timing, and size of past surface ruptures for the right-lateral Lim??n and Pedro Miguel faults in central Panam??. These faults are part of a system of conjugate faults that accommodate the internal deformation of Panam?? resulting from the ongoing collision of Central and South America. There have been at least three surface ruptures on the Lim??n fault in the past 950-1400 years, with the most recent during the past 365 years. Displacement in this young event is at least 1.2 m (based on trenching) and may be 1.6-2 m (based on small channel offsets). Awell-preserved 4.2 m offset suggests that the penultimate event also sustained significant displacement. The Holocene slip rate has averaged about 6 mm=yr, based on a 30-m offset terrace riser incised into a 5-ka abandoned channel. The Pedro Miguel fault has sustained three surface ruptures in the past 1600 years, the most recent being the 2 May 1621 earthquake that partially destroyed Panam?? Viejo. At least 2.1 m of slip occurred in this event near the Canal, with geomorphic offsets suggesting 2.5-3 m. The historic Camino de Cruces is offset 2.8 m, indicating multimeter displacement over at least 20 km of fault length. Channel offsets of 100-400 m, together with a climate-induced incision model, suggest a Late Quaternary slip rate of about 5 mm=yr, which is consistent with the paleoseismic results. Comparison of the timing of surface ruptures between the Lim??n and Pedro Miguel faults suggests that large earthquakes may rupture both faults with 2-3 m of displacement for over 40 km, such as is likely in earthquakes in the M 7 range. Altogether, our observations indicate that the Lim??n and Pedro Miguel faults represent a significant seismic hazard to central Panam?? and, specifically, to the Canal and Panam?? City.

  5. Comparison of direct selective versus nonselective agar media plus LIM broth enrichment for determination of group B streptococcus colonization status in pregnant women.

    PubMed

    Elsayed, Sameer; Gregson, Daniel B; Church, Deirdre L

    2003-06-01

    Group B streptococcus (GBS) is the most common cause of early-onset neonatal sepsis in developed countries, and determination of the GBS colonization status in pregnant patients near term is essential for the provision of prophylactic measures to prevent early-onset disease. To determine if GBS recovery rates and/or result turnaround times for vaginal or combined vaginal/rectal swab specimens from pregnant patients near term are enhanced if swabs are inoculated initially onto selective versus nonselective agar media, in addition to the standard Centers for Disease Control and Prevention method. Prospective laboratory analysis. Urban health region/centralized diagnostic microbiology laboratory. Pregnant women presenting for routine obstetrical care and collection of vaginal or combined vaginal/rectal swab specimens for GBS testing at 35 to 37 weeks' gestation. Culture of specimens directly onto selective (5% sheep blood with colistin and nalidixic acid) or nonselective (5% sheep blood) agar media, in addition to LIM broth enrichment and terminal subculture. Group B streptococcus recovery rate and culture result turnaround time. A total of 639 specimens were tested, with 128 (20%) positive for GBS. Sixty-three isolates were recovered on direct agar media at 24 hours, of which 16 (12.5%) were isolated on selective plates only. An additional 38 isolates were recovered at 48 hours from direct plates. Twenty-seven (21.1%) isolates that failed to grow on direct plates were recovered from the LIM broth subculture only. Three (2.3%) isolates not recovered from LIM broths were detected at 48 hours on the direct selective (2 isolates) and nonselective (1 isolate) agar plates. A 24-hour result turnaround time was achieved for 63 (49.2%) and 47 (36.7%) of the 128 culture-positive specimens for direct selective and nonselective plates, respectively (chi2 = 76.63, P <.001). Use of direct selective agar media, in addition to LIM broth enrichment, for the determination of the GBS

  6. An overview of wave-mean flow interactions during the winter of 1978-79 derived from LIMS observations. [Limb Infrared Monitor of Stratosphere

    NASA Technical Reports Server (NTRS)

    Gille, J. C.; Lyjak, L. V.

    1984-01-01

    Gradient winds, Eliassen-Palm (EP) fluxes and flux divergences, and the squared refractive index for planetary waves have been calculated from mapped data from the Limb Infrared Monitor of the Stratosphere (LIMS) experiment on Nimbus 7. The changes in the zonal mean atmospheric state, from early winter through 3 disturbances, is described. Convergence or divergence of the EP fluxes clearly produces changes in the zonal mean wind. The steering of the waves by the refractive index structure is not as clear on a daily basis.

  7. Detection of group B streptococci in Lim broth by use of group B streptococcus peptide nucleic acid fluorescent in situ hybridization and selective and nonselective agars.

    PubMed

    Montague, Naomi S; Cleary, Timothy J; Martinez, Octavio V; Procop, Gary W

    2008-10-01

    The sensitivity, specificity, and positive and negative predictive values for the detection of group B streptococci from Lim enrichment broth with sheep blood agar (SBA), with selective Streptococcus agar (SSA), and by a peptide nucleic acid fluorescent in situ hybridization (PNA FISH) assay were as follows: for culture on SBA, 68.4%, 100%, 100%, and 87.9%, respectively; for culture on SSA, 85.5%, 100%, 100%, and 94.1%, respectively; and for the PNA FISH assay, 97.4%, 98.3%, 96.1%, and 98.9%, respectively.

  8. Detection of Group B Streptococci in Lim Broth by Use of Group B Streptococcus Peptide Nucleic Acid Fluorescent In Situ Hybridization and Selective and Nonselective Agars▿

    PubMed Central

    Montague, Naomi S.; Cleary, Timothy J.; Martinez, Octavio V.; Procop, Gary W.

    2008-01-01

    The sensitivity, specificity, and positive and negative predictive values for the detection of group B streptococci from Lim enrichment broth with sheep blood agar (SBA), with selective Streptococcus agar (SSA), and by a peptide nucleic acid fluorescent in situ hybridization (PNA FISH) assay were as follows: for culture on SBA, 68.4%, 100%, 100%, and 87.9%, respectively; for culture on SSA, 85.5%, 100%, 100%, and 94.1%, respectively; and for the PNA FISH assay, 97.4%, 98.3%, 96.1%, and 98.9%, respectively. PMID:18667597

  9. Software component quality evaluation

    NASA Technical Reports Server (NTRS)

    Clough, A. J.

    1991-01-01

    The paper describes a software inspection process that can be used to evaluate the quality of software components. Quality criteria, process application, independent testing of the process and proposed associated tool support are covered. Early results indicate that this technique is well suited for assessing software component quality in a standardized fashion. With automated machine assistance to facilitate both the evaluation and selection of software components, such a technique should promote effective reuse of software components.

  10. Thermodynamic and dynamic ice thickness contributions in the Canadian Arctic Archipelago in NEMO-LIM2 numerical simulations

    NASA Astrophysics Data System (ADS)

    Hu, Xianmin; Sun, Jingfan; Chan, Ting On; Myers, Paul G.

    2018-04-01

    Sea ice thickness evolution within the Canadian Arctic Archipelago (CAA) is of great interest to science, as well as local communities and their economy. In this study, based on the NEMO numerical framework including the LIM2 sea ice module, simulations at both 1/4 and 1/12° horizontal resolution were conducted from 2002 to 2016. The model captures well the general spatial distribution of ice thickness in the CAA region, with very thick sea ice (˜ 4 m and thicker) in the northern CAA, thick sea ice (2.5 to 3 m) in the west-central Parry Channel and M'Clintock Channel, and thin ( < 2 m) ice (in winter months) on the east side of CAA (e.g., eastern Parry Channel, Baffin Island coast) and in the channels in southern areas. Even though the configurations still have resolution limitations in resolving the exact observation sites, simulated ice thickness compares reasonably (seasonal cycle and amplitudes) with weekly Environment and Climate Change Canada (ECCC) New Ice Thickness Program data at first-year landfast ice sites except at the northern sites with high concentration of old ice. At 1/4 to 1/12° scale, model resolution does not play a significant role in the sea ice simulation except to improve local dynamics because of better coastline representation. Sea ice growth is decomposed into thermodynamic and dynamic (including all non-thermodynamic processes in the model) contributions to study the ice thickness evolution. Relatively smaller thermodynamic contribution to ice growth between December and the following April is found in the thick and very thick ice regions, with larger contributions in the thin ice-covered region. No significant trend in winter maximum ice volume is found in the northern CAA and Baffin Bay while a decline (r2 ≈ 0.6, p < 0.01) is simulated in Parry Channel region. The two main contributors (thermodynamic growth and lateral transport) have high interannual variabilities which largely balance each other, so that maximum ice volume can

  11. Software Quality Assurance Metrics

    NASA Technical Reports Server (NTRS)

    McRae, Kalindra A.

    2004-01-01

    Software Quality Assurance (SQA) is a planned and systematic set of activities that ensures conformance of software life cycle processes and products conform to requirements, standards and procedures. In software development, software quality means meeting requirements and a degree of excellence and refinement of a project or product. Software Quality is a set of attributes of a software product by which its quality is described and evaluated. The set of attributes includes functionality, reliability, usability, efficiency, maintainability, and portability. Software Metrics help us understand the technical process that is used to develop a product. The process is measured to improve it and the product is measured to increase quality throughout the life cycle of software. Software Metrics are measurements of the quality of software. Software is measured to indicate the quality of the product, to assess the productivity of the people who produce the product, to assess the benefits derived from new software engineering methods and tools, to form a baseline for estimation, and to help justify requests for new tools or additional training. Any part of the software development can be measured. If Software Metrics are implemented in software development, it can save time, money, and allow the organization to identify the caused of defects which have the greatest effect on software development. The summer of 2004, I worked with Cynthia Calhoun and Frank Robinson in the Software Assurance/Risk Management department. My task was to research and collect, compile, and analyze SQA Metrics that have been used in other projects that are not currently being used by the SA team and report them to the Software Assurance team to see if any metrics can be implemented in their software assurance life cycle process.

  12. Software Engineering Program: Software Process Improvement Guidebook

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The purpose of this document is to provide experience-based guidance in implementing a software process improvement program in any NASA software development or maintenance community. This guidebook details how to define, operate, and implement a working software process improvement program. It describes the concept of the software process improvement program and its basic organizational components. It then describes the structure, organization, and operation of the software process improvement program, illustrating all these concepts with specific NASA examples. The information presented in the document is derived from the experiences of several NASA software organizations, including the SEL, the SEAL, and the SORCE. Their experiences reflect many of the elements of software process improvement within NASA. This guidebook presents lessons learned in a form usable by anyone considering establishing a software process improvement program within his or her own environment. This guidebook attempts to balance general and detailed information. It provides material general enough to be usable by NASA organizations whose characteristics do not directly match those of the sources of the information and models presented herein. It also keeps the ideas sufficiently close to the sources of the practical experiences that have generated the models and information.

  13. Software Defined Radio with Parallelized Software Architecture

    NASA Technical Reports Server (NTRS)

    Heckler, Greg

    2013-01-01

    This software implements software-defined radio procession over multicore, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to approx.50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.

  14. Software Defined Radio with Parallelized Software Architecture

    NASA Technical Reports Server (NTRS)

    Heckler, Greg

    2013-01-01

    This software implements software-defined radio procession over multi-core, multi-CPU systems in a way that maximizes the use of CPU resources in the system. The software treats each processing step in either a communications or navigation modulator or demodulator system as an independent, threaded block. Each threaded block is defined with a programmable number of input or output buffers; these buffers are implemented using POSIX pipes. In addition, each threaded block is assigned a unique thread upon block installation. A modulator or demodulator system is built by assembly of the threaded blocks into a flow graph, which assembles the processing blocks to accomplish the desired signal processing. This software architecture allows the software to scale effortlessly between single CPU/single-core computers or multi-CPU/multi-core computers without recompilation. NASA spaceflight and ground communications systems currently rely exclusively on ASICs or FPGAs. This software allows low- and medium-bandwidth (100 bps to .50 Mbps) software defined radios to be designed and implemented solely in C/C++ software, while lowering development costs and facilitating reuse and extensibility.

  15. Payload software technology: Software technology development plan

    NASA Technical Reports Server (NTRS)

    1977-01-01

    Programmatic requirements for the advancement of software technology are identified for meeting the space flight requirements in the 1980 to 1990 time period. The development items are described, and software technology item derivation worksheets are presented along with the cost/time/priority assessments.

  16. Space Station Software Recommendations

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor)

    1985-01-01

    Four panels of invited experts and NASA representatives focused on the following topics: software management, software development environment, languages, and software standards. Each panel deliberated in private, held two open sessions with audience participation, and developed recommendations for the NASA Space Station Program. The major thrusts of the recommendations were as follows: (1) The software management plan should establish policies, responsibilities, and decision points for software acquisition; (2) NASA should furnish a uniform modular software support environment and require its use for all space station software acquired (or developed); (3) The language Ada should be selected for space station software, and NASA should begin to address issues related to the effective use of Ada; and (4) The space station software standards should be selected (based upon existing standards where possible), and an organization should be identified to promulgate and enforce them. These and related recommendations are described in detail in the conference proceedings.

  17. Use of Mobile Clinical Decision Support Software by Junior Doctors at a UK Teaching Hospital: Identification and Evaluation of Barriers to Engagement.

    PubMed

    Patel, Rakesh; Green, William; Shahzad, Muhammad Waseem; Larkin, Chris

    2015-08-13

    Clinical decision support (CDS) tools improve clinical diagnostic decision making and patient safety. The availability of CDS to health care professionals has grown in line with the increased prevalence of apps and smart mobile devices. Despite these benefits, patients may have safety concerns about the use of mobile devices around medical equipment. This research explored the engagement of junior doctors (JDs) with CDS and the perceptions of patients about their use. There were three objectives for this research: (1) to measure the actual usage of CDS tools on mobile devices (mCDS) by JDs, (2) to explore the perceptions of JDs about the drivers and barriers to using mCDS, and (3) to explore the perceptions of patients about the use of mCDS. This study used a mixed-methods approach to study the engagement of JDs with CDS accessed through mobile devices. Usage data were collected on the number of interactions by JDs with mCDS. The perceived drivers and barriers for JDs to using CDS were then explored by interviews. Finally, these findings were contrasted with the perception of patients about the use of mCDS by JDs. Nine of the 16 JDs made a total of 142 recorded interactions with the mCDS over a 4-month period. Only 27 of the 114 interactions (24%) that could be categorized as on-shift or off-shift occurred on-shift. Eight individual, institutional, and cultural barriers to engagement emerged from interviews with the user group. In contrast to reported cautions and concerns about the impact of clinicians' use of mobile phone on patient health and safety, patients had positive perceptions about the use of mCDS. Patients reported positive perceptions toward mCDS. The usage of mCDS to support clinical decision making was considered to be positive as part of everyday clinical practice. The degree of engagement was found to be limited due to a number of individual, institutional, and cultural barriers. The majority of mCDS engagement occurred outside of the workplace

  18. Optimization and life-cycle cost of health clinic PV system for a rural area in southern Iraq using HOMER software

    SciTech Connect

    Al-Karaghouli, Ali; Kazmerski, L.L.

    2010-04-15

    This paper addresses the need for electricity of rural areas in southern Iraq and proposes a photovoltaic (PV) solar system to power a health clinic in that region. The total daily health clinic load is 31.6 kW h and detailed loads are listed. The National Renewable Energy Laboratory (NREL) optimization computer model for distributed power, ''HOMER,'' is used to estimate the system size and its life-cycle cost. The analysis shows that the optimal system's initial cost, net present cost, and electricity cost is US$ 50,700, US$ 60,375, and US$ 0.238/kW h, respectively. These values for the PV system are comparedmore » with those of a generator alone used to supply the load. We found that the initial cost, net present cost of the generator system, and electricity cost are US$ 4500, US$ 352,303, and US$ 1.332/kW h, respectively. We conclude that using the PV system is justified on humanitarian, technical, and economic grounds. (author)« less

  19. MVO Automation Platform: Addressing Unmet Needs in Clinical Laboratories with Microcontrollers, 3D Printing, and Open-Source Hardware/Software.

    PubMed

    Iglehart, Brian

    2018-05-01

    Laboratory automation improves test reproducibility, which is vital to patient care in clinical laboratories. Many small and specialty laboratories are excluded from the benefits of automation due to low sample number, cost, space, and/or lack of automation expertise. The Minimum Viable Option (MVO) automation platform was developed to address these hurdles and fulfill an unmet need. Consumer 3D printing enabled rapid iterative prototyping to allow for a variety of instrumentation and assay setups and procedures. Three MVO versions have been produced. MVOv1.1 successfully performed part of a clinical assay, and results were comparable to those of commercial automation. Raspberry Pi 3 Model B (RPI3) single-board computers with Sense Hardware Attached on Top (HAT) and Raspberry Pi Camera Module V2 hardware were remotely accessed and evaluated for their suitability to qualify the latest MVOv1.2 platform. Sense HAT temperature, barometric pressure, and relative humidity sensors were stable in climate-controlled environments and are useful in identifying appropriate laboratory spaces for automation placement. The RPI3 with camera plus digital dial indicator logged axis travel experiments. RPI3 with camera and Sense HAT as a light source showed promise when used for photometric dispensing tests. Individual well standard curves were necessary for well-to-well light and path length compensations.

  20. Human ESP1/CRP2, a member of the LIM domain protein family: Characterization of the cDNA and assignment of the gene locus to chromosome 14q32.3

    SciTech Connect

    Karim, Mohammad Azharul; Ohta, Kohji; Matsuda, Ichiro

    1996-01-15

    The LIM domain is present in a wide variety of proteins with diverse functions and exhibits characteristic arrangements of Cys and His residues with a novel zinc-binding motif. LIM domain proteins have been implicated in development, cell regulation, and cell structure. A LIM domain protein was identified by screening a human cDNA library with rat cysteine-rich intestinal protein (CRIP) as a probe, under conditions of low stringency. Comparison of the predicted amino acid sequence with several LIM domain proteins revealed 93% of the residues to be identical to rat LIM domain protein, termed ESP1 or CRP2. Thus, the protein ismore » hereafter referred to as human ESP1/CRP2. The cDNA encompasses a 1171-base region, including 26, 624, and 521 bases in the 5{prime}-noncoding region, coding region, and 3{prime}-noncoding regions, respectively, and encodes the entire ESP1/CRP2 protein has two LIM domains, and each shares 35.1% and 77 or 79% identical residues with human cysteine-rich protein (CRP) and rat CRIP, respectively. Northern blot analysis of ESP1/CRP2 in various human tissues showed distinct tissue distributions compared with CRP and CRIP, suggesting that each might serve related but specific roles in tissue organization or function. Using a panel of human-rodent somatic cell hybrids, the ESP1/CRP2 locus was assigned to chromosome 14. Fluorescence in situ hybridization, using cDNA and a genome DNA fragment of the ESP1/CRP2 as probes, confirms this assignment and relegates regional localization to band 14q32.3 47 refs., 7 figs.« less

  1. RAPID-L Highly Automated Fast Reactor Concept Without Any Control Rods (2) Critical experiment of lithium-6 used in LEM and LIM

    SciTech Connect

    Tsunoda, Hirokazu; Sato, Osamu; Okajima, Shigeaki

    2002-07-01

    In order to achieve fully automated reactor operation of RAPID-L reactor, innovative reactivity control systems LEM, LIM, and LRM are equipped with lithium-6 as a liquid poison. Because lithium-6 has not been used as a neutron absorbing material of conventional fast reactors, measurements of the reactivity worth of Lithium-6 were performed at the Fast Critical Assembly (FCA) of Japan Atomic Energy Research Institute (JAERI). The FCA core was composed of highly enriched uranium and stainless steel samples so as to simulate the core spectrum of RAPID-L. The samples of 95% enriched lithium-6 were inserted into the core parallel to themore » core axis for the measurement of the reactivity worth at each position. It was found that the measured reactivity worth in the core region well agreed with calculated value by the method for the core designs of RAPID-L. Bias factors for the core design method were obtained by comparing between experimental and calculated results. The factors were used to determine the number of LEM and LIM equipped in the core to achieve fully automated operation of RAPID-L. (authors)« less

  2. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

    PubMed Central

    2009-01-01

    Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community. PMID:19941647

  3. Successful Teaching of Radiobiology Students in the Medical Management of Acute Radiation Effects From Real Case Histories Using Clinical Signs and Symptoms and Taking Advantage of Recently Developed Software Tools.

    PubMed

    Majewski, Matthäus; Combs, Stephanie E; Trott, Klaus-Rüdiger; Abend, Michael; Port, Matthias

    2018-07-01

    In 2015, the Bundeswehr Institute of Radiobiology organized a North Atlantic Treaty Organization exercise to examine the significance of clinical signs and symptoms for the prediction of late-occurring acute radiation syndrome. Cases were generated using either the Medical Treatment Protocols for Radiation Accident Victims (METREPOL, n = 167) system or using real-case descriptions extracted from a database system for evaluation and archiving of radiation accidents based on case histories (SEARCH, n = 24). The cases ranged from unexposed [response category 0 (RC 0, n = 89)] to mild (RC 1, n = 45), moderate (RC 2, n = 19), severe (RC 3, n = 20), and lethal (RC 4, n = 18) acute radiation syndrome. During the previous exercise, expert teams successfully predicted hematological acute radiation syndrome severity, determined whether hospitalization was required, and gave treatment recommendations, taking advantage of different software tools developed by the North Atlantic Treaty Organization teams. The authors provided the same data set to radiobiology students who were introduced to the medical management of acute effects after radiation exposure and the software tools during a class lasting 15 h. Corresponding to the previous results, difficulties in the discrimination between RC 0/RC 1 and RC 3/RC 4, as well as a systematic underestimation of RC 1 and RC 2, were observed. Nevertheless, after merging reported response categories into clinically relevant groups (RC 0-1, RC 2-3, and RC 3-4), it was found that the majority of cases (95.2% ± 2.2 standard deviations) were correctly identified and that 94.7% (±2.6 standard deviations) developing acute radiation syndrome and z96.4% (±1.6 standard deviations) requiring hospitalization were identified correctly. Two out of three student teams also provided a dose estimate. These results are comparable to the best-performing team of the 2015 North Atlantic Treaty Organization exercise (response category: 92.5%; acute

  4. Design software for reuse

    NASA Technical Reports Server (NTRS)

    Tracz, Will

    1990-01-01

    Viewgraphs are presented on the designing of software for reuse. Topics include terminology, software reuse maxims, the science of programming, an interface design example, a modularization example, and reuse and implementation guidelines.

  5. Software service history report

    DOT National Transportation Integrated Search

    2002-01-01

    The safe and reliable operation of software within civil aviation systems and equipment has historically been assured through the application of rigorous design assurance applied during the software development process. Increasingly, manufacturers ar...

  6. Software assurance standard

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This standard specifies the software assurance program for the provider of software. It also delineates the assurance activities for the provider and the assurance data that are to be furnished by the provider to the acquirer. In any software development effort, the provider is the entity or individual that actually designs, develops, and implements the software product, while the acquirer is the entity or individual who specifies the requirements and accepts the resulting products. This standard specifies at a high level an overall software assurance program for software developed for and by NASA. Assurance includes the disciplines of quality assurance, quality engineering, verification and validation, nonconformance reporting and corrective action, safety assurance, and security assurance. The application of these disciplines during a software development life cycle is called software assurance. Subsequent lower-level standards will specify the specific processes within these disciplines.

  7. Software Engineering Improvement Plan

    NASA Technical Reports Server (NTRS)

    2006-01-01

    In performance of this task order, bd Systems personnel provided support to the Flight Software Branch and the Software Working Group through multiple tasks related to software engineering improvement and to activities of the independent Technical Authority (iTA) Discipline Technical Warrant Holder (DTWH) for software engineering. To ensure that the products, comments, and recommendations complied with customer requirements and the statement of work, bd Systems personnel maintained close coordination with the customer. These personnel performed work in areas such as update of agency requirements and directives database, software effort estimation, software problem reports, a web-based process asset library, miscellaneous documentation review, software system requirements, issue tracking software survey, systems engineering NPR, and project-related reviews. This report contains a summary of the work performed and the accomplishments in each of these areas.

  8. Guidelines for software inspections

    NASA Technical Reports Server (NTRS)

    1983-01-01

    Quality control inspections are software problem finding procedures which provide defect removal as well as improvements in software functionality, maintenance, quality, and development and testing methodology is discussed. The many side benefits include education, documentation, training, and scheduling.

  9. Experimentation in software engineering

    NASA Technical Reports Server (NTRS)

    Basili, V. R.; Selby, R. W.; Hutchens, D. H.

    1986-01-01

    Experimentation in software engineering supports the advancement of the field through an iterative learning process. In this paper, a framework for analyzing most of the experimental work performed in software engineering over the past several years is presented. A variety of experiments in the framework is described and their contribution to the software engineering discipline is discussed. Some useful recommendations for the application of the experimental process in software engineering are included.

  10. DSS command software update

    NASA Technical Reports Server (NTRS)

    Stinnett, W. G.

    1980-01-01

    The modifications, additions, and testing results for a version of the Deep Space Station command software, generated for support of the Voyager Saturn encounter, are discussed. The software update requirements included efforts to: (1) recode portions of the software to permit recovery of approximately 2000 words of memory; (2) correct five Voyager Ground data System liens; (3) provide capability to automatically turn off the command processor assembly local printer during periods of low activity; and (4) correct anomalies existing in the software.

  11. Automating Software Design Metrics.

    DTIC Science & Technology

    1984-02-01

    INTRODUCTION 1 ", ... 0..1 1.2 HISTORICAL PERSPECTIVE High quality software is of interest to both the software engineering com- munity and its users. As...contributions of many other software engineering efforts, most notably [MCC 77] and [Boe 83b], which have defined and refined a framework for quantifying...AUTOMATION OF DESIGN METRICS Software metrics can be useful within the context of an integrated soft- ware engineering environment. The purpose of this

  12. Guidance and Control Software,

    DTIC Science & Technology

    1980-05-01

    commitments of function, cost, and schedule . The phrase "software engineering" was intended to contrast with the phrase "computer science" the latter aims...the software problems of cost, delivery schedule , and quality were gradually being recognized at the highest management levels. Thus, in a project... schedule dates. Although the analysis of software problems indicated that the entire software development process (figure 1) needed new methods, only

  13. Java for flight software

    NASA Technical Reports Server (NTRS)

    Benowitz, E.; Niessner, A.

    2003-01-01

    This work involves developing representative mission-critical spacecraft software using the Real-Time Specification for Java (RTSJ). This work currently leverages actual flight software used in the design of actual flight software in the NASA's Deep Space 1 (DSI), which flew in 1998.

  14. Software - Naval Oceanography Portal

    Science.gov Websites

    section Advanced Search... Sections Home Time Earth Orientation Astronomy Meteorology Oceanography Ice You are here: Home › USNO › Earth Orientation › Software USNO Logo USNO Navigation Earth Orientation Search databases Auxiliary Software Supporting Software Form Folder Earth Orientation Matrix Calculator

  15. Software Architecture Evolution

    ERIC Educational Resources Information Center

    Barnes, Jeffrey M.

    2013-01-01

    Many software systems eventually undergo changes to their basic architectural structure. Such changes may be prompted by new feature requests, new quality attribute requirements, changing technology, or other reasons. Whatever the causes, architecture evolution is commonplace in real-world software projects. Today's software architects, however,…

  16. Complexity, Systems, and Software

    DTIC Science & Technology

    2014-08-14

    2014 Carnegie Mellon University Complexity, Systems, and Software Software Engineering Institute Carnegie Mellon University Pittsburgh, PA...this collection of information, including suggestions for reducing this burden, to Washington Headquarters Services , Directorate for Information...OMB control number. 1. REPORT DATE 29 OCT 2014 2. REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE Complexity, Systems, and Software

  17. Astronomical Software Directory Service

    NASA Technical Reports Server (NTRS)

    Hanisch, R. J.; Payne, H.; Hayes, J.

    1998-01-01

    This is the final report on the development of the Astronomical Software Directory Service (ASDS), a distributable, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URL's indexed for full-text searching.

  18. Specifications for Thesaurus Software.

    ERIC Educational Resources Information Center

    Milstead, Jessica L.

    1991-01-01

    Presents specifications for software that is designed to support manual development and maintenance of information retrieval thesauri. Evaluation of existing software and design of custom software is discussed, requirements for integration with larger systems and for the user interface are described, and relationships among terms are discussed.…

  19. Problem-Solving Software

    NASA Technical Reports Server (NTRS)

    1992-01-01

    CBR Express software solves problems by adapting sorted solutions to new problems specified by a user. It is applicable to a wide range of situations. The technology was originally developed by Inference Corporation for Johnson Space Center's Advanced Software Development Workstation. The project focused on the reuse of software designs, and Inference used CBR as part of the ACCESS prototype software. The commercial CBR Express is used as a "help desk" for customer support, enabling reuse of existing information when necessary. It has been adopted by several companies, among them American Airlines, which uses it to solve reservation system software problems.

  20. Payload software technology

    NASA Technical Reports Server (NTRS)

    1976-01-01

    A software analysis was performed of known STS sortie payload elements and their associated experiments. This provided basic data for STS payload software characteristics and sizes. A set of technology drivers was identified based on a survey of future technology needs and an assessment of current software technology. The results will be used to evolve a planned approach to software technology development. The purpose of this plan is to ensure that software technology is advanced at a pace and a depth sufficient to fulfill the identified future needs.

  1. Healthcare Software Assurance

    PubMed Central

    Cooper, Jason G.; Pauley, Keith A.

    2006-01-01

    Software assurance is a rigorous, lifecycle phase-independent set of activities which ensure completeness, safety, and reliability of software processes and products. This is accomplished by guaranteeing conformance to all requirements, standards, procedures, and regulations. These assurance processes are even more important when coupled with healthcare software systems, embedded software in medical instrumentation, and other healthcare-oriented life-critical systems. The current Food and Drug Administration (FDA) regulatory requirements and guidance documentation do not address certain aspects of complete software assurance activities. In addition, the FDA’s software oversight processes require enhancement to include increasingly complex healthcare systems such as Hospital Information Systems (HIS). The importance of complete software assurance is introduced, current regulatory requirements and guidance discussed, and the necessity for enhancements to the current processes shall be highlighted. PMID:17238324

  2. Healthcare software assurance.

    PubMed

    Cooper, Jason G; Pauley, Keith A

    2006-01-01

    Software assurance is a rigorous, lifecycle phase-independent set of activities which ensure completeness, safety, and reliability of software processes and products. This is accomplished by guaranteeing conformance to all requirements, standards, procedures, and regulations. These assurance processes are even more important when coupled with healthcare software systems, embedded software in medical instrumentation, and other healthcare-oriented life-critical systems. The current Food and Drug Administration (FDA) regulatory requirements and guidance documentation do not address certain aspects of complete software assurance activities. In addition, the FDA's software oversight processes require enhancement to include increasingly complex healthcare systems such as Hospital Information Systems (HIS). The importance of complete software assurance is introduced, current regulatory requirements and guidance discussed, and the necessity for enhancements to the current processes shall be highlighted.

  3. Microcomputer software development facilities

    NASA Technical Reports Server (NTRS)

    Gorman, J. S.; Mathiasen, C.

    1980-01-01

    A more efficient and cost effective method for developing microcomputer software is to utilize a host computer with high-speed peripheral support. Application programs such as cross assemblers, loaders, and simulators are implemented in the host computer for each of the microcomputers for which software development is a requirement. The host computer is configured to operate in a time share mode for multiusers. The remote terminals, printers, and down loading capabilities provided are based on user requirements. With this configuration a user, either local or remote, can use the host computer for microcomputer software development. Once the software is developed (through the code and modular debug stage) it can be downloaded to the development system or emulator in a test area where hardware/software integration functions can proceed. The microcomputer software program sources reside in the host computer and can be edited, assembled, loaded, and then downloaded as required until the software development project has been completed.

  4. NASA software documentation standard software engineering program

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  5. Let's get physical!: Comment on" Physical methods for genetic transformation of fungi and yeast" by Ana L. Rivera, Denis Magaña-Ortíz, Miguel Gómez-Lim, Francisco Fernández and Achim M. Loske.

    USDA-ARS?s Scientific Manuscript database

    This comment analyses the paper “Physical methods for genetic transformation of fungi and yeast” by Ana L. Rivera, Denis Magaña-Ortíz , Miguel Gómez-Lim , Francisco Fernández and Achim M. Loske. I examine the methods described and their advantages and disadvantages. I further discuss the other more ...

  6. Science and Software

    NASA Astrophysics Data System (ADS)

    Zelt, C. A.

    2017-12-01

    Earth science attempts to understand how the earth works. This research often depends on software for modeling, processing, inverting or imaging. Freely sharing open-source software is essential to prevent reinventing the wheel and allows software to be improved and applied in ways the original author may never have envisioned. For young scientists, releasing software can increase their name ID when applying for jobs and funding, and create opportunities for collaborations when scientists who collect data want the software's creator to be involved in their project. However, we frequently hear scientists say software is a tool, it's not science. Creating software that implements a new or better way of earth modeling or geophysical processing, inverting or imaging should be viewed as earth science. Creating software for things like data visualization, format conversion, storage, or transmission, or programming to enhance computational performance, may be viewed as computer science. The former, ideally with an application to real data, can be published in earth science journals, the latter possibly in computer science journals. Citations in either case should accurately reflect the impact of the software on the community. Funding agencies need to support more software development and open-source releasing, and the community should give more high-profile awards for developing impactful open-source software. Funding support and community recognition for software development can have far reaching benefits when the software is used in foreseen and unforeseen ways, potentially for years after the original investment in the software development. For funding, an open-source release that is well documented should be required, with example input and output files. Appropriate funding will provide the incentive and time to release user-friendly software, and minimize the need for others to duplicate the effort. All funded software should be available through a single web site

  7. RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

    PubMed

    Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A; Standley, Daron M

    2015-03-01

    RNA-LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal "limiting" restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA-LIM analysis programs along with detailed instructions for their use are available on request from the authors. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

  8. How Safe Is Control Software

    NASA Technical Reports Server (NTRS)

    Dunn, William R.; Corliss, Lloyd D.

    1991-01-01

    Paper examines issue of software safety. Presents four case histories of software-safety analysis. Concludes that, to be safe, software, for all practical purposes, must be free of errors. Backup systems still needed to prevent catastrophic software failures.

  9. Solar Asset Management Software

    SciTech Connect

    Iverson, Aaron; Zviagin, George

    Ra Power Management (RPM) has developed a cloud based software platform that manages the financial and operational functions of third party financed solar projects throughout their lifecycle. RPM’s software streamlines and automates the sales, financing, and management of a portfolio of solar assets. The software helps solar developers automate the most difficult aspects of asset management, leading to increased transparency, efficiency, and reduction in human error. More importantly, our platform will help developers save money by improving their operating margins.

  10. Assuring Software Reliability

    DTIC Science & Technology

    2014-08-01

    technologies and processes to achieve a required level of confidence that software systems and services function in the intended manner. 1.3 Security Example...that took three high-voltage lines out of service and a software fail- ure (a race condition3) that disabled the computing service that notified the... service had failed. Instead of analyzing the details of the alarm server failure, the reviewers asked why the following software assurance claim had

  11. NASA's Software Safety Standard

    NASA Technical Reports Server (NTRS)

    Ramsay, Christopher M.

    2005-01-01

    NASA (National Aeronautics and Space Administration) relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft (manned or unmanned) launched that did not have a computer on board that provided vital command and control services. Despite this growing dependence on software control and monitoring, there has been no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Led by the NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard (STD-18l9.13B) has recently undergone a significant update in an attempt to provide that consistency. This paper will discuss the key features of the new NASA Software Safety Standard. It will start with a brief history of the use and development of software in safety critical applications at NASA. It will then give a brief overview of the NASA Software Working Group and the approach it took to revise the software engineering process across the Agency.

  12. Dtest Testing Software

    NASA Technical Reports Server (NTRS)

    Jain, Abhinandan; Cameron, Jonathan M.; Myint, Steven

    2013-01-01

    This software runs a suite of arbitrary software tests spanning various software languages and types of tests (unit level, system level, or file comparison tests). The dtest utility can be set to automate periodic testing of large suites of software, as well as running individual tests. It supports distributing multiple tests over multiple CPU cores, if available. The dtest tool is a utility program (written in Python) that scans through a directory (and its subdirectories) and finds all directories that match a certain pattern and then executes any tests in that directory as described in simple configuration files.

  13. Software Reuse Issues

    NASA Technical Reports Server (NTRS)

    Voigt, Susan J. (Editor); Smith, Kathryn A. (Editor)

    1989-01-01

    NASA Langley Research Center sponsored a Workshop on NASA Research in Software Reuse on November 17-18, 1988 in Melbourne, Florida, hosted by Software Productivity Solutions, Inc. Participants came from four NASA centers and headquarters, eight NASA contractor companies, and three research institutes. Presentations were made on software reuse research at the four NASA centers; on Eli, the reusable software synthesis system designed and currently under development by SPS; on Space Station Freedom plans for reuse; and on other reuse research projects. This publication summarizes the presentations made and the issues discussed during the workshop.

  14. Software Security Knowledge: Training

    DTIC Science & Technology

    2011-05-01

    eliminating those erro~rs. It can be found at http:ffcwe.mitre.org/top25. Any programmer who writes C’Ode \\r-Vith~out betng aware of those proble ~ms a·nd...time on security. Ultimately, these reasons stem from an underlying problem in the software market . B~cause software is essentially a black·box, it is...security of software and start to effect change in the software market . Nevertheless, we still frequently get pushback when we advocate for security

  15. Classification software technique assessment

    NASA Technical Reports Server (NTRS)

    Jayroe, R. R., Jr.; Atkinson, R.; Dasarathy, B. V.; Lybanon, M.; Ramapryian, H. K.

    1976-01-01

    A catalog of software options is presented for the use of local user communities to obtain software for analyzing remotely sensed multispectral imagery. The resources required to utilize a particular software program are described. Descriptions of how a particular program analyzes data and the performance of that program for an application and data set provided by the user are shown. An effort is made to establish a statistical performance base for various software programs with regard to different data sets and analysis applications, to determine the status of the state-of-the-art.

  16. Software Management Metrics

    DTIC Science & Technology

    1988-05-01

    obtained from Dr. Barry Boehm’s Software 5650, Contract No. F19628-86-C-O001, Engineering Economics [1] and from T. J. ESD/MITRE Software Center Acquisition...of References 1. Boehm, Barry W., SoJtware Engineering 3. Halstead, M. H., Elements of SoJhtare Economics, Englewood Cliffs, New Science, New York...1983, pp. 639-648. 35 35 - Bibliography Beizer, B., Software System Testing and Pressman , Roger S., Software Engineering:QualtyO Assurance, New York: Van

  17. On Software Compatibility.

    ERIC Educational Resources Information Center

    Ershov, Andrei P.

    The problem of compatibility of software hampers the development of computer application. One solution lies in standardization of languages, terms, peripherais, operating systems and computer characteristics. (AB)

  18. Synchronization software for automation in anesthesia.

    PubMed

    Bressan, Nadja; Castro, Ana; Brás, Susana; Oliveira, Hélder P; Ribeiro, Lénio; Ferreira, David A; Antunes, Luís; Amorim, Pedro; Nunes, Catarina S

    2007-01-01

    This work presents the development of a software for data acquisition and control (ASYS) on a clinical setup. Similar to the industrial Supervisory Control And Data Acquisition (SCADA) the software assembles a Target Controlled Infusion (TCI) monitoring and supervisory control data in real time from devices in a surgical room. The software is not a full controller since the TCI systems comprehend permanent interaction from the anesthesiologist. Based on pharmacokinetic models, the effect-site and plasma concentrations can be related with the drug dose infused and vice versa. The software determines the infusion rates of the drug which are given as commands to the infusion pumps. This software provides the anesthesiologist with a trustworthy tool for managing a safe and balanced anesthesia. Since it also incorporates the acquisition and display of patients brain signals.

  19. Statistical modelling of software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1991-01-01

    During the six-month period from 1 April 1991 to 30 September 1991 the following research papers in statistical modeling of software reliability appeared: (1) A Nonparametric Software Reliability Growth Model; (2) On the Use and the Performance of Software Reliability Growth Models; (3) Research and Development Issues in Software Reliability Engineering; (4) Special Issues on Software; and (5) Software Reliability and Safety.

  20. NASA's Software Safety Standard

    NASA Technical Reports Server (NTRS)

    Ramsay, Christopher M.

    2007-01-01

    NASA relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft launched that does not have a computer on board that will provide command and control services. There have been recent incidents where software has played a role in high-profile mission failures and hazardous incidents. For example, the Mars Orbiter, Mars Polar Lander, the DART (Demonstration of Autonomous Rendezvous Technology), and MER (Mars Exploration Rover) Spirit anomalies were all caused or contributed to by software. The Mission Control Centers for the Shuttle, ISS, and unmanned programs are highly dependant on software for data displays, analysis, and mission planning. Despite this growing dependence on software control and monitoring, there has been little to no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Meanwhile, academia and private industry have been stepping forward with procedures and standards for safety critical systems and software, for example Dr. Nancy Leveson's book Safeware: System Safety and Computers. The NASA Software Safety Standard, originally published in 1997, was widely ignored due to its complexity and poor organization. It also focused on concepts rather than definite procedural requirements organized around a software project lifecycle. Led by NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard has recently undergone a significant update. This new standard provides the procedures and guidelines for evaluating a project for safety criticality and then lays out the minimum project lifecycle requirements to assure the software is created, operated, and maintained in the safest possible manner. This update of the standard clearly delineates the minimum set of software safety requirements for a project without detailing the implementation for those

  1. Selecting the Right Software.

    ERIC Educational Resources Information Center

    Shearn, Joseph

    1987-01-01

    Selection of administrative software requires analyzing present needs and, to meet future needs, choosing software that will function with a more powerful computer system. Other important factors to include are a professional system demonstration, maintenance and training, and financial considerations that allow leasing or renting alternatives.…

  2. ARC Software and Models

    Science.gov Websites

    produce software code and methodologies that are transferred to TARDEC and industry partners. These constraints", ASME Dynamic Systems and Control Conference, 2013, DOI:10.1115/DSCC2013-3935 Software Monitoring",IEEE Transactions on Control Systems Technology, DOI:10.1109/TCST.2012.2217143 Fast

  3. SOFTWARE ENGINEERING INSTITUTE (SEI)

    EPA Science Inventory

    The Software Engineering Institute (SEI) is a federally funded research and development center established in 1984 by the U.S. Department of Defense and operated by Carnegie Mellon University. SEI has a broad charter to provide leadership in the practice of software engineering t...

  4. Learning from Software Localization.

    ERIC Educational Resources Information Center

    Guo, She-Sen

    2003-01-01

    Localization is the process of adapting a product to meet the language, cultural and other requirements of a specific target environment or market. This article describes ways in which software localization impacts upon curriculum, and discusses what students will learn from software localization. (AEF)

  5. PREVAPORATION PERFORMANCE PREDICTION SOFTWARE

    EPA Science Inventory

    The Pervaporation, Performance, Prediction Software and Database (PPPS&D) computer software program is currently being developed within the USEPA, NRMRL. The purpose of the PPPS&D program is to educate and assist potential users in identifying opportunities for using pervaporati...

  6. UWB Tracking Software Development

    NASA Technical Reports Server (NTRS)

    Gross, Julia; Arndt, Dickey; Ngo, Phong; Phan, Chau; Dusl, John; Ni, Jianjun; Rafford, Melinda

    2006-01-01

    An Ultra-Wideband (UWB) two-cluster Angle of Arrival (AOA) tracking prototype system is currently being developed and tested at NASA Johnson Space Center for space exploration applications. This talk discusses the software development efforts for this UWB two-cluster AOA tracking system. The role the software plays in this system is to take waveform data from two UWB radio receivers as an input, feed this input into an AOA tracking algorithm, and generate the target position as an output. The architecture of the software (Input/Output Interface and Algorithm Core) will be introduced in this talk. The development of this software has three phases. In Phase I, the software is mostly Matlab driven and calls C++ socket functions to provide the communication links to the radios. This is beneficial in the early stage when it is necessary to frequently test changes in the algorithm. Phase II of the development is to have the software mostly C++ driven and call a Matlab function for the AOA tracking algorithm. This is beneficial in order to send the tracking results to other systems and also to improve the tracking update rate of the system. The third phase is part of future work and is to have the software completely C++ driven with a graphics user interface. This software design enables the fine resolution tracking of the UWB two-cluster AOA tracking system.

  7. Cartographic applications software

    USGS Publications Warehouse

    ,

    1992-01-01

    The Office of the Assistant Division Chief for Research, National Mapping Division, develops computer software for the solution of geometronic problems in the fields of surveying, geodesy, remote sensing, and photogrammetry. Software that has been developed using public funds is available on request for a nominal charge to recover the cost of duplication.

  8. The Software Problem.

    ERIC Educational Resources Information Center

    Walker, Decker F.

    This paper addresses the reasons that it is difficult to find good educational software and proposes measures for coping with this problem. The fundamental problem is a shortange of educational software that can be used as a major part of the teaching of academic subjects in elementary and secondary schools--a shortage that is both the effect and…

  9. Software process assessments

    NASA Technical Reports Server (NTRS)

    Miller, Sharon E.; Tucker, George T.; Verducci, Anthony J., Jr.

    1992-01-01

    Software process assessments (SPA's) are part of an ongoing program of continuous quality improvements in AT&T. Their use was found to be very beneficial by software development organizations in identifying the issues facing the organization and the actions required to increase both quality and productivity in the organization.

  10. Software measurement guidebook

    NASA Technical Reports Server (NTRS)

    Bassman, Mitchell J.; Mcgarry, Frank; Pajerski, Rose

    1994-01-01

    This software Measurement Guidebook presents information on the purpose and importance of measurement. It discusses the specific procedures and activities of a measurement program and the roles of the people involved. The guidebook also clarifies the roles that measurement can and must play in the goal of continual, sustained improvement for all software production and maintenance efforts.

  11. Computer Software Reviews.

    ERIC Educational Resources Information Center

    Hawaii State Dept. of Education, Honolulu. Office of Instructional Services.

    Intended to provide guidance in the selection of the best computer software available to support instruction and to make optimal use of schools' financial resources, this publication provides a listing of computer software programs that have been evaluated according to their currency, relevance, and value to Hawaii's educational programs. The…

  12. SEED Software Annotations.

    ERIC Educational Resources Information Center

    Bethke, Dee; And Others

    This document provides a composite index of the first five sets of software annotations produced by Project SEED. The software has been indexed by title, subject area, and grade level, and it covers sets of annotations distributed in September 1986, April 1987, September 1987, November 1987, and February 1988. The date column in the index…

  13. Software Solution Saves Dollars

    ERIC Educational Resources Information Center

    Trotter, Andrew

    2004-01-01

    This article discusses computer software that can give classrooms and computer labs the capabilities of costly PC's at a small fraction of the cost. A growing number of cost-conscious school districts are finding budget relief in low-cost computer software known as "open source" that can do everything from manage school Web sites to equip…

  14. Software engineering ethics

    NASA Technical Reports Server (NTRS)

    Bown, Rodney L.

    1991-01-01

    Software engineering ethics is reviewed. The following subject areas are covered: lack of a system viewpoint; arrogance of PC DOS software vendors; violation od upward compatibility; internet worm; internet worm revisited; student cheating and company hiring interviews; computing practitioners and the commodity market; new projects and old programming languages; schedule and budget; and recent public domain comments.

  15. Reusable Software Technology

    NASA Technical Reports Server (NTRS)

    Morgan, Timothy E.

    1995-01-01

    The objective of the Reusable Software System (RSS) is to provide NASA Langley Research Center and its contractor personnel with a reusable software technology through the Internet. The RSS is easily accessible, provides information that is extractable, and the capability to submit information or data for the purpose of scientific research at NASA Langley Research Center within the Atmospheric Science Division.

  16. NASA Software Documentation Standard

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as "Standard") is designed to support the documentation of all software developed for NASA; its goal is to provide a framework and model for recording the essential information needed throughout the development life cycle and maintenance of a software system. The NASA Software Documentation Standard can be applied to the documentation of all NASA software. The Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. The basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  17. NASA Software Safety Standard

    NASA Technical Reports Server (NTRS)

    Rosenberg, Linda

    1997-01-01

    If software is a critical element in a safety critical system, it is imperative to implement a systematic approach to software safety as an integral part of the overall system safety programs. The NASA-STD-8719.13A, "NASA Software Safety Standard", describes the activities necessary to ensure that safety is designed into software that is acquired or developed by NASA, and that safety is maintained throughout the software life cycle. A PDF version, is available on the WWW from Lewis. A Guidebook that will assist in the implementation of the requirements in the Safety Standard is under development at the Lewis Research Center (LeRC). After completion, it will also be available on the WWW from Lewis.

  18. Software quality in 1997

    SciTech Connect

    Jones, C.

    1997-11-01

    For many years, software quality assurance lagged behind hardware quality assurance in terms of methods, metrics, and successful results. New approaches such as Quality Function Deployment (QFD) the ISO 9000-9004 standards, the SEI maturity levels, and Total Quality Management (TQM) are starting to attract wide attention, and in some cases to bring software quality levels up to a parity with manufacturing quality levels. Since software is on the critical path for many engineered products, and for internal business systems as well, the new approaches are starting to affect global competition and attract widespread international interest. It can be hypothesized thatmore » success in mastering software quality will be a key strategy for dominating global software markets in the 21st century.« less

  19. Data warehouse implementation with clinical pharmacokinetic/pharmacodynamic data.

    PubMed

    Koprowski, S P; Barrett, J S

    2002-03-01

    We have created a data warehouse for human pharmacokinetic (PK) and pharmacodynamic (PD) data generated primarily within the Clinical PK Group of the Drug Metabolism and Pharmacokinetics (DM&PK) Department of DuPont Pharmaceuticals. Data which enters an Oracle-based LIMS directly from chromatography systems or through files from contract research organizations are accessed via SAS/PH.Kinetics, GLP-compliant data analysis software residing on individual users' workstations. Upon completion of the final PK or PD analysis, data are pushed to a predefined location. Data analyzed/created with other software (i.e., WinNonlin, NONMEM, Adapt, etc.) are added to this file repository as well. The warehouse creates views to these data and accumulates metadata on all data sources defined in the warehouse. The warehouse is managed via the SAS/Warehouse Administrator product that defines the environment, creates summarized data structures, and schedules data refresh. The clinical PK/PD warehouse encompasses laboratory, biometric, PK and PD data streams. Detailed logical tables for each compound are created/updated as the clinical PK/PD data warehouse is populated. The data model defined to the warehouse is based on a star schema. Summarized data structures such as multidimensional data bases (MDDB), infomarts, and datamarts are created from detail tables. Data mining and querying of highly summarized data as well as drill-down to detail data is possible via the creation of exploitation tools which front-end the warehouse data. Based on periodic refreshing of the warehouse data, these applications are able to access the most current data available and do not require a manual interface to update/populate the data store. Prototype applications have been web-enabled to facilitate their usage to varied data customers across platform and location. The warehouse also contains automated mechanisms for the construction of study data listings and SAS transport files for eventual

  20. 21 CFR 862.2570 - Instrumentation for clinical multiplex test systems.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical... hardware components, as well as raw data storage mechanisms, data acquisition software, and software to...

  1. Software for Better Documentation of Other Software

    NASA Technical Reports Server (NTRS)

    Pinedo, John

    2003-01-01

    The Literate Programming Extraction Engine is a Practical Extraction and Reporting Language- (PERL-)based computer program that facilitates and simplifies the implementation of a concept of self-documented literate programming in a fashion tailored to the typical needs of scientists. The advantage for the programmer is that documentation and source code are written side-by-side in the same file, reducing the likelihood that the documentation will be inconsistent with the code and improving the verification that the code performs its intended functions. The advantage for the user is the knowledge that the documentation matches the software because they come from the same file. This program unifies the documentation process for a variety of programming languages, including C, C++, and several versions of FORTRAN. This program can process the documentation in any markup language, and incorporates the LaTeX typesetting software. The program includes sample Makefile scripts for automating both the code-compilation (when appropriate) and documentation-generation processes into a single command-line statement. Also included are macro instructions for the Emacs display-editor software, making it easy for a programmer to toggle between editing in a code or a documentation mode.

  2. Software Measurement Guidebook

    NASA Technical Reports Server (NTRS)

    1995-01-01

    This Software Measurement Guidebook is based on the extensive experience of several organizations that have each developed and applied significant measurement programs over a period of at least 10 years. The lessons derived from those experiences reflect not only successes but also failures. By applying those lessons, an organization can minimize, or at least reduce, the time, effort, and frustration of introducing a software measurement program. The Software Measurement Guidebook is aimed at helping organizations to begin or improve a measurement program. It does not provide guidance for the extensive application of specific measures (such as how to estimate software cost or analyze software complexity) other than by providing examples to clarify points. It does contain advice for establishing and using an effective software measurement program and for understanding some of the key lessons that other organizations have learned. Some of that advice will appear counterintuitive, but it is all based on actual experience. Although all of the information presented in this guidebook is derived from specific experiences of mature measurement programs, the reader must keep in mind that the characteristics of every organization are unique. Some degree of measurement is critical for all software development and maintenance organizations, and most of the key rules captured in this report will be generally applicable. Nevertheless, each organization must strive to understand its own environment so that the measurement program can be tailored to suit its characteristics and needs.

  3. The STARLINK software collection

    NASA Astrophysics Data System (ADS)

    Penny, A. J.; Wallace, P. T.; Sherman, J. C.; Terret, D. L.

    1993-12-01

    A demonstration will be given of some recent Starlink software. STARLINK is: a network of computers used by UK astronomers; a collection of programs for the calibration and analysis of astronomical data; a team of people giving hardware, software and administrative support. The Starlink Project has been in operation since 1980 to provide UK astronomers with interactive image processing and data reduction facilities. There are now Starlink computer systems at 25 UK locations, serving about 1500 registered users. The Starlink software collection now has about 25 major packages covering a wide range of astronomical data reduction and analysis techniques, as well as many smaller programs and utilities. At the core of most of the packages is a common `software environment', which provides many of the functions which applications need and offers standardized methods of structuring and accessing data. The software environment simplifies programming and support, and makes it easy to use different packages for different stages of the data reduction. Users see a consistent style, and can mix applications without hitting problems of differing data formats. The Project group coordinates the writing and distribution of this software collection, which is Unix based. Outside the UK, Starlink is used at a large number of places, which range from installations at major UK telescopes, which are Starlink-compatible and managed like Starlink sites, to individuals who run only small parts of the Starlink software collection.

  4. Software Formal Inspections Guidebook

    NASA Technical Reports Server (NTRS)

    1993-01-01

    The Software Formal Inspections Guidebook is designed to support the inspection process of software developed by and for NASA. This document provides information on how to implement a recommended and proven method for conducting formal inspections of NASA software. This Guidebook is a companion document to NASA Standard 2202-93, Software Formal Inspections Standard, approved April 1993, which provides the rules, procedures, and specific requirements for conducting software formal inspections. Application of the Formal Inspections Standard is optional to NASA program or project management. In cases where program or project management decide to use the formal inspections method, this Guidebook provides additional information on how to establish and implement the process. The goal of the formal inspections process as documented in the above-mentioned Standard and this Guidebook is to provide a framework and model for an inspection process that will enable the detection and elimination of defects as early as possible in the software life cycle. An ancillary aspect of the formal inspection process incorporates the collection and analysis of inspection data to effect continual improvement in the inspection process and the quality of the software subjected to the process.

  5. Evidence synthesis software.

    PubMed

    Park, Sophie Elizabeth; Thomas, James

    2018-06-07

    It can be challenging to decide which evidence synthesis software to choose when doing a systematic review. This article discusses some of the important questions to consider in relation to the chosen method and synthesis approach. Software can support researchers in a range of ways. Here, a range of review conditions and software solutions. For example, facilitating contemporaneous collaboration across time and geographical space; in-built bias assessment tools; and line-by-line coding for qualitative textual analysis. EPPI-Reviewer is a review software for research synthesis managed by the EPPI-centre, UCL Institute of Education. EPPI-Reviewer has text mining automation technologies. Version 5 supports data sharing and re-use across the systematic review community. Open source software will soon be released. EPPI-Centre will continue to offer the software as a cloud-based service. The software is offered via a subscription with a one-month (extendible) trial available and volume discounts for 'site licences'. It is free to use for Cochrane and Campbell reviews. The next EPPI-Reviewer version is being built in collaboration with National Institute for Health and Care Excellence using 'surveillance' of newly published research to support 'living' iterative reviews. This is achieved using a combination of machine learning and traditional information retrieval technologies to identify the type of research each new publication describes and determine its relevance for a particular review, domain or guideline. While the amount of available knowledge and research is constantly increasing, the ways in which software can support the focus and relevance of data identification are also developing fast. Software advances are maximising the opportunities for the production of relevant and timely reviews. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise

  6. Software packager user's guide

    NASA Technical Reports Server (NTRS)

    Callahan, John R.

    1995-01-01

    Software integration is a growing area of concern for many programmers and software managers because the need to build new programs quickly from existing components is greater than ever. This includes building versions of software products for multiple hardware platforms and operating systems, building programs from components written in different languages, and building systems from components that must execute on different machines in a distributed network. The goal of software integration is to make building new programs from existing components more seamless -- programmers should pay minimal attention to the underlying configuration issues involved. Libraries of reusable components and classes are important tools but only partial solutions to software development problems. Even though software components may have compatible interfaces, there may be other reasons, such as differences between execution environments, why they cannot be integrated. Often, components must be adapted or reimplemented to fit into another application because of implementation differences -- they are implemented in different programming languages, dependent on different operating system resources, or must execute on different physical machines. The software packager is a tool that allows programmers to deal with interfaces between software components and ignore complex integration details. The packager takes modular descriptions of the structure of a software system written in the package specification language and produces an integration program in the form of a makefile. If complex integration tools are needed to integrate a set of components, such as remote procedure call stubs, their use is implied by the packager automatically and stub generation tools are invoked in the corresponding makefile. The programmer deals only with the components themselves and not the details of how to build the system on any given platform.

  7. Ascent/Descent Software

    NASA Technical Reports Server (NTRS)

    Brown, Charles; Andrew, Robert; Roe, Scott; Frye, Ronald; Harvey, Michael; Vu, Tuan; Balachandran, Krishnaiyer; Bly, Ben

    2012-01-01

    The Ascent/Descent Software Suite has been used to support a variety of NASA Shuttle Program mission planning and analysis activities, such as range safety, on the Integrated Planning System (IPS) platform. The Ascent/Descent Software Suite, containing Ascent Flight Design (ASC)/Descent Flight Design (DESC) Configuration items (Cis), lifecycle documents, and data files used for shuttle ascent and entry modeling analysis and mission design, resides on IPS/Linux workstations. A list of tools in Navigation (NAV)/Prop Software Suite represents tool versions established during or after the IPS Equipment Rehost-3 project.

  8. Advanced fingerprint verification software

    NASA Astrophysics Data System (ADS)

    Baradarani, A.; Taylor, J. R. B.; Severin, F.; Maev, R. Gr.

    2016-05-01

    We have developed a fingerprint software package that can be used in a wide range of applications from law enforcement to public and private security systems, and to personal devices such as laptops, vehicles, and door- locks. The software and processing units are a unique implementation of new and sophisticated algorithms that compete with the current best systems in the world. Development of the software package has been in line with the third generation of our ultrasonic fingerprinting machine1. Solid and robust performance is achieved in the presence of misplaced and low quality fingerprints.

  9. Orbit Software Suite

    NASA Technical Reports Server (NTRS)

    Osgood, Cathy; Williams, Kevin; Gentry, Philip; Brownfield, Dana; Hallstrom, John; Stuit, Tim

    2012-01-01

    Orbit Software Suite is used to support a variety of NASA/DM (Dependable Multiprocessor) mission planning and analysis activities on the IPS (Intrusion Prevention System) platform. The suite of Orbit software tools (Orbit Design and Orbit Dynamics) resides on IPS/Linux workstations, and is used to perform mission design and analysis tasks corresponding to trajectory/ launch window, rendezvous, and proximity operations flight segments. A list of tools in Orbit Software Suite represents tool versions established during/after the Equipment Rehost-3 Project.

  10. Towards a software profession

    NASA Technical Reports Server (NTRS)

    Berard, Edward V.

    1986-01-01

    An increasing number of programmers have attempted to change their image. They have made it plain that they wish not only to be taken seriously, but they also wish to be regarded as professionals. Many programmers now wish to referred to as software engineers. If programmers wish to be considered professionals in every sense of the word, two obstacles must be overcome: the inability to think of software as a product, and the idea that little or no skill is required to create and handle software throughout its life cycle. The steps to be taken toward professionalization are outlined along with recommendations.

  11. Investing in Software Sustainment

    DTIC Science & Technology

    2015-04-30

    colored arrows simply represent a reinforcing  loop called the “ Bandwagon   Effect ”.  This  effect   simply means that a series of successful missions will...the Software Engineering Institute (SEI) developed a simulation model for analyzing the effects of changes in demand for software sustainment and the...developed a simulation model for analyzing the effects of changes in demand for software sustainment and the corresponding funding decisions. The model

  12. Criteria for software modularization

    NASA Technical Reports Server (NTRS)

    Card, David N.; Page, Gerald T.; Mcgarry, Frank E.

    1985-01-01

    A central issue in programming practice involves determining the appropriate size and information content of a software module. This study attempted to determine the effectiveness of two widely used criteria for software modularization, strength and size, in reducing fault rate and development cost. Data from 453 FORTRAN modules developed by professional programmers were analyzed. The results indicated that module strength is a good criterion with respect to fault rate, whereas arbitrary module size limitations inhibit programmer productivity. This analysis is a first step toward defining empirically based standards for software modularization.

  13. Multiphase flow calculation software

    DOEpatents

    Fincke, James R.

    2003-04-15

    Multiphase flow calculation software and computer-readable media carrying computer executable instructions for calculating liquid and gas phase mass flow rates of high void fraction multiphase flows. The multiphase flow calculation software employs various given, or experimentally determined, parameters in conjunction with a plurality of pressure differentials of a multiphase flow, preferably supplied by a differential pressure flowmeter or the like, to determine liquid and gas phase mass flow rates of the high void fraction multiphase flows. Embodiments of the multiphase flow calculation software are suitable for use in a variety of applications, including real-time management and control of an object system.

  14. Error Free Software

    NASA Technical Reports Server (NTRS)

    1985-01-01

    A mathematical theory for development of "higher order" software to catch computer mistakes resulted from a Johnson Space Center contract for Apollo spacecraft navigation. Two women who were involved in the project formed Higher Order Software, Inc. to develop and market the system of error analysis and correction. They designed software which is logically error-free, which, in one instance, was found to increase productivity by 600%. USE.IT defines its objectives using AXES -- a user can write in English and the system converts to computer languages. It is employed by several large corporations.

  15. Educational Software Acquisition for Microcomputers.

    ERIC Educational Resources Information Center

    Erikson, Warren; Turban, Efraim

    1985-01-01

    Examination of issues involved in acquiring appropriate microcomputer software for higher education focuses on the following points: developing your own software; finding commercially available software; using published evaluations; pre-purchase testing; customizing and adapting commercial software; post-purchase testing; and software use. A…

  16. A Symphony of Software.

    ERIC Educational Resources Information Center

    Currents, 2002

    2002-01-01

    Offers a descriptive table of databases that help higher education institutions orchestrate advancement operations. Information includes vendor, contact, software, price, database engine/server platform, recommended reporting tools, record capacity, and client type. (EV)

  17. Error-Free Software

    NASA Technical Reports Server (NTRS)

    1989-01-01

    001 is an integrated tool suited for automatically developing ultra reliable models, simulations and software systems. Developed and marketed by Hamilton Technologies, Inc. (HTI), it has been applied in engineering, manufacturing, banking and software tools development. The software provides the ability to simplify the complex. A system developed with 001 can be a prototype or fully developed with production quality code. It is free of interface errors, consistent, logically complete and has no data or control flow errors. Systems can be designed, developed and maintained with maximum productivity. Margaret Hamilton, President of Hamilton Technologies, also directed the research and development of USE.IT, an earlier product which was the first computer aided software engineering product in the industry to concentrate on automatically supporting the development of an ultrareliable system throughout its life cycle. Both products originated in NASA technology developed under a Johnson Space Center contract.

  18. Software interface verifier

    NASA Technical Reports Server (NTRS)

    Soderstrom, Tomas J.; Krall, Laura A.; Hope, Sharon A.; Zupke, Brian S.

    1994-01-01

    A Telos study of 40 recent subsystem deliveries into the DSN at JPL found software interface testing to be the single most expensive and error-prone activity, and the study team suggested creating an automated software interface test tool. The resulting Software Interface Verifier (SIV), which was funded by NASA/JPL and created by Telos, employed 92 percent software reuse to quickly create an initial version which incorporated early user feedback. SIV is now successfully used by developers for interface prototyping and unit testing, by test engineers for formal testing, and by end users for non-intrusive data flow tests in the operational environment. Metrics, including cost, are included. Lessons learned include the need for early user training. SIV is ported to many platforms and can be successfully used or tailored by other NASA groups.

  19. Computer Center: Software Review.

    ERIC Educational Resources Information Center

    Duhrkopf, Richard, Ed.; Belshe, John F., Ed.

    1988-01-01

    Reviews a software package, "Mitosis-Meiosis," available for Apple II or IBM computers with colorgraphics capabilities. Describes the documentation, presentation and flexibility of the program. Rates the program based on graphics and usability in a biology classroom. (CW)

  20. Evaluation of Visualization Software

    NASA Technical Reports Server (NTRS)

    Globus, Al; Uselton, Sam

    1995-01-01

    Visualization software is widely used in scientific and engineering research. But computed visualizations can be very misleading, and the errors are easy to miss. We feel that the software producing the visualizations must be thoroughly evaluated and the evaluation process as well as the results must be made available. Testing and evaluation of visualization software is not a trivial problem. Several methods used in testing other software are helpful, but these methods are (apparently) often not used. When they are used, the description and results are generally not available to the end user. Additional evaluation methods specific to visualization must also be developed. We present several useful approaches to evaluation, ranging from numerical analysis of mathematical portions of algorithms to measurement of human performance while using visualization systems. Along with this brief survey, we present arguments for the importance of evaluations and discussions of appropriate use of some methods.

  1. HOMER® Energy Modeling Software

    SciTech Connect

    Lambert, Tom

    2000-12-31

    The HOMER® energy modeling software is a tool for designing and analyzing hybrid power systems, which contain a mix of conventional generators, cogeneration, wind turbines, solar photovoltaic, hydropower, batteries, fuel cells, hydropower, biomass and other inputs.

  2. Software For Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Wang, Lui; Bayer, Steve E.

    1992-01-01

    SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.

  3. GFAST Software Demonstration

    NASA Image and Video Library

    2017-03-17

    NASA engineers and test directors gather in Firing Room 3 in the Launch Control Center at NASA's Kennedy Space Center in Florida, to watch a demonstration of the automated command and control software for the agency's Space Launch System (SLS) and Orion spacecraft. The software is called the Ground Launch Sequencer. It will be responsible for nearly all of the launch commit criteria during the final phases of launch countdowns. The Ground and Flight Application Software Team (GFAST) demonstrated the software. It was developed by the Command, Control and Communications team in the Ground Systems Development and Operations (GSDO) Program. GSDO is helping to prepare the center for the first test flight of Orion atop the SLS on Exploration Mission 1.

  4. Tier2 Submit Software

    EPA Pesticide Factsheets

    Download this tool for Windows or Mac, which helps facilities prepare a Tier II electronic chemical inventory report. The data can also be exported into the CAMEOfm (Computer-Aided Management of Emergency Operations) emergency planning software.

  5. GFAST Software Demonstration

    NASA Image and Video Library

    2017-03-17

    NASA engineers and test directors gather in Firing Room 3 in the Launch Control Center at NASA's Kennedy Space Center in Florida, to watch a demonstration of the automated command and control software for the agency's Space Launch System (SLS) and Orion spacecraft. In front, far right, is Charlie Blackwell-Thompson, launch director for Exploration Mission 1 (EM-1). The software is called the Ground Launch Sequencer. It will be responsible for nearly all of the launch commit criteria during the final phases of launch countdowns. The Ground and Flight Application Software Team (GFAST) demonstrated the software. It was developed by the Command, Control and Communications team in the Ground Systems Development and Operations (GSDO) Program. GSDO is helping to prepare the center for the first test flight of Orion atop the SLS on EM-1.

  6. SEER Data & Software

    Cancer.gov

    Options for accessing datasets for incidence, mortality, county populations, standard populations, expected survival, and SEER-linked and specialized data. Plus variable definitions, documentation for reporting and using datasets, statistical software (SEER*Stat), and observational research resources.

  7. Astronomical Software Directory Service

    NASA Astrophysics Data System (ADS)

    Hanisch, Robert J.; Payne, Harry; Hayes, Jeffrey

    1997-01-01

    With the support of NASA's Astrophysics Data Program (NRA 92-OSSA-15), we have developed the Astronomical Software Directory Service (ASDS): a distributed, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URLs indexed for full-text searching. Users are performing about 400 searches per month. A new aspect of our service is the inclusion of telescope and instrumentation manuals, which prompted us to change the name to the Astronomical Software and Documentation Service. ASDS was originally conceived to serve two purposes: to provide a useful Internet service in an area of expertise of the investigators (astronomical software), and as a research project to investigate various architectures for searching through a set of documents distributed across the Internet. Two of the co-investigators were then installing and maintaining astronomical software as their primary job responsibility. We felt that a service which incorporated our experience in this area would be more useful than a straightforward listing of software packages. The original concept was for a service based on the client/server model, which would function as a directory/referral service rather than as an archive. For performing the searches, we began our investigation with a decision to evaluate the Isite software from the Center for Networked Information Discovery and Retrieval (CNIDR). This software was intended as a replacement for Wide-Area Information Service (WAIS), a client/server technology for performing full-text searches through a set of documents. Isite had some additional features that we considered attractive, and we enjoyed the cooperation of the Isite developers, who were happy to have ASDS as a demonstration project. We ended up staying with the software throughout the project, making modifications to take advantage of new features as they came along, as well as

  8. Neogene-quaternary Ostracoda and paleoenvironments, of the Limón basin, Costa Rica, and Bocas del Toro basin, Panama

    USGS Publications Warehouse

    Borne, P.F.; Cronin, T. M.; Hazel, J.E.

    1999-01-01

    Tropical marine ostracodes from Neogene and Quaternary sediments of the Central American Caribbean region have been the subject of biostratigraphic, ecological, taxonomic, and evolutionary studies. As part of the Panama Paleontology Project (PPP), Neogene and Quaternary ostracodes are being studied from the Central American region. The overall goal of this research is to evaluate the impact of the emergence of the Central American Isthmus as a land barrier between the Caribbean/tropical Atlantic and the Pacific oceans on marine ostracode biodiversity and the oceanic environments in which extant ostracodes evolved. Due to the ecological specificity of many living tropical ostracode species, they are ideally suited for reconstructing paleoenvironments on the basis of their occurrence in fossil assemblages, which in turn can lead to a better understanding of the tropical climatic and tectonic history of Central America. The principal aims of this chapter are: (a) to document the composition of the ostracode assemblages from the Limón Basin of Costa Rica and the Bocas del Toro Basin of Panama, two areas yielding extensive ma rine ostracode assemblages; (b) to describe the environments of deposition within these basins; and (c) to document the stratigraphic distribution of potentially agediagnostic ostracode species in the Limón and Bocas del Toro basins in order to enhance their use in Central American biostratigraphy. A secondary, but none-the-less important goal is to assemble a database on the distribution of modem ostracode species in the Caribbean and adjacent areas as a basis for comparison with fossil assemblages. Although the ecological, biostratigraphic and paleoenvironmental conclusions presented here will improve as additional material is studied, these fossil and modem ostracode databases constitute the foundation for future evolutionary and geochernical studies of tropical Caribbean and eastern Pacific Ocean ostracodes. Moreover, we present here evidence

  9. Image Processing Software

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The Ames digital image velocimetry technology has been incorporated in a commercially available image processing software package that allows motion measurement of images on a PC alone. The software, manufactured by Werner Frei Associates, is IMAGELAB FFT. IMAGELAB FFT is a general purpose image processing system with a variety of other applications, among them image enhancement of fingerprints and use by banks and law enforcement agencies for analysis of videos run during robberies.

  10. Engineering and Software Engineering

    NASA Astrophysics Data System (ADS)

    Jackson, Michael

    The phrase ‘software engineering' has many meanings. One central meaning is the reliable development of dependable computer-based systems, especially those for critical applications. This is not a solved problem. Failures in software development have played a large part in many fatalities and in huge economic losses. While some of these failures may be attributable to programming errors in the narrowest sense—a program's failure to satisfy a given formal specification—there is good reason to think that most of them have other roots. These roots are located in the problem of software engineering rather than in the problem of program correctness. The famous 1968 conference was motivated by the belief that software development should be based on “the types of theoretical foundations and practical disciplines that are traditional in the established branches of engineering.” Yet after forty years of currency the phrase ‘software engineering' still denotes no more than a vague and largely unfulfilled aspiration. Two major causes of this disappointment are immediately clear. First, too many areas of software development are inadequately specialised, and consequently have not developed the repertoires of normal designs that are the indispensable basis of reliable engineering success. Second, the relationship between structural design and formal analytical techniques for software has rarely been one of fruitful synergy: too often it has defined a boundary between competing dogmas, at which mutual distrust and incomprehension deprive both sides of advantages that should be within their grasp. This paper discusses these causes and their effects. Whether the common practice of software development will eventually satisfy the broad aspiration of 1968 is hard to predict; but an understanding of past failure is surely a prerequisite of future success.

  11. Software Engineering Education Directory

    DTIC Science & Technology

    1988-01-01

    Dana Hausman and Suzanne Woolf were crucial to the successful completion of this edition of the directory. Their teamwork, energy, and dedication...for this directory began in the summer of 1986 with a questionnaire mailed to schools selected from Peterson’s Graduate Programs in Engineering and...Christoper, and Siegel, Stan Software Cost Estimation and Life-Cycle Control by Putnam, Lawrence H. Software Quality Assurance: A Practical Approach by

  12. Software Cost Estimating,

    DTIC Science & Technology

    1982-05-13

    Size Of The Software. A favourite measure for software system size is linos of operational code, or deliverable code (operational code plus...regression models, these conversions are either derived from productivity measures using the "cost per instruction" type of equation or they are...appropriate to different development organisattons, differert project types, different sets of units for measuring e and s, and different items

  13. Software Reliability 2002

    NASA Technical Reports Server (NTRS)

    Wallace, Dolores R.

    2003-01-01

    In FY01 we learned that hardware reliability models need substantial changes to account for differences in software, thus making software reliability measurements more effective, accurate, and easier to apply. These reliability models are generally based on familiar distributions or parametric methods. An obvious question is 'What new statistical and probability models can be developed using non-parametric and distribution-free methods instead of the traditional parametric method?" Two approaches to software reliability engineering appear somewhat promising. The first study, begin in FY01, is based in hardware reliability, a very well established science that has many aspects that can be applied to software. This research effort has investigated mathematical aspects of hardware reliability and has identified those applicable to software. Currently the research effort is applying and testing these approaches to software reliability measurement, These parametric models require much project data that may be difficult to apply and interpret. Projects at GSFC are often complex in both technology and schedules. Assessing and estimating reliability of the final system is extremely difficult when various subsystems are tested and completed long before others. Parametric and distribution free techniques may offer a new and accurate way of modeling failure time and other project data to provide earlier and more accurate estimates of system reliability.

  14. Encyclopedia of software components

    NASA Technical Reports Server (NTRS)

    Vanwarren, Lloyd (Inventor); Beckman, Brian C. (Inventor)

    1991-01-01

    Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

  15. Software Process Assessment (SPA)

    NASA Technical Reports Server (NTRS)

    Rosenberg, Linda H.; Sheppard, Sylvia B.; Butler, Scott A.

    1994-01-01

    NASA's environment mirrors the changes taking place in the nation at large, i.e. workers are being asked to do more work with fewer resources. For software developers at NASA's Goddard Space Flight Center (GSFC), the effects of this change are that we must continue to produce quality code that is maintainable and reusable, but we must learn to produce it more efficiently and less expensively. To accomplish this goal, the Data Systems Technology Division (DSTD) at GSFC is trying a variety of both proven and state-of-the-art techniques for software development (e.g., object-oriented design, prototyping, designing for reuse, etc.). In order to evaluate the effectiveness of these techniques, the Software Process Assessment (SPA) program was initiated. SPA was begun under the assumption that the effects of different software development processes, techniques, and tools, on the resulting product must be evaluated in an objective manner in order to assess any benefits that may have accrued. SPA involves the collection and analysis of software product and process data. These data include metrics such as effort, code changes, size, complexity, and code readability. This paper describes the SPA data collection and analysis methodology and presents examples of benefits realized thus far by DSTD's software developers and managers.

  16. Software for the EVLA

    NASA Astrophysics Data System (ADS)

    Butler, Bryan J.; van Moorsel, Gustaaf; Tody, Doug

    2004-09-01

    The Expanded Very Large Array (EVLA) project is the next generation instrument for high resolution long-millimeter to short-meter wavelength radio astronomy. It is currently funded by NSF, with completion scheduled for 2012. The EVLA will upgrade the VLA with new feeds, receivers, data transmission hardware, correlator, and a new software system to enable the instrument to achieve its full potential. This software includes both that required for controlling and monitoring the instrument and that involved with the scientific dataflow. We concentrate here on a portion of the dataflow software, including: proposal preparation, submission, and handling; observation preparation, scheduling, and remote monitoring; data archiving; and data post-processing, including both automated (pipeline) and manual processing. The primary goals of the software are: to maximize the scientific return of the EVLA; provide ease of use, for both novices and experts; exploit commonality amongst all NRAO telescopes where possible. This last point is both a bane and a blessing: we are not at liberty to do whatever we want in the software, but on the other hand we may borrow from other projects (notably ALMA and GBT) where appropriate. The software design methodology includes detailed initial use-cases and requirements from the scientists, intimate interaction between the scientists and the programmers during design and implementation, and a thorough testing and acceptance plan.

  17. Encyclopedia of Software Components

    NASA Technical Reports Server (NTRS)

    Warren, Lloyd V. (Inventor); Beckman, Brian C. (Inventor)

    1997-01-01

    Intelligent browsing through a collection of reusable software components is facilitated with a computer having a video monitor and a user input interface such as a keyboard or a mouse for transmitting user selections, by presenting a picture of encyclopedia volumes with respective visible labels referring to types of software, in accordance with a metaphor in which each volume includes a page having a list of general topics under the software type of the volume and pages having lists of software components for each one of the generic topics, altering the picture to open one of the volumes in response to an initial user selection specifying the one volume to display on the monitor a picture of the page thereof having the list of general topics and altering the picture to display the page thereof having a list of software components under one of the general topics in response to a next user selection specifying the one general topic, and then presenting a picture of a set of different informative plates depicting different types of information about one of the software components in response to a further user selection specifying the one component.

  18. HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

    PubMed

    Prilusky, Jaime; Oueillet, Eric; Ulryck, Nathalie; Pajon, Anne; Bernauer, Julie; Krimm, Isabelle; Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Liger, Dominique; Trésaugues, Lionel; Sussman, Joel L; Janin, Joël; van Tilbeurgh, Herman; Poupon, Anne

    2005-06-01

    Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

  19. Computing and software

    USGS Publications Warehouse

    White, Gary C.; Hines, J.E.

    2004-01-01

    The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methodsavailable. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them.In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented.Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004).Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years.Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood

  20. Modulation of light-driven arousal by LIM-homeodomain transcription factor Apterous in large PDF-positive lateral neurons of the Drosophila brain

    PubMed Central

    Shimada, Naoto; Inami, Show; Sato, Shoma; Kitamoto, Toshihiro; Sakai, Takaomi

    2016-01-01

    Apterous (Ap), the best studied LIM-homeodomain transcription factor in Drosophila, cooperates with the cofactor Chip (Chi) to regulate transcription of specific target genes. Although Ap regulates various developmental processes, its function in the adult brain remains unclear. Here, we report that Ap and Chi in the neurons expressing PDF, a neuropeptide, play important roles in proper sleep/wake regulation in adult flies. PDF-expressing neurons consist of two neuronal clusters: small ventral-lateral neurons (s-LNvs) acting as the circadian pacemaker and large ventral-lateral neurons (l-LNvs) regulating light-driven arousal. We identified that Ap localizes to the nuclei of s-LNvs and l-LNvs. In light-dark (LD) cycles, RNAi knockdown or the targeted expression of dominant-negative forms of Ap or Chi in PDF-expressing neurons or l-LNvs promoted arousal. In contrast, in constant darkness, knockdown of Ap in PDF-expressing neurons did not promote arousal, indicating that a reduced Ap function in PDF-expressing neurons promotes light-driven arousal. Furthermore, Ap expression in l-LNvs showed daily rhythms (peaking at midnight), which are generated by a direct light-dependent mechanism rather than by the endogenous clock. These results raise the possibility that the daily oscillation of Ap expression in l-LNvs may contribute to the buffering of light-driven arousal in wild-type flies. PMID:27853240

  1. Modulation of light-driven arousal by LIM-homeodomain transcription factor Apterous in large PDF-positive lateral neurons of the Drosophila brain.

    PubMed

    Shimada, Naoto; Inami, Show; Sato, Shoma; Kitamoto, Toshihiro; Sakai, Takaomi

    2016-11-17

    Apterous (Ap), the best studied LIM-homeodomain transcription factor in Drosophila, cooperates with the cofactor Chip (Chi) to regulate transcription of specific target genes. Although Ap regulates various developmental processes, its function in the adult brain remains unclear. Here, we report that Ap and Chi in the neurons expressing PDF, a neuropeptide, play important roles in proper sleep/wake regulation in adult flies. PDF-expressing neurons consist of two neuronal clusters: small ventral-lateral neurons (s-LNvs) acting as the circadian pacemaker and large ventral-lateral neurons (l-LNvs) regulating light-driven arousal. We identified that Ap localizes to the nuclei of s-LNvs and l-LNvs. In light-dark (LD) cycles, RNAi knockdown or the targeted expression of dominant-negative forms of Ap or Chi in PDF-expressing neurons or l-LNvs promoted arousal. In contrast, in constant darkness, knockdown of Ap in PDF-expressing neurons did not promote arousal, indicating that a reduced Ap function in PDF-expressing neurons promotes light-driven arousal. Furthermore, Ap expression in l-LNvs showed daily rhythms (peaking at midnight), which are generated by a direct light-dependent mechanism rather than by the endogenous clock. These results raise the possibility that the daily oscillation of Ap expression in l-LNvs may contribute to the buffering of light-driven arousal in wild-type flies.

  2. The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types.

    PubMed

    Zhang, Feifan; Bhattacharya, Abhishek; Nelson, Jessica C; Abe, Namiko; Gordon, Patricia; Lloret-Fernandez, Carla; Maicas, Miren; Flames, Nuria; Mann, Richard S; Colón-Ramos, Daniel A; Hobert, Oliver

    2014-01-01

    Transcription factors that drive neuron type-specific terminal differentiation programs in the developing nervous system are often expressed in several distinct neuronal cell types, but to what extent they have similar or distinct activities in individual neuronal cell types is generally not well explored. We investigate this problem using, as a starting point, the C. elegans LIM homeodomain transcription factor ttx-3, which acts as a terminal selector to drive the terminal differentiation program of the cholinergic AIY interneuron class. Using a panel of different terminal differentiation markers, including neurotransmitter synthesizing enzymes, neurotransmitter receptors and neuropeptides, we show that ttx-3 also controls the terminal differentiation program of two additional, distinct neuron types, namely the cholinergic AIA interneurons and the serotonergic NSM neurons. We show that the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors. One of the collaborating transcription factors is the POU homeobox gene unc-86, which collaborates with ttx-3 to determine the identity of the serotonergic NSM neurons. unc-86 in turn operates independently of ttx-3 in the anterior ganglion where it collaborates with the ARID-type transcription factor cfi-1 to determine the cholinergic identity of the IL2 sensory and URA motor neurons. In conclusion, transcription factors operate as terminal selectors in distinct combinations in different neuron types, defining neuron type-specific identity features.

  3. Drosophila melanogaster muscle LIM protein and alpha-actinin function together to stabilize muscle cytoarchitecture: a potential role for Mlp84B in actin-crosslinking.

    PubMed

    Clark, Kathleen A; Kadrmas, Julie L

    2013-06-01

    Stabilization of tissue architecture during development and growth is essential to maintain structural integrity. Because of its contractile nature, muscle is especially susceptible to physiological stresses, and has multiple mechanisms to maintain structural integrity. The Drosophila melanogaster Muscle LIM Protein (MLP), Mlp84B, participates in muscle maintenance, yet its precise mechanism of action is still controversial. Through a candidate approach, we identified α-actinin as a protein that functions with Mlp84B to ensure muscle integrity. α-actinin RNAi animals die primarily as pupae, and Mlp84B RNAi animals are adult viable. RNAi knockdown of Mlp84B and α-actinin together produces synergistic early larval lethality and destabilization of Z-line structures. We recapitulated these phenotypes using combinations of traditional loss-of-function alleles and single-gene RNAi. We observe that Mlp84B induces the formation of actin loops in muscle cell nuclei in the absence of nuclear α-actinin, suggesting Mlp84B has intrinsic actin cross-linking activity, which may complement α-actinin cross-linking activity at sites of actin filament anchorage. These results reveal a molecular mechanism for MLP stabilization of muscle and implicate reduced actin crosslinking as the primary destabilizing defect in MLP-associated cardiomyopathies. Our data support a model in which α-actinin and Mlp84B have important and overlapping functions at sites of actin filament anchorage to preserve muscle structure and function. Copyright © 2013 Wiley Periodicals, Inc.

  4. Four and a Half LIM Domains 1b (Fhl1b) Is Essential for Regulating the Liver versus Pancreas Fate Decision and for β-Cell Regeneration

    PubMed Central

    Xu, Jin; Cui, Jiaxi; Del Campo, Aranzazu; Shin, Chong Hyun

    2016-01-01

    The liver and pancreas originate from overlapping embryonic regions, and single-cell lineage tracing in zebrafish has shown that Bone morphogenetic protein 2b (Bmp2b) signaling is essential for determining the fate of bipotential hepatopancreatic progenitors towards the liver or pancreas. Despite its pivotal role, the gene regulatory networks functioning downstream of Bmp2b signaling in this process are poorly understood. We have identified four and a half LIM domains 1b (fhl1b), which is primarily expressed in the prospective liver anlage, as a novel target of Bmp2b signaling. fhl1b depletion compromised liver specification and enhanced induction of pancreatic cells from endodermal progenitors. Conversely, overexpression of fhl1b favored liver specification and inhibited induction of pancreatic cells. By single-cell lineage tracing, we showed that fhl1b depletion led lateral endodermal cells, destined to become liver cells, to become pancreatic cells. Reversely, when fhl1b was overexpressed, medially located endodermal cells, fated to differentiate into pancreatic and intestinal cells, contributed to the liver by directly or indirectly modulating the discrete levels of pdx1 expression in endodermal progenitors. Moreover, loss of fhl1b increased the regenerative capacity of β-cells by increasing pdx1 and neurod expression in the hepatopancreatic ductal system. Altogether, these data reveal novel and critical functions of Fhl1b in the hepatic versus pancreatic fate decision and in β-cell regeneration. PMID:26845333

  5. Chemical obtaining of LiMO2 and LiM2O4 (M=Co, Mn) oxides, for cathodic applications in Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Y Neira-Guio, A.; Gómez Cuaspud, J. A.; López, E. Vera; Pineda Triana, Y.

    2017-12-01

    This paper describes the synthesis and characterization of two spinel and olivine-type multicomponent oxides based on LiMO2 and LiM2O4 systems (M=Co and Mn), which represent the current state of the art in the development of cathodes for Li-ion batteries. A simple combustion synthesis process was employed to obtain the nanometric oxides in powder form (crystal sizes around 5-8nm), with a number of improved surface characteristics. The characterization by X-Ray Diffraction (XRD), Scanning and Transmission Electron Microscopy (SEM, TEM) and X-Ray Fluorescence (XRF), allowed to evaluate the morphology and the stoichiometric compositions of solids, obtaining a concordant pure crystalline phase of LiCoO2 and LiMn2O4 oxides identified in a rhombohedral and cubic phase with punctual group R-3m (1 6 6) and Fm-3m (2 2 5) respectively. The electrical characterization of materials developed by impedance spectroscopy solid state, allowed to determine a p-type semiconducting behaviour with conductivity values of 6.2×10-3 and 2.7×10-7 S for LiCoO2 and LiMn2O4 systems, consistent with the state of the art for such materials.

  6. Impact of Agile Software Development Model on Software Maintainability

    ERIC Educational Resources Information Center

    Gawali, Ajay R.

    2012-01-01

    Software maintenance and support costs account for up to 60% of the overall software life cycle cost and often burdens tightly budgeted information technology (IT) organizations. Agile software development approach delivers business value early, but implications on software maintainability are still unknown. The purpose of this quantitative study…

  7. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 15

    NASA Technical Reports Server (NTRS)

    1997-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  8. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 13

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  9. Software Engineering Laboratory Series: Collected Software Engineering Papers. Volume 14

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The Software Engineering Laboratory (SEL) is an organization sponsored by NASA/GSFC and created to investigate the effectiveness of software engineering technologies when applied to the development of application software. The activities, findings, and recommendations of the SEL are recorded in the Software Engineering Laboratory Series, a continuing series of reports that includes this document.

  10. Software cost/resource modeling: Software quality tradeoff measurement

    NASA Technical Reports Server (NTRS)

    Lawler, R. W.

    1980-01-01

    A conceptual framework for treating software quality from a total system perspective is developed. Examples are given to show how system quality objectives may be allocated to hardware and software; to illustrate trades among quality factors, both hardware and software, to achieve system performance objectives; and to illustrate the impact of certain design choices on software functionality.

  11. Aircraft Design Software

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Successful commercialization of the AirCraft SYNThesis (ACSYNT) tool has resulted in the creation of Phoenix Integration, Inc. ACSYNT has been exclusively licensed to the company, an outcome of a seven year, $3 million effort to provide unique software technology to a focused design engineering market. Ames Research Center formulated ACSYNT and in working with the Virginia Polytechnic Institute CAD Laboratory, began to design and code a computer-aided design for ACSYNT. Using a Joint Sponsored Research Agreement, Ames formed an industry-government-university alliance to improve and foster research and development for the software. As a result of the ACSYNT Institute, the software is becoming a predominant tool for aircraft conceptual design. ACSYNT has been successfully applied to high- speed civil transport configuration, subsonic transports, and supersonic fighters.

  12. Automated software development workstation

    NASA Technical Reports Server (NTRS)

    Prouty, Dale A.; Klahr, Philip

    1988-01-01

    A workstation is being developed that provides a computational environment for all NASA engineers across application boundaries, which automates reuse of existing NASA software and designs, and efficiently and effectively allows new programs and/or designs to be developed, catalogued, and reused. The generic workstation is made domain specific by specialization of the user interface, capturing engineering design expertise for the domain, and by constructing/using a library of pertinent information. The incorporation of software reusability principles and expert system technology into this workstation provide the obvious benefits of increased productivity, improved software use and design reliability, and enhanced engineering quality by bringing engineering to higher levels of abstraction based on a well tested and classified library.

  13. libdrdc: software standards library

    NASA Astrophysics Data System (ADS)

    Erickson, David; Peng, Tie

    2008-04-01

    This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

  14. AMBER instrument control software

    NASA Astrophysics Data System (ADS)

    Le Coarer, Etienne P.; Zins, Gerard; Gluck, Laurence; Duvert, Gilles; Driebe, Thomas; Ohnaka, Keiichi; Heininger, Matthias; Connot, Claus; Behrend, Jan; Dugue, Michel; Clausse, Jean Michel; Millour, Florentin

    2004-09-01

    AMBER (Astronomical Multiple BEam Recombiner) is a 3 aperture interferometric recombiner operating between 1 and 2.5 um, for the Very Large Telescope Interferometer (VLTI). The control software of the instrument, based on the VLT Common Software, has been written to comply with specific features of the AMBER hardware, such as the Infrared detector read out modes or piezo stage drivers, as well as with the very specific operation modes of an interferomtric instrument. In this respect, the AMBER control software was designed to insure that all operations, from the preparation of the observations to the control/command of the instrument during the observations, would be kept as simple as possible for the users and operators, opening the use of an interferometric instrument to the largest community of astronomers. Peculiar attention was given to internal checks and calibration procedures both to evaluate data quality in real time, and improve the successes of long term UV plane coverage observations.

  15. Astronomers as Software Developers

    NASA Astrophysics Data System (ADS)

    Pildis, Rachel A.

    2016-01-01

    Astronomers know that their research requires writing, adapting, and documenting computer software. Furthermore, they often have to learn new computer languages and figure out how existing programs work without much documentation or guidance and with extreme time pressure. These are all skills that can lead to a software development job, but recruiters and employers probably won't know that. I will discuss all the highly useful experience that astronomers may not know that they already have, and how to explain that knowledge to others when looking for non-academic software positions. I will also talk about some of the pitfalls I have run into while interviewing for jobs and working as a developer, and encourage you to embrace the curiosity employers might have about your non-standard background.

  16. Software reliability perspectives

    NASA Technical Reports Server (NTRS)

    Wilson, Larry; Shen, Wenhui

    1987-01-01

    Software which is used in life critical functions must be known to be highly reliable before installation. This requires a strong testing program to estimate the reliability, since neither formal methods, software engineering nor fault tolerant methods can guarantee perfection. Prior to the final testing software goes through a debugging period and many models have been developed to try to estimate reliability from the debugging data. However, the existing models are poorly validated and often give poor performance. This paper emphasizes the fact that part of their failures can be attributed to the random nature of the debugging data given to these models as input, and it poses the problem of correcting this defect as an area of future research.

  17. CONRAD Software Architecture

    NASA Astrophysics Data System (ADS)

    Guzman, J. C.; Bennett, T.

    2008-08-01

    The Convergent Radio Astronomy Demonstrator (CONRAD) is a collaboration between the computing teams of two SKA pathfinder instruments, MeerKAT (South Africa) and ASKAP (Australia). Our goal is to produce the required common software to operate, process and store the data from the two instruments. Both instruments are synthesis arrays composed of a large number of antennas (40 - 100) operating at centimeter wavelengths with wide-field capabilities. Key challenges are the processing of high volume of data in real-time as well as the remote mode of operations. Here we present the software architecture for CONRAD. Our design approach is to maximize the use of open solutions and third-party software widely deployed in commercial applications, such as SNMP and LDAP, and to utilize modern web-based technologies for the user interfaces, such as AJAX.

  18. The EOSDIS software challenge

    NASA Astrophysics Data System (ADS)

    Jaworski, Allan

    1993-08-01

    The Earth Observing System (EOS) Data and Information System (EOSDIS) will serve as a major resource for the earth science community, supporting both command and control of complex instruments onboard the EOS spacecraft and the archiving, distribution, and analysis of data. The scale of EOSDIS and the volume of multidisciplinary research to be conducted using EOSDIS resources will produce unparalleled needs for technology transparency, data integration, and system interoperability. The scale of this effort far outscopes any previous scientific data system in its breadth or operational and performance needs. Modern hardware technology can meet the EOSDIS technical challenge. Multiprocessing speeds of many giga-flops are being realized by modern computers. Online storage disk, optical disk, and videocassette libraries with storage capacities of many terabytes are now commercially available. Radio frequency and fiber optics communications networks with gigabit rates are demonstrable today. It remains, of course, to perform the system engineering to establish the requirements, architectures, and designs that will implement the EOSDIS systems. Software technology, however, has not enjoyed the price/performance advances of hardware. Although we have learned to engineer hardware systems which have several orders of magnitude greater complexity and performance than those built in the 1960's, we have not made comparable progress in dramatically reducing the cost of software development. This lack of progress may significantly reduce our capabilities to achieve economically the types of highly interoperable, responsive, integraded, and productive environments which are needed by the earth science community. This paper describes some of the EOSDIS software requirements and current activities in the software community which are applicable to meeting the EOSDIS challenge. Some of these areas include intelligent user interfaces, software reuse libraries, and domain engineering

  19. Needs challenge software

    SciTech Connect

    NONE

    1997-07-01

    New hardware and software tools build on existing platforms and add performance and ease-of-use benefits as the struggle to find and produce hydrocarbons at the lowest cost becomes more and more competitive. Software tools now provide geoscientists and petroleum engineers with a better understanding of reservoirs from the shape and makeup of formation to behavior projections as hydrocarbons are extracted. Petroleum software tools allow scientists to simulate oil flow, predict the life expectancy of a reservoir, and even help determine how to extend the life and economic viability of the reservoir. The requirement of the petroleum industry to find andmore » extract petroleum more efficiently drives the solutions provided by software and service companies. To one extent or another, most of the petroleum software products available today have achieved an acceptable level of competency. Innovative, high-impact products from small, focussed companies often were bought out by larger companies with deeper pockets if their developers couldn`t fund their expansion. Other products disappeared from the scene, because they were unable to evolve fast enough to compete. There are still enough small companies around producing excellent products to prevent the marketplace from feeling too narrow and lacking in choice. Oil companies requiring specific solutions to their problems have helped fund product development within the commercial sector. As the industry has matured, strategic alliances between vendors, both hardware and software, have provided market advantages, often combining strengths to enter new and undeveloped areas for technology. The pace of technological development has been fast and constant.« less

  20. Secure software practices among Malaysian software practitioners: An exploratory study

    NASA Astrophysics Data System (ADS)

    Mohamed, Shafinah Farvin Packeer; Baharom, Fauziah; Deraman, Aziz; Yahya, Jamaiah; Mohd, Haslina

    2016-08-01

    Secure software practices is increasingly gaining much importance among software practitioners and researchers due to the rise of computer crimes in the software industry. It has become as one of the determinant factors for producing high quality software. Even though its importance has been revealed, its current practice in the software industry is still scarce, particularly in Malaysia. Thus, an exploratory study is conducted among software practitioners in Malaysia to study their experiences and practices in the real-world projects. This paper discusses the findings from the study, which involved 93 software practitioners. Structured questionnaire is utilized for data collection purpose whilst statistical methods such as frequency, mean, and cross tabulation are used for data analysis. Outcomes from this study reveal that software practitioners are becoming increasingly aware on the importance of secure software practices, however, they lack of appropriate implementation, which could affect the quality of produced software.

  1. Real World Software Engineering

    DTIC Science & Technology

    1994-07-15

    Corvision Cortex Corporation Daisys S /Cubed, Inc. Design/IDF & CPN Meta Software Corp. 22 EasyCase Professional Evergreen CASE Tools 8522 150th 4th Ave NE...Final RSUoTL 28 Sep 92-31 May 94 4. TITLE AND SUBTITLE S . FUNDING NUMBERS Real World Software Engineering 6. AUTHOR( S ) Donald Gotterbarn Robert Riser . a...nin• Sm-i t’h 7. PERFORMING ORGANIZATION NAME( S ) AND AOORESS(ES1 8. PERFORMING ORGANIZATION REPORT NUMBER East Tennessee State University Department

  2. Security System Software

    NASA Technical Reports Server (NTRS)

    1993-01-01

    C Language Integration Production System (CLIPS), a NASA-developed expert systems program, has enabled a security systems manufacturer to design a new generation of hardware. C.CURESystem 1 Plus, manufactured by Software House, is a software based system that is used with a variety of access control hardware at installations around the world. Users can manage large amounts of information, solve unique security problems and control entry and time scheduling. CLIPS acts as an information management tool when accessed by C.CURESystem 1 Plus. It asks questions about the hardware and when given the answer, recommends possible quick solutions by non-expert persons.

  3. Machine Tool Software

    NASA Technical Reports Server (NTRS)

    1988-01-01

    A NASA-developed software package has played a part in technical education of students who major in Mechanical Engineering Technology at William Rainey Harper College. Professor Hack has been using (APT) Automatically Programmed Tool Software since 1969 in his CAD/CAM Computer Aided Design and Manufacturing curriculum. Professor Hack teaches the use of APT programming languages for control of metal cutting machines. Machine tool instructions are geometry definitions written in APT Language to constitute a "part program." The part program is processed by the machine tool. CAD/CAM students go from writing a program to cutting steel in the course of a semester.

  4. Automated software development workstation

    NASA Technical Reports Server (NTRS)

    1986-01-01

    Engineering software development was automated using an expert system (rule-based) approach. The use of this technology offers benefits not available from current software development and maintenance methodologies. A workstation was built with a library or program data base with methods for browsing the designs stored; a system for graphical specification of designs including a capability for hierarchical refinement and definition in a graphical design system; and an automated code generation capability in FORTRAN. The workstation was then used in a demonstration with examples from an attitude control subsystem design for the space station. Documentation and recommendations are presented.

  5. Provider software buyer's guide.

    PubMed

    1994-03-01

    To help long term care providers find new ways to improve quality of care and efficiency, Provider magazine presents the fourth annual listing of software firms marketing computer programs for all areas of nursing facility operations. On the following five pages, more than 80 software firms display their wares, with programs such as minimum data set and care planning, dietary, accounting and financials, case mix, and medication administration records. The guide also charts compatible hardware, integration ability, telephone numbers, company contacts, and easy-to-use reader service numbers.

  6. Provider software buyer's guide.

    PubMed

    1993-03-01

    To help long term care providers find new ways to improve quality of care and efficiency. Provider magazine presents the third annual listing of software firms marketing computer programs for all areas of nursing facility operations. On the following five pages, more than 80 software firms display their wares, with programs such as minimum data set and care planning, dietary, accounting and financials, case mix, and medication administration records. The guide also charts compatible hardware, integration ability, telephone numbers, company contacts, and easy-to-use reader service numbers.

  7. TIA Software User's Manual

    NASA Technical Reports Server (NTRS)

    Cramer, K. Elliott; Syed, Hazari I.

    1995-01-01

    This user's manual describes the installation and operation of TIA, the Thermal-Imaging acquisition and processing Application, developed by the Nondestructive Evaluation Sciences Branch at NASA Langley Research Center, Hampton, Virginia. TIA is a user friendly graphical interface application for the Macintosh 2 and higher series computers. The software has been developed to interface with the Perceptics/Westinghouse Pixelpipe(TM) and PixelStore(TM) NuBus cards and the GW Instruments MacADIOS(TM) input-output (I/O) card for the Macintosh for imaging thermal data. The software is also capable of performing generic image-processing functions.

  8. Software Models Impact Stresses

    NASA Technical Reports Server (NTRS)

    Hanshaw, Timothy C.; Roy, Dipankar; Toyooka, Mark

    1991-01-01

    Generalized Impact Stress Software designed to assist engineers in predicting stresses caused by variety of impacts. Program straightforward, simple to implement on personal computers, "user friendly", and handles variety of boundary conditions applied to struck body being analyzed. Applications include mathematical modeling of motions and transient stresses of spacecraft, analysis of slamming of piston, of fast valve shutoffs, and play of rotating bearing assembly. Provides fast and inexpensive analytical tool for analysis of stresses and reduces dependency on expensive impact tests. Written in FORTRAN 77. Requires use of commercial software package PLOT88.

  9. The Software Engineering Prototype.

    DTIC Science & Technology

    1983-06-01

    34. sThis cnly means that the ’claim’, i.e., "accepted wisdcu" in systems design, was set up as the aiternative to the hypcthesis, in accord with tra dit ion...conflict and its resolution are m~~lyto occur when users can exercise their influence 4n the levelc2- inert prcezss. Ccnflict 4itsslY os snotr lead...the traditional method of software de- velopment often has poor results. Recently, a new approach to software development, the prototype approach

  10. Software Management System

    NASA Technical Reports Server (NTRS)

    1994-01-01

    A software management system, originally developed for Goddard Space Flight Center (GSFC) by Century Computing, Inc. has evolved from a menu and command oriented system to a state-of-the art user interface development system supporting high resolution graphics workstations. Transportable Applications Environment (TAE) was initially distributed through COSMIC and backed by a TAE support office at GSFC. In 1993, Century Computing assumed the support and distribution functions and began marketing TAE Plus, the system's latest version. The software is easy to use and does not require programming experience.

  11. Center for Adaptive Optics | Software

    Science.gov Websites

    Center for Adaptive Optics A University of California Science and Technology Center home Adaptive Optics Software The Center for Adaptive Optics acts as a clearing house for distributing Software to Institutes it gives specialists in Adaptive Optics a place to distribute their software. All software is

  12. Sustaining Software-Intensive Systems

    DTIC Science & Technology

    2006-05-01

    2.2 Multi- Service Operational Test and Evaluation .......................................4 2.3 Stable Software Baseline...or equivalent document • completed Multi- Service Operational Test and Evaluation (MOT&E) for the potential production software package (or OT&E if...not multi- service ) • stable software production baseline • complete and current software documentation • Authority to Operate (ATO) for an

  13. Software tool for physics chart checks.

    PubMed

    Li, H Harold; Wu, Yu; Yang, Deshan; Mutic, Sasa

    2014-01-01

    Physics chart check has long been a central quality assurance (QC) measure in radiation oncology. The purpose of this work is to describe a software tool that aims to accomplish simplification, standardization, automation, and forced functions in the process. Nationally recognized guidelines, including American College of Radiology and American Society for Radiation Oncology guidelines and technical standards, and the American Association of Physicists in Medicine Task Group reports were identified, studied, and summarized. Meanwhile, the reported events related to physics chart check service were analyzed using an event reporting and learning system. A number of shortfalls in the chart check process were identified. To address these problems, a software tool was designed and developed under Microsoft. Net in C# to hardwire as many components as possible at each stage of the process. The software consists of the following 4 independent modules: (1) chart check management; (2) pretreatment and during treatment chart check assistant; (3) posttreatment chart check assistant; and (4) quarterly peer-review management. The users were a large group of physicists in the author's radiation oncology clinic. During over 1 year of use the tool has proven very helpful in chart checking management, communication, documentation, and maintaining consistency. The software tool presented in this work aims to assist physicists at each stage of the physics chart check process. The software tool is potentially useful for any radiation oncology clinics that are either in the process of pursuing or maintaining the American College of Radiology accreditation.

  14. Microcomputer Software Technician Curriculum.

    ERIC Educational Resources Information Center

    EASTCONN Regional Educational Services Center, North Windham, CT.

    This curriculum guide, developed for high schools in Connecticut, outlines a 4-year program for training microcomputer software technicians. Following a list of nine general objectives of the program, the guide provides a list of competencies that students are expected to develop in each of the courses of the 4-year program. The guide then…

  15. Book and Software Review.

    ERIC Educational Resources Information Center

    Ludlow, Barbara L.; Foshay, John D.

    2003-01-01

    This column describes several commercial Web sites seen to be helpful in special education and disability services programs and personnel preparation. These include sites of the Laureate Learning Company, the Slater Software Company, the Intellitools Company, the Attainment Company, and the Don Johnston Company. Potential uses for these sites are…

  16. Software Geometry in Simulations

    NASA Astrophysics Data System (ADS)

    Alion, Tyler; Viren, Brett; Junk, Tom

    2015-04-01

    The Long Baseline Neutrino Experiment (LBNE) involves many detectors. The experiment's near detector (ND) facility, may ultimately involve several detectors. The far detector (FD) will be significantly larger than any other Liquid Argon (LAr) detector yet constructed; many prototype detectors are being constructed and studied to motivate a plethora of proposed FD designs. Whether it be a constructed prototype or a proposed ND/FD design, every design must be simulated and analyzed. This presents a considerable challenge to LBNE software experts; each detector geometry must be described to the simulation software in an efficient way which allows for multiple authors to easily collaborate. Furthermore, different geometry versions must be tracked throughout their use. We present a framework called General Geometry Description (GGD), written and developed by LBNE software collaborators for managing software to generate geometries. Though GGD is flexible enough to be used by any experiment working with detectors, we present it's first use in generating Geometry Description Markup Language (GDML) files to interface with LArSoft, a framework of detector simulations, event reconstruction, and data analyses written for all LAr technology users at Fermilab. Brett is the other of the framework discussed here, the General Geometry Description (GGD).

  17. Social Software in Academia

    ERIC Educational Resources Information Center

    Bryant, Todd

    2006-01-01

    Considerable buzz has appeared on the Internet over a group of new tools labeled social software. These tools can expand discussion beyond the classroom and provide new ways for students to collaborate and communicate within their class or around the world. Dickinson College has implemented two of the best-known tools, the wiki and the blog, in…

  18. INTERIM -- Starlink Software Environment

    NASA Astrophysics Data System (ADS)

    Pearce, Dave; Pavelin, Cliff; Lawden, M. D.

    Early versions of this paper were based on a number of other papers produced at a very early stage of the Starlink project. They contained a description of a specific implementation of a subroutine library, speculations on the desirable attributes of a software environment, and future development plans. They reflected the experimental nature of the Starlink software environment at that time. Since then, the situation has changed. The implemented subroutine library, INTERIM_DIR:INTERIM.OLB, is now a well established and widely used piece of software. A completely new Starlink software environment (ADAM) has been developed and distributed. Thus the library released in 1980 as `STARLINK' and now called `INTERIM' has reached the end of its development cycle and is now frozen in its current state, apart from bug corrections. This paper has, therefore, been completely rewritten and restructured to reflect the new situation. Its aim is to describe the facilities of the INTERIM subroutine library as clearly and concisely as possible. It avoids speculation, discussion of design decisions, and announcements of future plans.

  19. Engaging New Software.

    ERIC Educational Resources Information Center

    Allen, Denise

    1994-01-01

    Reviews three educational computer software products: (1) a compact disc-read only memory (CD-ROM) bundle of five mathematics programs from the Apple Education Series; (2) "Sammy's Science House," with science activities for preschool through second grade (Edmark); and (3) "The Cat Came Back," an interactive CD-ROM game designed to build language…

  20. CALIPSO Data Read Software

    Atmospheric Science Data Center

    2018-06-14

      CALIPSO Data Read Software Callable routines in Interactive Data Language (IDL) provide basic read access to CALIPSO science data files. ... Release 4.30  (PDF) Standard Data Sets: LIDAR L1:  CAL_LID_L1-Standard-V4-10 LIDAR L2: ...

  1. Software Carpentry: lessons learned

    PubMed Central

    Wilson, Greg

    2016-01-01

    Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to improve researchers' computing skills. This paper explains what we have learned along the way, the challenges we now face, and our plans for the future. PMID:24715981

  2. Starlink Software Developments

    NASA Astrophysics Data System (ADS)

    Bly, M. J.; Giaretta, D.; Currie, M. J.; Taylor, M.

    Some current and upcoming software developments from Starlink were demonstrated. These included invoking traditional Starlink applications via web services, the current version of the ORAC-DR reduction pipeline, and some new Java-based tools including Treeview, an interactive explorer of hierarchical data structures.

  3. Software Product Liability

    DTIC Science & Technology

    1993-08-01

    disclaimers should be a top priority. Contract law involves the Uniform Commercial Code (UCC). This is an agreement between all the states (except...to contract law than this, the basic issue with software is that the sup- plier is generally an expert on an arcane and sophisticated technology and

  4. Basic Internet Software Toolkit.

    ERIC Educational Resources Information Center

    Buchanan, Larry

    1998-01-01

    Once schools are connected to the Internet, the next step is getting network workstations configured for Internet access. This article describes a basic toolkit comprising software currently available on the Internet for free or modest cost. Lists URLs for Web browser, Telnet, FTP, file decompression, portable document format (PDF) reader,…

  5. Software reliability studies

    NASA Technical Reports Server (NTRS)

    Wilson, Larry W.

    1989-01-01

    The longterm goal of this research is to identify or create a model for use in analyzing the reliability of flight control software. The immediate tasks addressed are the creation of data useful to the study of software reliability and production of results pertinent to software reliability through the analysis of existing reliability models and data. The completed data creation portion of this research consists of a Generic Checkout System (GCS) design document created in cooperation with NASA and Research Triangle Institute (RTI) experimenters. This will lead to design and code reviews with the resulting product being one of the versions used in the Terminal Descent Experiment being conducted by the Systems Validations Methods Branch (SVMB) of NASA/Langley. An appended paper details an investigation of the Jelinski-Moranda and Geometric models for software reliability. The models were given data from a process that they have correctly simulated and asked to make predictions about the reliability of that process. It was found that either model will usually fail to make good predictions. These problems were attributed to randomness in the data and replication of data was recommended.

  6. AOFlagger: RFI Software

    NASA Astrophysics Data System (ADS)

    Offringa, A. R.

    2010-10-01

    The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers. The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++. The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms. The software is published under the GNU General Public License version 3.

  7. NASA's Software Bank (CLIPS)

    NASA Technical Reports Server (NTRS)

    1991-01-01

    C Language Integrated Production System (CLIPS) is a NASA Johnson Space Center developed software shell for developing expert systems, is used by researchers at Ohio State University to determine solid waste disposal sites to assist in historic preservation. The program has various other applications and has even been included in a widely-used textbook.

  8. MOCASSIN-prot software

    USDA-ARS?s Scientific Manuscript database

    MOCASSIN-prot is a software, implemented in Perl and Matlab, for constructing protein similarity networks to classify proteins. Both domain composition and quantitative sequence similarity information are utilized in constructing the directed protein similarity networks. For each reference protein i...

  9. The FARE Software

    ERIC Educational Resources Information Center

    Pitarello, Adriana

    2015-01-01

    This article highlights the importance of immediate corrective feedback in tutorial software for language teaching in an academic learning environment. We aim to demonstrate that, rather than simply reporting on the performance of the foreign language learner, this feedback can act as a mediator of students' cognitive and metacognitive activity.…

  10. ESTSC - Software Best Practices

    Science.gov Websites

    OSTI, located in Oak Ridge, TN, serves as the DOE's software management facility for the announcement fundamental operability of automated data processing equipment, whether supplied by the manufacturer of the , completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that

  11. SEER*Stat Software

    Cancer.gov

    If you have access to SEER Research Data, use SEER*Stat to analyze SEER and other cancer-related databases. View individual records and produce statistics including incidence, mortality, survival, prevalence, and multiple primary. Tutorials and related analytic software tools are available.

  12. Landscape analysis software tools

    Treesearch

    Don Vandendriesche

    2008-01-01

    Recently, several new computer programs have been developed to assist in landscape analysis. The “Sequential Processing Routine for Arraying Yields” (SPRAY) program was designed to run a group of stands with particular treatment activities to produce vegetation yield profiles for forest planning. SPRAY uses existing Forest Vegetation Simulator (FVS) software coupled...

  13. Open Source Software Development

    DTIC Science & Technology

    2011-01-01

    Software, 2002, 149(1), 3-17. 3. DiBona , C., Cooper, D., and Stone, M. (Eds.), Open Sources 2.0, 2005, O’Reilly Media, Sebastopol, CA. Also see, C... DiBona , S. Ockman, and M. Stone (Eds.). Open Sources: Vocides from the Open Source Revolution, 1999. O’Reilly Media, Sebastopol, CA. 4. Ducheneaut, N

  14. Writing testable software requirements

    SciTech Connect

    Knirk, D.

    1997-11-01

    This tutorial identifies common problems in analyzing requirements in the problem and constructing a written specification of what the software is to do. It deals with two main problem areas: identifying and describing problem requirements, and analyzing and describing behavior specifications.

  15. Software reliability report

    NASA Technical Reports Server (NTRS)

    Wilson, Larry

    1991-01-01

    There are many software reliability models which try to predict future performance of software based on data generated by the debugging process. Unfortunately, the models appear to be unable to account for the random nature of the data. If the same code is debugged multiple times and one of the models is used to make predictions, intolerable variance is observed in the resulting reliability predictions. It is believed that data replication can remove this variance in lab type situations and that it is less than scientific to talk about validating a software reliability model without considering replication. It is also believed that data replication may prove to be cost effective in the real world, thus the research centered on verification of the need for replication and on methodologies for generating replicated data in a cost effective manner. The context of the debugging graph was pursued by simulation and experimentation. Simulation was done for the Basic model and the Log-Poisson model. Reasonable values of the parameters were assigned and used to generate simulated data which is then processed by the models in order to determine limitations on their accuracy. These experiments exploit the existing software and program specimens which are in AIR-LAB to measure the performance of reliability models.

  16. Generic Kalman Filter Software

    NASA Technical Reports Server (NTRS)

    Lisano, Michael E., II; Crues, Edwin Z.

    2005-01-01

    The Generic Kalman Filter (GKF) software provides a standard basis for the development of application-specific Kalman-filter programs. Historically, Kalman filters have been implemented by customized programs that must be written, coded, and debugged anew for each unique application, then tested and tuned with simulated or actual measurement data. Total development times for typical Kalman-filter application programs have ranged from months to weeks. The GKF software can simplify the development process and reduce the development time by eliminating the need to re-create the fundamental implementation of the Kalman filter for each new application. The GKF software is written in the ANSI C programming language. It contains a generic Kalman-filter-development directory that, in turn, contains a code for a generic Kalman filter function; more specifically, it contains a generically designed and generically coded implementation of linear, linearized, and extended Kalman filtering algorithms, including algorithms for state- and covariance-update and -propagation functions. The mathematical theory that underlies the algorithms is well known and has been reported extensively in the open technical literature. Also contained in the directory are a header file that defines generic Kalman-filter data structures and prototype functions and template versions of application-specific subfunction and calling navigation/estimation routine code and headers. Once the user has provided a calling routine and the required application-specific subfunctions, the application-specific Kalman-filter software can be compiled and executed immediately. During execution, the generic Kalman-filter function is called from a higher-level navigation or estimation routine that preprocesses measurement data and post-processes output data. The generic Kalman-filter function uses the aforementioned data structures and five implementation- specific subfunctions, which have been developed by the user on

  17. Flight Software Math Library

    NASA Technical Reports Server (NTRS)

    McComas, David

    2013-01-01

    The flight software (FSW) math library is a collection of reusable math components that provides typical math utilities required by spacecraft flight software. These utilities are intended to increase flight software quality reusability and maintainability by providing a set of consistent, well-documented, and tested math utilities. This library only has dependencies on ANSI C, so it is easily ported. Prior to this library, each mission typically created its own math utilities using ideas/code from previous missions. Part of the reason for this is that math libraries can be written with different strategies in areas like error handling, parameters orders, naming conventions, etc. Changing the utilities for each mission introduces risks and costs. The obvious risks and costs are that the utilities must be coded and revalidated. The hidden risks and costs arise in miscommunication between engineers. These utilities must be understood by both the flight software engineers and other subsystem engineers (primarily guidance navigation and control). The FSW math library is part of a larger goal to produce a library of reusable Guidance Navigation and Control (GN&C) FSW components. A GN&C FSW library cannot be created unless a standardized math basis is created. This library solves the standardization problem by defining a common feature set and establishing policies for the library s design. This allows the libraries to be maintained with the same strategy used in its initial development, which supports a library of reusable GN&C FSW components. The FSW math library is written for an embedded software environment in C. This places restrictions on the language features that can be used by the library. Another advantage of the FSW math library is that it can be used in the FSW as well as other environments like the GN&C analyst s simulators. This helps communication between the teams because they can use the same utilities with the same feature set and syntax.

  18. Formal Validation of Aerospace Software

    NASA Astrophysics Data System (ADS)

    Lesens, David; Moy, Yannick; Kanig, Johannes

    2013-08-01

    Any single error in critical software can have catastrophic consequences. Even though failures are usually not advertised, some software bugs have become famous, such as the error in the MIM-104 Patriot. For space systems, experience shows that software errors are a serious concern: more than half of all satellite failures from 2000 to 2003 involved software. To address this concern, this paper addresses the use of formal verification of software developed in Ada.

  19. Self-assembling software generator

    DOEpatents

    Bouchard, Ann M [Albuquerque, NM; Osbourn, Gordon C [Albuquerque, NM

    2011-11-25

    A technique to generate an executable task includes inspecting a task specification data structure to determine what software entities are to be generated to create the executable task, inspecting the task specification data structure to determine how the software entities will be linked after generating the software entities, inspecting the task specification data structure to determine logic to be executed by the software entities, and generating the software entities to create the executable task.

  20. Product-oriented Software Certification Process for Software Synthesis

    NASA Technical Reports Server (NTRS)

    Nelson, Stacy; Fischer, Bernd; Denney, Ewen; Schumann, Johann; Richardson, Julian; Oh, Phil

    2004-01-01

    The purpose of this document is to propose a product-oriented software certification process to facilitate use of software synthesis and formal methods. Why is such a process needed? Currently, software is tested until deemed bug-free rather than proving that certain software properties exist. This approach has worked well in most cases, but unfortunately, deaths still occur due to software failure. Using formal methods (techniques from logic and discrete mathematics like set theory, automata theory and formal logic as opposed to continuous mathematics like calculus) and software synthesis, it is possible to reduce this risk by proving certain software properties. Additionally, software synthesis makes it possible to automate some phases of the traditional software development life cycle resulting in a more streamlined and accurate development process.

  1. Nuclear localization of lymphocyte-specific protein tyrosine kinase (Lck) and its role in regulating LIM domain only 2 (Lmo2) gene

    SciTech Connect

    Venkitachalam, Srividya; Chueh, Fu-Yu; Yu, Chao-Lan, E-mail: chaolan.yu@rosalindfranklin.edu

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer Lmo2 expression is elevated in Lck-transformed cells. Black-Right-Pointing-Pointer Both endogenous and exogenous Lck localize in the nucleus. Black-Right-Pointing-Pointer Nuclear Lck is active in Lck-transformed cells. Black-Right-Pointing-Pointer Lck binds to the promoter region of Lmo2 gene in vivo. Black-Right-Pointing-Pointer In contrast to JAK2, Lck does not increase histone H3 phosphorylation on Tyr 41. -- Abstract: LIM domain only protein 2 (Lmo2) is a transcription factor that plays a critical role in the development of T-acute lymphoblastic leukemia (T-ALL). A previous report established a link between Lmo2 expression and the nuclear presence of oncogenic Janus kinase 2 (JAK2), a non-receptormore » protein tyrosine kinase. The oncogenic JAK2 kinase phosphorylates histone H3 on Tyr 41 that leads to the relief of Lmo2 promoter repression and subsequent gene expression. Similar to JAK2, constitutive activation of lymphocyte-specific protein tyrosine kinase (Lck) has been implicated in lymphoid malignancies. However, it is not known whether oncogenic Lck regulates Lmo2 expression through a similar mechanism. We show here that Lmo2 expression is significantly elevated in T cell leukemia LSTRA overexpressing active Lck kinase and in HEK 293 cells expressing oncogenic Y505FLck kinase. Nuclear localization of active Lck kinase was confirmed in both Lck-transformed cells by subcellular fractionation and immunofluorescence microscopy. More importantly, in contrast to oncogenic JAK2, oncogenic Lck kinase does not result in significant increase in histone H3 phosphorylation on Tyr 41. Instead, chromatin immunoprecipitation experiment shows that oncogenic Y505FLck kinase binds to the Lmo2 promoter in vivo. This result raises the possibility that oncogenic Lck may activate Lmo2 promoter through direct interaction.« less

  2. Nanosized LiM YMn 2- YO 4 (M = Cr, Co and Ni) spinels synthesized by a sucrose-aided combustion method . Structural characterization and electrochemical properties

    NASA Astrophysics Data System (ADS)

    Amarilla, J. M.; Rojas, R. M.; Pico, F.; Pascual, L.; Petrov, K.; Kovacheva, D.; Lazarraga, M. G.; Lejona, I.; Rojo, J. M.

    Spinels of composition LiM YMn 2- YO 4, M = Cr 3+, Co 3+, or Ni 2+, Y = 0.1 and 1 for the Cr and Co dopants, Y = 0.05 and 0.5 for the Ni sample, have been synthesized by a sucrose-aided combustion method. The samples as prepared require of an additional thermal treatment at 700 °C, 1 h to get stoichiometric single-phase spinels. The samples consist of aggregated particles of small size (45-50 nm) as deduced from transmission electron microscopy and X-ray powder diffraction. The electrochemical behaviour of the six spinels as cathodes in lithium cells has been analysed at 5 and 4 V under high current, 1 C rate. At 5 V the discharge capacity of LiNi 0.5Mn 1.5O 4 is higher than the one shown by LiCrMnO 4 and LiCoMnO 4, and it shows an elevated cyclability, i.e. capacity retention of 85.3% after 100 cycles. At 4 V the discharge capacity is similar for LiNi 0.05Mn 1.95O 4, LiCr 0.1Mn 1.9O 4 and LiCo 0.1Mn 1.9O 4, and all the three spinels show similar and very high cyclability, i.e. capacity retention >90% after 100 cycles. The spinels preserve their starting capacity up to currents as high as 2 C rate. The nanometric size of the samples explains the high rate capability of the synthesized spinels.

  3. Exome sequencing identifies variants in two genes encoding the LIM-proteins NRAP and FHL1 in an Italian patient with BAG3 myofibrillar myopathy.

    PubMed

    D'Avila, Francesca; Meregalli, Mirella; Lupoli, Sara; Barcella, Matteo; Orro, Alessandro; De Santis, Francesca; Sitzia, Clementina; Farini, Andrea; D'Ursi, Pasqualina; Erratico, Silvia; Cristofani, Riccardo; Milanesi, Luciano; Braga, Daniele; Cusi, Daniele; Poletti, Angelo; Barlassina, Cristina; Torrente, Yvan

    2016-06-01

    Myofibrillar myopathies (MFMs) are genetically heterogeneous dystrophies characterized by the disintegration of Z-disks and myofibrils and are associated with mutations in genes encoding Z-disk or Z-disk-related proteins. The c.626 C > T (p.P209L) mutation in the BAG3 gene has been described as causative of a subtype of MFM. We report a sporadic case of a 26-year-old Italian woman, affected by MFM with axonal neuropathy, cardiomyopathy, rigid spine, who carries the c.626 C > T mutation in the BAG3 gene. The patient and her non-consanguineous healthy parents and brother were studied with whole exome sequencing (WES) to further investigate the genetic basis of this complex phenotype. In the patient, we found that the BAG3 mutation is associated with variants in the NRAP and FHL1 genes that encode muscle-specific, LIM domain containing proteins. Quantitative real time PCR, immunohistochemistry and Western blot analysis of the patient's muscular biopsy showed the absence of NRAP expression and FHL1 accumulation in aggregates in the affected skeletal muscle tissue. Molecular dynamic analysis of the mutated FHL1 domain showed a modification in its surface charge, which could affect its capability to bind its target proteins. To our knowledge this is the first study reporting, in a BAG3 MFM, the simultaneous presence of genetic variants in the BAG3 and FHL1 genes (previously described as independently associated with MFMs) and linking the NRAP gene to MFM for the first time.

  4. Suppression of LIM and SH3 Domain Protein 1 (LASP1) Negatively Regulated by Androgen Receptor Delays Castration Resistant Prostate Cancer Progression.

    PubMed

    Dejima, Takashi; Imada, Kenjiro; Takeuchi, Ario; Shiota, Masaki; Leong, Jeffrey; Tombe, Tabitha; Tam, Kevin; Fazli, Ladan; Naito, Seiji; Gleave, Martin E; Ong, Christopher J

    2017-02-01

    LIM and SH3 domain protein 1 (LASP1) has been implicated in several human malignancies and has been shown to predict PSA recurrence in prostate cancer. However, the anti-tumor effect of LASP1 knockdown and the association between LASP1 and the androgen receptor (AR) remains unclear. The aim of this study is to clarify the significance of LASP1 as a target for prostate cancer, and to test the effect of silencing LASP1 in vivo using antisense oligonucleotides (ASO). A tissue microarray (TMA) was performed to characterize the differences in LASP1 expression in prostate cancer treated after hormone deprivation therapy. Flow cytometry was used to analyze cell cycle. We designed LASP1 ASO for knockdown of LASP1 in vivo studies. The expression of LASP1 in TMA was increased after androgen ablation and persisted in castration resistant prostate cancer (CRPC). Also in TMA, compared with LNCaP cell, LASP1 expression is elevated in CRPC cell lines (C4-2 and VehA cells). Interestingly, suppression of AR elevated LASP1 expression conversely, AR activation decreased LASP1 expression. Silencing of LASP1 reduced cell growth through G1 arrest which was accompanied by a decrease of cyclin D1. Forced overexpression of LASP1 promoted cell cycle and induced cell growth which was accompanied by an increase of cyclin D1. Systemic administration of LASP1 ASO with athymic mice significantly inhibited tumor growth in CRPC xenografts. These results indicate that LASP1 is negatively regulated by AR at the transcriptional level and promotes tumor growth through induction of cell cycle, ultimately suggesting that LASP1 may be a potential target in prostate cancer treatment. Prostate 77:309-320, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  5. Nutrient profiles discriminate between foods according to their contribution to nutritionally adequate diets: a validation study using linear programming and the SAIN,LIM system.

    PubMed

    Darmon, Nicole; Vieux, Florent; Maillot, Matthieu; Volatier, Jean-Luc; Martin, Ambroise

    2009-04-01

    The nutrient profile concept implies that it is possible to discriminate between foods according to their contribution to a healthy diet on the basis of their nutrient contents only. The objective was to test the compatibility between nutrient profiling and nutrient-based recommendations by using diet modeling with linear programming. Food consumption data from the French "Individuelle et Nationale sur les Consommations Alimentaires" dietary survey and its associated food-composition database were used as input data. Each food was allocated to 1 of 4 classes, according to the SAIN,LIM system -- a nutrient profiling system based on 2 independent scores, including a total of 8 basic plus 4 optional nutrients. The possibility to model diets fulfilling a set of 40 nutrient recommendations (healthy models) was tested by using foods from a given nutrient profile class only or from a combination of classes. The possibility to fulfill a set of nutrient constraints in contradiction with the recommendations (unhealthy models) was also tested. For each model, the feasible energy range was assessed by minimizing and maximizing total energy content. With foods from the most favorable nutrient profile class, healthy diets could be modeled, but it was impossible to design unhealthy diets within a realistic range of energy intake with these foods. With foods from the least favorable class, unhealthy, but not healthy, diets could be designed. Both healthy and unhealthy diets could be designed with foods from intermediate classes. On the basis of a few key nutrients, it is possible to predict the ability of a given food to facilitate -- or to impair -- the fulfillment of a large number of nutrient recommendations.

  6. [Intestinal parasites in white-faced capuchin monkeys Cebus capucinus (Primates: Cebidae) inhabiting a protected area in the Limón province of Northeastern Costa Rica].

    PubMed

    Chinchilla, Misael; Urbani, Bernardo; Valerio, Idalia; Vanegas, Juan Carlos

    2010-12-01

    Deforestation of tropical forests is threatening monkey biodiversity and their health status, dependent of an ecologically undisturbed area. To asses this relationship, we analyzed parasite occurrence in their intestines. The study was conducted at the Estación Biológica La Suerte (EBLS), Limón, Costa Rica. The group of white-faced capuchin monkeys (Cebus capucinus) was observed between March and December of 2006. A total of 75 feces samples were obtained. Once a sample was collected, the eaten plant type was identified to family and species level, and feces were processed in the laboratory to determine parasite incidence. Results showed that Moraceae was the most represented family in the samples. Among parasites, Strongyloides spp. and Acanthocephala were the most common. Positive prevalence of parasites was found similar and independent of sex and age of capuchin individuals. Microsporids were mainly reported in feces associated with Piperaceae. A low presence of these parasites was found in samples associated with Myrtaceae, with possible anti-parasite active components. The occurrence of parasites was relatively high in EBLS, when compared to other regions in Costa Rica. The higher occurrence of parasites observed in capuchins at EBLS may be due to the fact that this rain forest is surrounded by areas affected by human activities. We suggest the promotion of research in neotropical primates parasitology, for a better comprehension of the parasite-host relationship, and in a long term, being able to understand the ecosystems where they coexist, and consequently, preserve the biodiversity of the whole region.

  7. Thrombin selectively engages LIM kinase 1 and slingshot-1L phosphatase to regulate NF-κB activation and endothelial cell inflammation

    PubMed Central

    Leonard, Antony; Marando, Catherine; Rahman, Arshad

    2013-01-01

    Endothelial cell (EC) inflammation is a central event in the pathogenesis of many pulmonary diseases such as acute lung injury and its more severe form acute respiratory distress syndrome. Alterations in actin cytoskeleton are shown to be crucial for NF-κB regulation and EC inflammation. Previously, we have described a role of actin binding protein cofilin in mediating cytoskeletal alterations essential for NF-κB activation and EC inflammation. The present study describes a dynamic mechanism in which LIM kinase 1 (LIMK1), a cofilin kinase, and slingshot-1Long (SSH-1L), a cofilin phosphatase, are engaged by procoagulant and proinflammatory mediator thrombin to regulate these responses. Our data show that knockdown of LIMK1 destabilizes whereas knockdown of SSH-1L stabilizes the actin filaments through modulation of cofilin phosphorylation; however, in either case thrombin-induced NF-κB activity and expression of its target genes (ICAM-1 and VCAM-1) is inhibited. Further mechanistic analyses reveal that knockdown of LIMK1 or SSH-1L each attenuates nuclear translocation and thereby DNA binding of RelA/p65. In addition, LIMK1 or SSH-1L depletion inhibited RelA/p65 phosphorylation at Ser536, a critical event conferring transcriptional competency to the bound NF-κB. However, unlike SSH-1L, LIMK1 knockdown also impairs the release of RelA/p65 by blocking IKKβ-dependent phosphorylation/degradation of IκBα. Interestingly, LIMK1 or SSH-1L depletion failed to inhibit TNF-α-induced RelA/p65 nuclear translocation and proinflammatory gene expression. Thus this study provides evidence for a novel role of LIMK1 and SSH-1L in selectively regulating EC inflammation associated with intravascular coagulation. PMID:24039253

  8. Thrombin selectively engages LIM kinase 1 and slingshot-1L phosphatase to regulate NF-κB activation and endothelial cell inflammation.

    PubMed

    Leonard, Antony; Marando, Catherine; Rahman, Arshad; Fazal, Fabeha

    2013-11-01

    Endothelial cell (EC) inflammation is a central event in the pathogenesis of many pulmonary diseases such as acute lung injury and its more severe form acute respiratory distress syndrome. Alterations in actin cytoskeleton are shown to be crucial for NF-κB regulation and EC inflammation. Previously, we have described a role of actin binding protein cofilin in mediating cytoskeletal alterations essential for NF-κB activation and EC inflammation. The present study describes a dynamic mechanism in which LIM kinase 1 (LIMK1), a cofilin kinase, and slingshot-1Long (SSH-1L), a cofilin phosphatase, are engaged by procoagulant and proinflammatory mediator thrombin to regulate these responses. Our data show that knockdown of LIMK1 destabilizes whereas knockdown of SSH-1L stabilizes the actin filaments through modulation of cofilin phosphorylation; however, in either case thrombin-induced NF-κB activity and expression of its target genes (ICAM-1 and VCAM-1) is inhibited. Further mechanistic analyses reveal that knockdown of LIMK1 or SSH-1L each attenuates nuclear translocation and thereby DNA binding of RelA/p65. In addition, LIMK1 or SSH-1L depletion inhibited RelA/p65 phosphorylation at Ser(536), a critical event conferring transcriptional competency to the bound NF-κB. However, unlike SSH-1L, LIMK1 knockdown also impairs the release of RelA/p65 by blocking IKKβ-dependent phosphorylation/degradation of IκBα. Interestingly, LIMK1 or SSH-1L depletion failed to inhibit TNF-α-induced RelA/p65 nuclear translocation and proinflammatory gene expression. Thus this study provides evidence for a novel role of LIMK1 and SSH-1L in selectively regulating EC inflammation associated with intravascular coagulation.

  9. Loss of the LIM-only protein Fhl2 impairs inflammatory reaction and scar formation after cardiac ischemia leading to better hemodynamic performance.

    PubMed

    Goltz, Diane; Hittetiya, Kanishka; Gevensleben, Heidrun; Kirfel, Jutta; Diehl, Linda; Meyer, Rainer; Büttner, Reinhard

    2016-04-15

    The pathogenesis of myocardial ischemia-reperfusion injury (MI/R) involves an inflammatory response. Since the four-and-a-half LIM domain-containing protein 2 (Fhl2) has been observed to modulate immune cell migration, we aimed to study the consequences of Fhl2(-/-) under MI/R with respect to immune reaction, scar formation, and hemodynamic performance. In a closed chest model of 1h MI/R, immune cell invasion of phagocytic monocytes was characterized by flow cytometry and immunohistochemistry. In addition, infarct size was assessed by triphenyltetrazolium chloride/Masson trichrome staining 24h/21days after reperfusion and a set of hemodynamic parameters was recorded by catheterisation in Fhl2(-/-) mice and controls. While flow cytometry did not reveal differences in myocardial CD45(high) immune cell infiltrate, histological analysis showed that infiltrating immune cells in Fhl2(-/-) animals were preferentially located in the perivascular area, whereas in wild type, immune cells were well dispersed within the area at risk. After 24h and 21days of reperfusion, infarct size was significantly reduced in Fhl2(-/-) compared to WT animals. In addition, hemodynamic performance was better in Fhl2(-/-) mice, compared to WT mice up to day 21 of reperfusion. The loss of Fhl2 leads to an altered immune response to myocardial ischemia, which results in smaller infarcts and better hemodynamic performance up to 21days after myocardial ischemia reperfusion. Immune cell invasion plays a pivotal role in the context of MI/R. Fhl2 significantly influences immune cell function and immune cell interaction with injured cardiac tissue leading to altered scar composition. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Statistical modeling of software reliability

    NASA Technical Reports Server (NTRS)

    Miller, Douglas R.

    1992-01-01

    This working paper discusses the statistical simulation part of a controlled software development experiment being conducted under the direction of the System Validation Methods Branch, Information Systems Division, NASA Langley Research Center. The experiment uses guidance and control software (GCS) aboard a fictitious planetary landing spacecraft: real-time control software operating on a transient mission. Software execution is simulated to study the statistical aspects of reliability and other failure characteristics of the software during development, testing, and random usage. Quantification of software reliability is a major goal. Various reliability concepts are discussed. Experiments are described for performing simulations and collecting appropriate simulated software performance and failure data. This data is then used to make statistical inferences about the quality of the software development and verification processes as well as inferences about the reliability of software versions and reliability growth under random testing and debugging.

  11. Relay Sequence Generation Software

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampompan, Teerapat

    2009-01-01

    Due to thermal and electromagnetic interactivity between the UHF (ultrahigh frequency) radio onboard the Mars Reconnaissance Orbiter (MRO), which performs relay sessions with the Martian landers, and the remainder of the MRO payloads, it is required to integrate and de-conflict relay sessions with the MRO science plan. The MRO relay SASF/PTF (spacecraft activity sequence file/ payload target file) generation software facilitates this process by generating a PTF that is needed to integrate the periods of time during which MRO supports relay activities with the rest of the MRO science plans. The software also generates the needed command products that initiate the relay sessions, some features of which are provided by the lander team, some are managed by MRO internally, and some being derived.

  12. Software error detection

    NASA Technical Reports Server (NTRS)

    Buechler, W.; Tucker, A. G.

    1981-01-01

    Several methods were employed to detect both the occurrence and source of errors in the operational software of the AN/SLQ-32. A large embedded real time electronic warfare command and control system for the ROLM 1606 computer are presented. The ROLM computer provides information about invalid addressing, improper use of privileged instructions, stack overflows, and unimplemented instructions. Additionally, software techniques were developed to detect invalid jumps, indices out of range, infinte loops, stack underflows, and field size errors. Finally, data are saved to provide information about the status of the system when an error is detected. This information includes I/O buffers, interrupt counts, stack contents, and recently passed locations. The various errors detected, techniques to assist in debugging problems, and segment simulation on a nontarget computer are discussed. These error detection techniques were a major factor in the success of finding the primary cause of error in 98% of over 500 system dumps.

  13. Software Configurable Multichannel Transceiver

    NASA Technical Reports Server (NTRS)

    Freudinger, Lawrence C.; Cornelius, Harold; Hickling, Ron; Brooks, Walter

    2009-01-01

    Emerging test instrumentation and test scenarios increasingly require network communication to manage complexity. Adapting wireless communication infrastructure to accommodate challenging testing needs can benefit from reconfigurable radio technology. A fundamental requirement for a software-definable radio system is independence from carrier frequencies, one of the radio components that to date has seen only limited progress toward programmability. This paper overviews an ongoing project to validate the viability of a promising chipset that performs conversion of radio frequency (RF) signals directly into digital data for the wireless receiver and, for the transmitter, converts digital data into RF signals. The Software Configurable Multichannel Transceiver (SCMT) enables four transmitters and four receivers in a single unit the size of a commodity disk drive, programmable for any frequency band between 1 MHz and 6 GHz.

  14. Software sensors for bioprocesses.

    PubMed

    Bogaerts, Ph; Vande Wouwer, A

    2003-10-01

    State estimation is a significant problem in biotechnological processes, due to the general lack of hardware sensor measurements of the variables describing the process dynamics. The objective of this paper is to review a number of software sensor design methods, including extended Kalman filters, receding-horizon observers, asymptotic observers, and hybrid observers, which can be efficiently applied to bioprocesses. These several methods are illustrated with simulation and real-life case studies.

  15. Software Engineering Education Directory

    DTIC Science & Technology

    1989-02-01

    engineering degree programs . In future editions of this directory, we plan to provide indices and cross tabulations showing a profile of ongoing software...Compilation of entries for this directory began in the summer of 1986 with a questionnaire mailed to schools selected from Peterson’s- Graduate Programs ...organized the directory by state and country. How to Use this Directory The directory is organized by state and province. Within each section, the

  16. Image Processing Software

    NASA Technical Reports Server (NTRS)

    1992-01-01

    To convert raw data into environmental products, the National Weather Service and other organizations use the Global 9000 image processing system marketed by Global Imaging, Inc. The company's GAE software package is an enhanced version of the TAE, developed by Goddard Space Flight Center to support remote sensing and image processing applications. The system can be operated in three modes and is combined with HP Apollo workstation hardware.

  17. Software Project Management

    DTIC Science & Technology

    1989-07-01

    incorporated into the sys- Kotler88 tem. Several interesting concepts are presented, but Kotler , P. Marketing Planning: Analysis, Planning, the bulk of the...Metzger87 Mantei, M. "The Effect of Programming Team Metzger, Philip W. Managing Programming Structures on Programming Tasks." Comm. ACM People: A Personal... Philips . Software Engi- Classic approach in organization theory. neering. Englewood Cliffs, N.J.: Prentice-Hall, 1988. Shannon75 An industrial approach

  18. Unified Engineering Software System

    NASA Technical Reports Server (NTRS)

    Purves, L. R.; Gordon, S.; Peltzman, A.; Dube, M.

    1989-01-01

    Collection of computer programs performs diverse functions in prototype engineering. NEXUS, NASA Engineering Extendible Unified Software system, is research set of computer programs designed to support full sequence of activities encountered in NASA engineering projects. Sequence spans preliminary design, design analysis, detailed design, manufacturing, assembly, and testing. Primarily addresses process of prototype engineering, task of getting single or small number of copies of product to work. Written in FORTRAN 77 and PROLOG.

  19. ThermalTracker Software

    SciTech Connect

    The software processes recorded thermal video and detects the flight tracks of birds and bats that passed through the camera's field of view. The output is a set of images that show complete flight tracks for any detections, with the direction of travel indicated and the thermal image of the animal delineated. A report of the descriptive features of each detected track is also output in the form of a comma-separated value text file.

  20. Aviation Design Software

    NASA Technical Reports Server (NTRS)

    1997-01-01

    DARcorporation developed a General Aviation CAD package through a Small Business Innovation Research contract from Langley Research Center. This affordable, user-friendly preliminary design system for General Aviation aircraft runs on the popular 486 IBM-compatible personal computers. Individuals taking the home-built approach, small manufacturers of General Aviation airplanes, as well as students and others interested in the analysis and design of aircraft are possible users of the package. The software can cut design and development time in half.