SaDA: From Sampling to Data Analysis-An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data.

PubMed

Singh, Kumar Saurabh; Thual, Dominique; Spurio, Roberto; Cannata, Nicola

2015-06-03

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. 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 most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies.

Assembling proteomics data as a prerequisite for the analysis of large scale experiments

PubMed Central

Schmidt, Frank; Schmid, Monika; Thiede, Bernd; Pleißner, Klaus-Peter; Böhme, Martina; Jungblut, Peter R

2009-01-01

Background Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments. Results In the present study, a database concept has been developed to address these issues and to offer complete information via a web interface. In our concept, the Oracle based data repository system SQL-LIMS plays the central role in the proteomics workflow and was applied to the proteomes of Mycobacterium tuberculosis, Helicobacter pylori, Salmonella typhimurium and protein complexes such as 20S proteasome. Technical operations of our proteomics labs were used as the standard for SQL-LIMS template creation. By means of a Java based data parser, post-processed data of different approaches, such as LC/ESI-MS, MALDI-MS and 2-D gel electrophoresis (2-DE), were stored in SQL-LIMS. A minimum set of the proteomics data were transferred in our public 2D-PAGE database using a Java based interface (Data Transfer Tool) with the requirements of the PEDRo standardization. Furthermore, the stored proteomics data were extractable out of SQL-LIMS via XML. Conclusion The Oracle based data repository system SQL-LIMS played the central role in the proteomics workflow concept. Technical operations of our proteomics labs were used as standards for SQL-LIMS templates. Using a Java based parser, post-processed data of different approaches such as LC/ESI-MS, MALDI-MS and 1-DE and 2-DE were stored in SQL-LIMS. Thus, unique data formats of different instruments were unified and stored in SQL-LIMS tables. Moreover, a unique submission identifier allowed fast access to all experimental data. This was the main advantage compared to multi software solutions, especially if personnel fluctuations are high. Moreover, large scale and high-throughput experiments must be managed in a comprehensive repository system such as SQL-LIMS, to query results in a systematic manner. On the other hand, these database systems are expensive and require at least one full time administrator and specialized lab manager. Moreover, the high technical dynamics in proteomics may cause problems to adjust new data formats. To summarize, SQL-LIMS met the requirements of proteomics data handling especially in skilled processes such as gel-electrophoresis or mass spectrometry and fulfilled the PSI standardization criteria. The data transfer into a public domain via DTT facilitated validation of proteomics data. Additionally, evaluation of mass spectra by post-processing using MS-Screener improved the reliability of mass analysis and prevented storage of data junk. PMID:19166578

2009 Navy ManTech Project Book

DTIC Science & Technology

2009-01-01

pieces which are welded together, filled with syntactic foam , and welded to the sail and hull structure. The ManTech project was successful in...cladding has demonstrated the required performance characteristics . The testing demonstrated manufacturability of optical fibers with enhanced hard...using Liquid Injection Molding Simulation (LIMS) and Polyworx software tools for infusion set-up optimization. Test articles fabricated are

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.

Recording information on protein complexes in an information management system

PubMed Central

Savitsky, Marc; Diprose, Jonathan M.; Morris, Chris; Griffiths, Susanne L.; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S.; Blake, Richard; Stuart, David I.; Esnouf, Robert M.

2011-01-01

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein–protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. PMID:21605682

Recording information on protein complexes in an information management system.

PubMed

Savitsky, Marc; Diprose, Jonathan M; Morris, Chris; Griffiths, Susanne L; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S; Blake, Richard; Stuart, David I; Esnouf, Robert M

2011-08-01

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. Copyright © 2011 Elsevier Inc. All rights reserved.

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 community. It is freely available under the GNU GPL v3 licence and can be accessed from, https://muccg.github.io/mastr-ms/.

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.

Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study.

PubMed

Prague, Mélanie; Commenges, Daniel; Gran, Jon Michael; Ledergerber, Bruno; Young, Jim; Furrer, Hansjakob; Thiébaut, Rodolphe

2017-03-01

Highly active antiretroviral therapy (HAART) has proved efficient in increasing CD4 counts in many randomized clinical trials. Because randomized trials have some limitations (e.g., short duration, highly selected subjects), it is interesting to assess the effect of treatments using observational studies. This is challenging because treatment is started preferentially in subjects with severe conditions. This general problem had been treated using Marginal Structural Models (MSM) relying on the counterfactual formulation. Another approach to causality is based on dynamical models. We present three discrete-time dynamic models based on linear increments models (LIM): the first one based on one difference equation for CD4 counts, the second with an equilibrium point, and the third based on a system of two difference equations, which allows jointly modeling CD4 counts and viral load. We also consider continuous-time models based on ordinary differential equations with non-linear mixed effects (ODE-NLME). These mechanistic models allow incorporating biological knowledge when available, which leads to increased statistical evidence for detecting treatment effect. Because inference in ODE-NLME is numerically challenging and requires specific methods and softwares, LIM are a valuable intermediary option in terms of consistency, precision, and complexity. We compare the different approaches in simulation and in illustration on the ANRS CO3 Aquitaine Cohort and the Swiss HIV Cohort Study. © 2016, The International Biometric Society.

Detection and Structural Characterization of Nucleophiles Trapped Reactive Metabolites of Limonin Using Liquid Chromatography-Mass Spectrometry

PubMed Central

Deng, Yujie; Fu, Yudong; Xu, Shumin; Wang, Ping; Yang, Nailong; Li, Chengqian

2018-01-01

Limonin (LIM), a furan-containing limonoid, is one of the most abundant components of Dictamnus dasycarpus Turcz. Recent studies demonstrated that LIM has great potential for inhibiting the activity of drug-metabolizing enzymes. However, the mechanisms of LIM-induced enzyme inactivation processes remain unexplored. The main objective of this study was to identify the reactive metabolites of LIM using liquid chromatography-mass spectrometry. Three nucleophiles, glutathione (GSH), N-acetyl cysteine (NAC), and N-acetyl lysine (NAL), were used to trap the reactive metabolites of LIM in in vitro and in vivo models. Two different types of mass spectrometry, a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometry and a LTQ velos Pro ion trap mass spectrometry, were employed to acquire structural information of nucleophile adducts of LIM. In total, six nucleophile adducts of LIM (M1–M6) with their isomers were identified; among them, M1 was a GSH and NAL conjugate of LIM, M2–M4 were glutathione adducts of LIM, M5 was a NAC and NAL conjugate of LIM, and M6 was a NAC adduct of LIM. Additionally, CYP3A4 was found to be the key enzyme responsible for the bioactivation of limonin. This metabolism study largely facilitates the understanding of mechanisms of limonin-induced enzyme inactivation processes. PMID:29850372

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.

PubMed

Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A

2016-10-15

Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules. With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Challenges in small screening laboratories: implementing an on-demand laboratory information management system.

PubMed

Lemmon, Vance P; Jia, Yuanyuan; Shi, Yan; Holbrook, S Douglas; Bixby, John L; Buchser, William

2011-11-01

The Miami Project to Cure Paralysis, part of the University of Miami Miller School of Medicine, includes a laboratory devoted to High Content Analysis (HCA) of neurons. The goal of the laboratory is to uncover signaling pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCA permits the quantification of neuronal morphology, including the lengths and numbers of axons. HCA of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. HCA itself produces vast amounts of information including images, well-based data and cell-based phenotypic measures. Documenting and integrating the experimental workflows, library data and extensive experimental results is challenging. For academic laboratories generating large data sets from experiments involving thousands of perturbagens, a Laboratory Information Management System (LIMS) is the data tracking solution of choice. With both productivity and efficiency as driving rationales, the Miami Project has equipped its HCA laboratory with an On Demand or Software As A Service (SaaS) LIMS to ensure the quality of its experiments and workflows. The article discusses how the system was selected and integrated into the laboratory. The advantages of a SaaS based LIMS over a client-server based system are described. © 2011 Bentham Science Publishers

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

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.

Designing Networks that are Capable of Self-Healing and Adapting

DTIC Science & Technology

2017-04-01

Undergrad. Res. Fellowship, visiting from Caltech. Undergraduate Eugene Park Math Duke Models of self-healing networks (undergrad. senior thesis...Graduate student Anastasia Deckard Math Duke 3rd/4th year PhD. Wrote software for simulation. Undergraduate Nick Day Math LIMS Summer project at...Harer gave a talk on this DTRA grant to undergraduate math majors at Duke. 11 Q UA D C HA R T Uploaded to the DTRA Basic and Fundamental Research

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

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

Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A.

PubMed

Uluisik, Rizvan; Romero, Elvira; Gadda, Giovanni

2017-11-01

The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[ 2 H 4 ]-choline as a substrate. The limiting rate constants k lim1 and k lim2 at saturating substrate were well separated (k lim1 /k lim2 >9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that k lim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that k lim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the k lim1 and k lim2 values increased with increasing temperature, allowing for the analyses of H + and H - transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the k lim1 value ( H2O k lim1 / D2O k lim1 ) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the k lim2 value gave lines with the slope (choline) >slope (D-choline) , suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

PubMed Central

Zhang, Jianwei; Kudrna, Dave; Mu, Ting; Li, Weiming; Copetti, Dario; Yu, Yeisoo; Goicoechea, Jose Luis; Lei, Yang; Wing, Rod A.

2016-01-01

Abstract Motivation: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool—Genome Puzzle Master (GPM)—that enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules. Results: With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to ‘group,’ ‘merge,’ ‘order and orient’ sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user’s total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. Availability and Implementation: The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS Contacts: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27318200

Estimating Mutual Information by Local Gaussian Approximation

DTIC Science & Technology

2015-07-13

suggesstions for reducing this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway...following conditions: lim N→∞ hi = 0 , lim N→∞ Nhi =∞, i = 1, 2, . . . , d. (9) Then the following holds: lim N→∞ E|f̂ (x)− f (x)| = 0 (10) lim N→∞ E|f̂ (x

BioSig-Air-Force

DOE Office of Scientific and Technical Information (OSTI.GOV)

2011-07-15

1) Configured servers: In coordination with the INSIGHT team, a hardware configuration was selected. Two nodes were purchased, configured, and shipped with compatible OS and database installation. The servers have been stress tested for reliability as they use leading edge technologies. Each node has two CPUs and 12 cores per CPU with maximum onboard memory for high performance. 2) LIM and Experimental module: The original BioSig system was developed for cancer research. Accordingly, the LIM system its corresponding web pages are being modified to facilitate (i) pathogene-donor interactions, (ii) media composition, (iii) chemical and siRNA plate configurations. The LIM systemmore » has been redesigned. The revised system allows design of new media and tracking it from lot-to-lot so that variations in the phenotypic responses can be tracked to a specific media and lot number. Similar associations are also possible with other experimental factors (e.g., donor-pathoge, siRNA, and chemical). Furthermore, the design of the experimental variables has also been revised to (i) interact with the newly developed LIM system, (ii) simplify experimental specifications, and (iii) test for potential operator's error during the data entry. Part of the complication has been due to the handshake between multiple teams that provide the small molecule plates and the team that creates assay plates. Our efforts have focused to harmonize these interactions (e.g., various data formats) so that each assay plate can be mapped to its source so that a correct set of experimental variables can be associated with each image. For example, depending upon the source of the chemical plates, they may have different formats. We have developed a canonical representation that registers SMILES code, for each chemical compound, along with its physiochemical properties. The schema for LIM conjunction with customized Web pages. 3) Import of Images and computed descriptors module: In coordination with the INSIGHT team, policies were designed to route images and computed representation into BioSig. This module (i) examines for completion of image analysis, and imports images, computed masks, and descriptors into BioSig. A database API for efficient retrieval of selection of descriptors (among thousands) was designed and implemented. 4) Computed segmentation masks from external software were imported, boundaries computed, and overlaid on images for quality control.« less

Time series comparisons of satellite and rocketsonde temperatures in 1978-1979

NASA Technical Reports Server (NTRS)

Remsberg, Ellis E.; Bhatt, Praful P.; Schmidlin, Francis J.

1994-01-01

The Limb Infrared Monitor of the Stratosphere (LIMS) experiment on Nimbus 7 yielded temperature-versus-pressure (T(p)) profiles for each radiance scan. The present report describes time series comparisons between LIMS and rocketsonde T(p) values at rocketsonde station locations. Sample size has increased up to 665 by this new approach, leading to better statistics for a T(p) validation. The results indicate no clearly significant bias for LIMS versus Datasonde from 10 kPa at low and mid latitudes. There is a positive LIMS bias of 2 to 3 K in the upper stratosphere at high latitudes for the Northern Hemisphere in both winter and spring. LIMS is progressively colder than Datasonde from 0.4 kPa (about -3 K) to 0.1 kPa (about -9 K) at all latitudes. A similar comparison between LIMS and the more accurate falling sphere measurements reveals an equivalent mid-latitude LIMS bias at 0.4 kPa but a much smaller bias at 0.1 kPa (-4.6 K). Because the biases do not vary noticeably with season, it is concluded that they are not a function of atmospheric state. This result confirms the robustness of the LIMS temperature retrieval technique.

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.

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).

Structure Characterization and Lead Detoxification Effect of Carboxymethylated Melanin Derived from Lachnum Sp.

PubMed

Zong, Shuai; Li, Lan; Li, Jinglei; Shaikh, Farnaz; Yang, Liu; Ye, Ming

2017-06-01

In the present study, an intracellular melanin, named LIM205, was separated from Lachnum YM205 mycelia and was purified on a Sephadex G-15 column. The molecular weight of LIM205 was determined as 522 Da, and its molecular formula was speculated as C 28 H 14 N 2 O 7 S. The possible chemical structure of LIM205 was determined according to the results of Fourier transform infrared (FT-IR), 1 H NMR, 13 C NMR, and pyrolysis/GC-MS analysis. With the aim to increase its water solubility, its carboxymethylated derivative, named CLIM205, was formed by the substitution of hydrogen atoms in LIM205 with one, two, and three carboxymethylate groups. FT-IR, UV, and ESI-MS analysis demonstrated that the carboxymethylate groups were conjugated onto LIM205. The lead detoxification activities of LIM205 and CLIM205 had also been investigated. In vivo test showed that both LIM205 and CLIM205 reduced the tissue lead concentration, enhanced lead excretion, and reversed lead-induced alterations in superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and malondialdehyde (MDA) concentrations in mice, with CLIM205 showed better efficacy. The study indicates that LIM205 and CLIM205 have significant lead detoxification effect which will contribute to solve related problems.

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.

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.

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.

Laser microprobe characterization of C species in Interplanetary Dust Particles (IDP)

NASA Technical Reports Server (NTRS)

Dibrozolo, F. R.; Bunch, T. E.; Chang, S.; Brownlee, D. E.

1986-01-01

Preliminary results of a study whose aim is the characterization of carbon (C) species in microvolumes of materials by means of laser ionization mass spectrometry (LIMS) are presented. The LIMS instrument employs a pulsed UV laser to produce nearly instantaneous vaporization and ionization of materials, followed by acceleration and time-of-flight analysis of the ions produced. LIMS provides a survey technique with nearly simultaneous acquisition of mass spectra covering the entire elemental range. The main limitation of the LIMS technique at present is its limited ability to perform quantitative analysis, due in part to insufficient knowledge of the mechanism of laser-solid interaction. However, considerable effort is now being directed at making LIMS a more quantitative technique. A variety of different C samples, both natural and man made were analyzed to establish the ability of LIMS to differentiate among the various C phases. The results of preliminary analyses performed on meteoritical and interplanetary dust samples are also presented. The C standards selected for the LIMS characterization range from essentially amorphous soot to diamond, which exhibits the highest degree of ordering.

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

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

PubMed

Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

2012-03-01

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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

Rail Brake System Using a Linear Induction Motor for Dynamic Braking

NASA Astrophysics Data System (ADS)

Sakamoto, Yasuaki; Kashiwagi, Takayuki; Tanaka, Minoru; Hasegawa, Hitoshi; Sasakawa, Takashi; Fujii, Nobuo

One type of braking system for railway vehicles is the eddy current brake. Because this type of brake has the problem of rail heating, it has not been used for practical applications in Japan. Therefore, we proposed the use of a linear induction motor (LIM) for dynamic braking in eddy current brake systems. The LIM reduces rail heating and uses an inverter for self excitation. In this paper, we estimated the performance of an LIM from experimental results of a fundamental test machine and confirmed that the LIM generates an approximately constant braking force under constant current excitation. At relatively low frequencies, this braking force remains unaffected by frequency changes. The reduction ratio of rail heating is also approximately proportional to the frequency. We also confirmed that dynamic braking resulting in no electrical output can be used for drive control of the LIM. These characteristics are convenient for the realization of the LIM rail brake system.

Low-index-metamaterial for gain enhancement of planar terahertz antenna

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Qing-Le; Si, Li-Ming, E-mail: lms@bit.edu.cn; Lv, Xin

2014-03-15

We theoretically present a high gain planar antenna at terahertz (THz) frequencies by combing a conventional log-periodic antenna (LPA) with a low-index-metamaterial (LIM, |n| < 1). The LIM is realized by properly designing a fishnet metamaterial using full-wave finite-element simulation. Owing to the impedance matching, the LIM can be placed seamlessly on the substrate of the LPA without noticeable reflection. The effectiveness of using LIM for antenna gain enhancement is confirmed by comparing the antenna performance with and without LIM, where significantly improved half-power beam-width (3-dB beam-width) and more than 4 dB gain enhancement are seen within a certain frequencymore » range. The presented LIM-enhanced planar THz antenna is compact, flat, low profile, and high gain, which has extensive applications in THz systems, including communications, radar, and spectroscopy.« less

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.

Lipase and its modulator from Pseudomonas sp. strain KFCC 10818: proline-to-glutamine substitution at position 112 induces formation of enzymatically active lipase in the absence of the modulator.

PubMed

Kim, E K; Jang, W H; Ko, J H; Kang, J S; Noh, M J; Yoo, O J

2001-10-01

A lipase gene, lipK, and a lipase modulator gene, limK, of Pseudomonas sp. strain KFCC 10818 have been cloned, sequenced, and expressed in Escherichia coli. The limK gene is located immediately downstream of the lipK gene. Enzymatically active lipase was produced only in the presence of the limK gene. The effect of the lipase modulator LimK on the expression of active lipase was similar to those of the Pseudomonas subfamily I.1 and I.2 lipase-specific foldases (Lifs). The deduced amino acid sequence of LimK shares low homology (17 to 19%) with the known Pseudomonas Lifs, suggesting that Pseudomonas sp. strain KFCC 10818 is only distantly related to the subfamily I.1 and I.2 Pseudomonas species. Surprisingly, a lipase variant that does not require LimK for its correct folding was isolated in the study to investigate the functional interaction between LipK and LimK. When expressed in the absence of LimK, the P112Q variant of LipK formed an active enzyme and displayed 63% of the activity of wild-type LipK expressed in the presence of LimK. These results suggest that the Pro(112) residue of LipK is involved in a key step of lipase folding. We expect that the novel finding of this study may contribute to future research on efficient expression or refolding of industrially important lipases and on the mechanism of lipase folding.

Lipase and Its Modulator from Pseudomonas sp. Strain KFCC 10818: Proline-to-Glutamine Substitution at Position 112 Induces Formation of Enzymatically Active Lipase in the Absence of the Modulator

PubMed Central

Kim, Eun Kyung; Jang, Won Hee; Ko, Jung Ho; Kang, Jong Seok; Noh, Moon Jong; Yoo, Ook Joon

2001-01-01

A lipase gene, lipK, and a lipase modulator gene, limK, of Pseudomonas sp. strain KFCC 10818 have been cloned, sequenced, and expressed in Escherichia coli. The limK gene is located immediately downstream of the lipK gene. Enzymatically active lipase was produced only in the presence of the limK gene. The effect of the lipase modulator LimK on the expression of active lipase was similar to those of the Pseudomonas subfamily I.1 and I.2 lipase-specific foldases (Lifs). The deduced amino acid sequence of LimK shares low homology (17 to 19%) with the known Pseudomonas Lifs, suggesting that Pseudomonas sp. strain KFCC 10818 is only distantly related to the subfamily I.1 and I.2 Pseudomonas species. Surprisingly, a lipase variant that does not require LimK for its correct folding was isolated in the study to investigate the functional interaction between LipK and LimK. When expressed in the absence of LimK, the P112Q variant of LipK formed an active enzyme and displayed 63% of the activity of wild-type LipK expressed in the presence of LimK. These results suggest that the Pro112 residue of LipK is involved in a key step of lipase folding. We expect that the novel finding of this study may contribute to future research on efficient expression or refolding of industrially important lipases and on the mechanism of lipase folding. PMID:11566993

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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.

Substance P, thyrotropin-releasing hormone, and monoamine metabolites in cerebrospinal fluid in sleep apnea patients.

PubMed

Gislason, T; Hedner, J; Terenius, L; Bisette, G; Nemeroff, C B

1992-09-01

The cerebrospinal fluid (CSF) concentrations of thyrotropin-releasing hormone (TRH), substance P (SP), 5-hydroxyindoleacetic acid (5-HIAA), homovanillic acid (HVA), and 3-methoxy-4-hydroxyphenyl glycol (MHPG) were measured in 15 consecutive patients with the sleep apnea syndrome (SAS) and in healthy control subjects. Second measurements were performed 6 months after surgical treatment in 10 of the patients. The mean (+/- SD) concentration of TRH-like immunoreactive material (TRH-LIM) (pg/ml) did not differ significantly between patients with SAS (8.1 +/- 2.8) and control subjects (7.5 +/- 2.2). However, postoperatively, this concentration was increased in the six clinically cured patients with SAS, from 6.9 +/- 2.7 to 9.4 +/- 1.6 (p less than 0.03). Substance P-like immunoreactive material (SP-LIM) was higher in untreated patients with SAS than in control subjects: 19.2 +/- 6.7 versus 14.4 +/- 4.2 fmol/ml (p less than 0.02), and the level remained high after operation in the group treated surgically. The HVA, 5-HIAA, and MHPG concentrations were similar in patients with SAS and control subjects, and no consistent changes were found postoperatively. The CSF deviations in TRH-LIM and SP-LIM concentrations in the patients may reflect a primary central nervous system defect or they may be secondary to intermittent nocturnal hypoxia, progressive hypercapnia, and/or sleep fragmentation. In this sense, both these systems may be markers of SAS-SP as a "trait" marker and TRH as an indicator of the current state.

Electromagnetic Performance Calculation of HTS Linear Induction Motor for Rail Systems

NASA Astrophysics Data System (ADS)

Liu, Bin; Fang, Jin; Cao, Junci; Chen, Jie; Shu, Hang; Sheng, Long

2017-07-01

According to a high temperature superconducting (HTS) linear induction motor (LIM) designed for rail systems, the influence of electromagnetic parameters and mechanical structure parameters on the electromagnetic horizontal thrust, vertical force of HTS LIM and the maximum vertical magnetic field of HTS windings are analyzed. Through the research on the vertical field of HTS windings, the development regularity of the HTS LIM maximum input current with different stator frequency and different thickness value of the secondary conductive plate is obtained. The theoretical results are of great significance to analyze the stability of HTS LIM. Finally, based on theory analysis, HTS LIM test platform was built and the experiment was carried out with load. The experimental results show that the theoretical analysis is correct and reasonable.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Ingestion of Sodium Bicarbonate (NaHCO3) Following a Fatiguing Bout of Exercise Accelerates Postexercise Acid-Base Balance Recovery and Improves Subsequent High-Intensity Cycling Time to Exhaustion.

PubMed

Gough, Lewis A; Rimmer, Steven; Osler, Callum J; Higgins, Matthew F

2017-10-01

This study evaluated the ingestion of sodium bicarbonate (NaHCO 3 ) on postexercise acid-base balance recovery kinetics and subsequent high-intensity cycling time to exhaustion. In a counterbalanced, crossover design, nine healthy and active males (age: 23 ± 2 years, height: 179 ± 5 cm, body mass: 74 ± 9 kg, peak mean minute power (W peak ) 256 ± 45 W, peak oxygen uptake (V̇O 2peak ) 46 ± 8 ml.kg -1 .min -1 ) performed a graded incremental exercise test, two familiarization and two experimental trials. Experimental trials consisted of cycling to volitional exhaustion (T LIM1 ) at 100% W PEAK on two occasions (T LIM1 and T LIM2 ) interspersed by a 90 min passive recovery period. Using a double-blind approach, 30 min into a 90 min recovery period participants ingested either 0.3 g.kg -1 body mass sodium bicarbonate (NaHCO 3 ) or a placebo (PLA) containing 0.1 g.kg -1 body mass sodium chloride (NaCl) mixed with 4 ml.kg -1 tap water and 1 ml.kg -1 orange squash. The mean differences between T LIM2 and T LIM1 was larger for PLA compared with NaHCO 3 (-53 ± 53 vs. -20 ± 48 s; p = .008, d = 0.7, CI =-0.3, 1.6), indicating superior subsequent exercise time to exhaustion following NaHCO 3 . Blood lactate [Bla - ] was similar between treatments post T LIM1 , but greater for NaHCO 3 post T LIM2 and 5 min post T LIM2 . Ingestion of NaHCO 3 induced marked increases (p < .01) in both blood pH (+0.07 ± 0.02, d = 2.6, CI = 1.2, 3.7) and bicarbonate ion concentration [HCO 3 - ] (+6.8 ± 1.6 mmo.l -1 , d = 3.4, CI = 1.8, 4.7) compared with the PLA treatment, before T LIM2 . It is likely both the acceleration of recovery, and the marked increases of acid-base after T LIM1 contributed to greater T LIM2 performance compared with the PLA condition.

Cost-effective and business-beneficial computer validation for bioanalytical laboratories.

PubMed

McDowall, Rd

2011-07-01

Computerized system validation is often viewed as a burden and a waste of time to meet regulatory requirements. This article presents a different approach by looking at validation in a bioanalytical laboratory from the business benefits that computer validation can bring. Ask yourself the question, have you ever bought a computerized system that did not meet your initial expectations? This article will look at understanding the process to be automated, the paper to be eliminated and the records to be signed to meet the requirements of the GLP or GCP and Part 11 regulations. This paper will only consider commercial nonconfigurable and configurable software such as plate readers and LC-MS/MS data systems rather than LIMS or custom applications. Two streamlined life cycle models are presented. The first one consists of a single document for validation of nonconfigurable software. The second is for configurable software and is a five-stage model that avoids the need to write functional and design specifications. Both models are aimed at managing the risk each type of software poses whist reducing the amount of documented evidence required for validation.

Reconstructing Common Era Climate Fields Using Data Assimilation, Proxies, and a Linear Climate Model

NASA Astrophysics Data System (ADS)

Perkins, W. A.; Hakim, G. J.

2016-12-01

In this work, we examine the skill of a new approach to performing climate field reconstructions (CFRs) using a form of online paleoclimate data assimilation (PDA). Many previous studies have foregone climate model forecasts during assimilation due to the computational expense of running coupled global climate models (CGCMs), and the relatively low skill of these forecasts on longer timescales. Here we greatly diminish the computational costs by employing an empirical forecast model (known as a linear inverse model; LIM), which has been shown to have comparable skill to CGCMs. CFRs of annually averaged 2m air temperature anomalies are compared between the Last Millennium Reanalysis framework (no forecasting or "offline"), a persistence forecast, and four LIM forecasting experiments over the instrumental period (1850 - 2000). We test LIM calibrations for observational (Berkeley Earth), reanalysis (20th Century Reanalysis), and CMIP5 climate model (CCSM4 and MPI) data. Generally, we find that the usage of LIM forecasts for online PDA increases reconstruction agreement with the instrumental record for both spatial and global mean temperature (GMT). The detrended GMT skill metrics show the most dramatic increases in skill with coefficient of efficiency (CE) improvements over the no-forecasting benchmark averaging 57%. LIM experiments display a common pattern of spatial field increases in CE skill over northern hemisphere land areas and in the high-latitude North Atlantic - Barents Sea corridor (Figure 1). However, the non-GCM-calibrated LIMs introduce other deficiencies into the spatial skill of these reconstructions, likely due to aspects of the LIM calibration process. Overall, the CMIP5 LIMs have the best performance when considering both spatial fields and GMT. A comparison with the persistence forecast experiment suggests that improvements are associated with the usage of the LIM forecasts, and not simple persistence of temperature anomalies over time. These results show that the use of LIM forecasting can help add further dynamical constraint to CFRs. As we move forward, this will be an important factor in fully utilizing dynamically consistent information from the proxy record while reconstructing the past millennium.

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,…

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.

Carbon and Nitrogen Enrichment Patterns in Planetary Nebulae

NASA Astrophysics Data System (ADS)

Dufour, Reginald

2011-10-01

The goal of this project is to assess the role played in carbon production by low and intermediate mass stars {LIMS}, i.e. the progenitors of planetary nebulae {PNe}. One of the most pressing problems in galactic chemical evolution today is understanding the relative roles of LIMS {1-8 M_sun} versus massive stars {8-120 M_sun} in affecting the cosmic level of the element C. We are launching a fresh, ambitious project whose purpose is to employ STIS to obtain UV spectra of unprecedented-quality of 10 carefully chosen, bright solar metallicity PNe spanning a broad range in progenitor mass. Line strength measurements of important emission lines of C, N, and O such as OIII] 1660-6, NIII] 1747-54, CIII] 1907-9, and {when He++ is strong} CIV] 1550 and OIV] 1400 in each object will be used along with our own in-house abundance software to determine ion and element abundances for these three species. In turn, these results will be used to assess stellar yields {productivity rates} available in the literature. Favored yield sets will be used to calculate our own chemical evolution models in order to assess directly the importance of intermediate-mass stars in the cosmic evolution of C.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Yanwu; Wang, Xiaoxia; Hawkins, Cheryl A.

The LIM-only adaptor PINCH (the particularly interesting cysteine- and histidine-rich protein) plays a pivotal role in the assembly of focal adhesions (FAs), supramolecular complexes that transmit mechanical and biochemical information between extracellular matrix and actin cytoskeleton, regulating diverse cell adhesive processes such as cell migration, cell spreading, and survival. A key step for the PINCH function is its localization to FAs, which depends critically on the tight binding of PINCH to integrin-linked kinase (ILK). Here we report the solution NMR structure of the core ILK {center_dot} PINCH complex (28 kDa, K{sub D} {approx} 68 nm) involving the N-terminal ankyrin repeatmore » domain (ARD) of ILK and the first LIM domain (LIM1) of PINCH. We show that the ILK ARD exhibits five sequentially stacked ankyrin repeat units, which provide a large concave surface to grip the two contiguous zinc fingers of the PINCH LIM1. The highly electrostatic interface is evolutionally conserved but differs drastically from those of known ARD and LIM bound to other types of protein domains. Consistently mutation of a hot spot in LIM1, which is not conserved in other LIM domains, disrupted the PINCH binding to ILK and abolished the PINCH targeting to FAs. These data provide atomic insight into a novel modular recognition and demonstrate how PINCH is specifically recruited by ILK to mediate the FA assembly and cell-extracellular matrix communication.« less

Are we near the predictability limit of tropical Indo-Pacific sea surface temperatures?

NASA Astrophysics Data System (ADS)

Newman, Matthew; Sardeshmukh, Prashant D.

2017-08-01

The predictability of seasonal anomalies worldwide rests largely on the predictability of tropical sea surface temperature (SST) anomalies. Tropical forecast skill is also a key metric of climate models. We find, however, that despite extensive model development, the tropical SST forecast skill of the operational North American Multi-Model Ensemble (NMME) of eight coupled atmosphere-ocean models remains close both regionally and temporally to that of a vastly simpler linear inverse model (LIM) derived from observed covariances of SST, sea surface height, and wind fields. The LIM clearly captures the essence of the predictable SST dynamics. The NMME and LIM skills also closely track and are only slightly lower than the potential skill estimated using the LIM's forecast signal-to-noise ratios. This suggests that the scope for further skill improvement is small in most regions, except in the western equatorial Pacific where the NMME skill is currently much lower than the LIM skill.

Excitation Method of Linear-Motor-Type Rail Brake without Using Power Sources by Dynamic Braking with Zero Electrical Output

NASA Astrophysics Data System (ADS)

Sakamoto, Yasuaki; Kashiwagi, Takayuki; Hasegawa, Hitoshi; Sasakawa, Takashi; Fujii, Nobuo

The eddy current rail brake is a type of braking system used in railway vehicles. Because of problems such as rail heating and problems associated with ensuring that power is supplied when the feeder malfunctions, this braking system has not been used for practical applications in Japan. Therefore, we proposed the use of linear induction motor (LIM) technology in eddy current rail brake systems. The LIM rail brake driven by dynamic braking can reduce rail heating and generate the energy required for self-excitation. In this paper, we present an excitation system and control method for the LIM rail brake driven by “dynamic braking with zero electrical output”. The proposed system is based on the concept that the LIM rail brake can be energized without using excitation power sources such as a feeder circuit and that high reliability can be realized by providing an independent excitation system. We have studied this system and conducted verification tests using a prototype LIM rail brake on a roller rig. The results show that the system performance is adequate for commercializing the proposed system, in which the LIM rail brake is driven without using any excitation power source.

Measuring topology of low-intensity DNA methylation sites for high-throughput assessment of epigenetic drug-induced effects in cancer cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gertych, Arkadiusz, E-mail: gertycha@cshs.org; Bioinformatics, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA; Farkas, Daniel L., E-mail: dlfarkas@gmail.com

2010-11-15

Epigenetic anti-cancer drugs with demethylating effects have shown to alter genome organization in mammalian cell nuclei. The interest in the development of novel epigenetic drugs has increased the demand for cell-based assays to evaluate drug performance in pre-clinical studies. An imaging-based cytometrical approach that can measure demethylation effects as changes in the spatial nuclear distributions of methylated cytosine and global DNA in cancer cells is introduced in this paper. The cells were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei. In the preprocessing step themore » segmentation of nuclei in three-dimensional images (3-D) is followed by an automated assessment of nuclear DAPI/MeC patterns to exclude dissimilar entities. Next, low-intensity MeC (LIM) and low-intensity DNA (LID) sites of similar nuclei are localized and processed to obtain specific nuclear density profiles. These profiles sampled at half of the total nuclear volume yielded two parameters: LIM{sub 0.5} and LID{sub 0.5}. The analysis shows that zebularine and 5-azacytidine-the two tested epigenetic drugs introduce changes in the spatial distribution of low-intensity DNA and MeC signals. LIM{sub 0.5} and LID{sub 0.5} were significantly different (p < 0.001) in 5-azacytidine treated (n = 660) and zebularine treated (n = 496) vs. untreated (n = 649) DU145 human prostate cancer cells. In the latter case the LIM sites were predominantly found at the nuclear border, whereas treated populations showed different degrees of increase in LIMs towards the interior nuclear space, in which a large portion of heterochromatin is located. The cell-by-cell evaluation of changes in the spatial reorganization of MeC/DAPI signals revealed that zebularine is a more gentle demethylating agent than 5-azacytidine. Measuring changes in the topology of low-intensity sites can potentially be a valuable component in the high-throughput assessment of demethylation and risk of chromatin reorganization in epigenetic-drug screening tasks.« less

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.

Lay information mediary behavior uncovered: exploring how nonprofessionals seek health information for themselves and others online.

PubMed

Abrahamson, Jennie A; Fisher, Karen E; Turner, Anne G; Durrance, Joan C; Turner, Tammara Combs

2008-10-01

This research studied motivations for, barriers to, and effects of online health information seeking and explored lay information mediary behavior (LIMB) characteristics in the consumer health information domain. Lay information mediaries (LIMs) seek information on behalf or because of others, without necessarily being asked to do so or engaging in follow up, and have represented more than 50% of health information seekers in prior studies. A web-based survey was posted on NC Health Info (NCHI) with 211 respondents, self-identified per the information need that brought them to NCHI as 20% LIMs (n = 43), 58% direct users (n = 122), and 22% health or information providers (n = 46). Follow-up telephone interviews were performed with 10% (n = 21). Interview analysis focused on lay participants (n = 15 LIMs and direct users combined). Interviewees were reclassified post-survey as 12 LIMs and 3 direct users when studied information behavior extended beyond NCHI search. Interview data were analyzed using grounded theory approach. Surveyed LIMs were 77% female (n = 33) and searched on behalf or because of family members (81%, n = 35) and people they felt "extremely close" to (77%, n = 33). LIMs reported various information seeking barriers "sometimes" to "often." LIMs searched mostly without prompting (51%, n = 22). Interview results triangulated survey findings regarding gender, tie strength, and prompting. LIMB may be related to gender and relationship tie strength and appears more internally than externally motivated. Further LIMB research is warranted.

Army-UNL Center for Trauma Mechanics

DTIC Science & Technology

2011-03-07

Jung Yul Lim, Dr. Joseph A. Turner, Dr. Florin Bobaru, Dr. Mehrdad Negahban University of Nebraska Research Grants & Contracts 303 Administration...none) 1. Matthew Nienaber,* Jeong Soon Lee,* Ruqiang Feng, Jung Yul Lim. Impulsive pressurization of neuronal cells for traumatic brain injury study...Toronto, Canada, October 16-18, 2010. 11. Jeong Soon Lee, Matthew Nienaber, Ruqiang Feng, Jung Yul Lim. Impulsive pressurization of neuronal cells for

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.

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.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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...

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

Islet-to-LMO stoichiometries control the function of transcription complexes that specify motor neuron and V2a interneuron identity

PubMed Central

Song, Mi-Ryoung; Sun, Yunfu; Bryson, Ami; Gill, Gordon N.; Evans, Sylvia M.; Pfaff, Samuel L.

2009-01-01

Summary LIM transcription factors bind to nuclear LIM interactor (Ldb/NLI/Clim) in specific ratios to form higher-order complexes that regulate gene expression. Here we examined how the dosage of LIM homeodomain proteins Isl1 and Isl2 and LIM-only protein Lmo4 influences the assembly and function of complexes involved in the generation of spinal motor neurons (MNs) and V2a interneurons (INs). Reducing the levels of Islet proteins using a graded series of mutations favored V2a IN differentiation at the expense of MN formation. Although LIM-only proteins (LMOs) are predicted to antagonize the function of Islet proteins, we found that the presence or absence of Lmo4 had little influence on MN or V2a IN specification. We did find, however, that the loss of MNs resulting from reduced Islet levels was rescued by eliminating Lmo4, unmasking a functional interaction between these proteins. Our findings demonstrate that MN and V2a IN fates are specified by distinct complexes that are sensitive to the relative stoichiometries of the constituent factors and we present a model to explain how LIM domain proteins modulate these complexes and, thereby, this binary-cell-fate decision. PMID:19666821

The Diversity of the Limnohabitans Genus, an Important Group of Freshwater Bacterioplankton, by Characterization of 35 Isolated Strains

PubMed Central

Kasalický, Vojtěch; Jezbera, Jan; Hahn, Martin W.; Šimek, Karel

2013-01-01

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology. PMID:23505469

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 .

[Observation on changes of oxygen partial pressure in the deep tissues along the large intestine meridian during acupuncture in healthy subjects].

PubMed

Chen, Ming; Hu, Xiang-long; Wu, Zu-xing

2010-06-01

To observe changes of the partial oxygen pressure in the deep tissues along the Large Intestine Meridian (LIM) during acupuncture stimulation, so as to reveal the characteristics of energy metabolism in the tissues along the LIM. Thirty-one healthy volunteer subjects were enlisted in the present study. Partial oxygen pressure (POP) in the tissues (at a depth of about 1.5 cm) of acupoints Binao (LI 14), Shouwuli (LI 13), Shousanli (LI 10), 2 non-acupoints [the midpoints between Quchi (LI 11) and LI 14, and between Yangxi (LI 5) and LI 11) of the LIM, and 10 non-meridian points, 1.5-2.0 cm lateral and medial to each of the tested points of the LIM was detected before, during and after electroacupuncture (EA) stimulation of Hegu (LI 4) by using a tissue oxygen tension needle-like sensor. In normal condition, the POP values in the deep tissues along the LIM were significantly higher than those of the non-meridian control points on its bilateral sides. During and after EA of Hegu (LI 4), the POP levels decreased significantly in the deep tissues along the LIM in comparison with pre-EA (P < 0.01), and had no apparent changes in the non-meridian control points (P > 0.05). POP is significantly higher in the deep tissues along the LIM of healthy subjects under normal conditions, which can be downregulated by EA of Hegu (LI 4), suggesting an increase of both the utilization rate of oxygen and energy metabolism after EA.

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. There are small biases in the middle to lower stratosphere for the ascending versus descending node LIMS ozone, due principally to not accounting for the asymmetric weighting of its radiances across the tangent layer. The estimates of total accuracy were assessed by comparing the daily zonal mean LIMS ozone distributions against those from the Nimbus 7 SBUV Version 8 (V8) dataset for the same period. Generally, the LIMS V6 ozone agrees well with SBUV, except perhaps in the tropical lower stratosphere where the LIMS ozone is less. Still, the accuracy for LIMS V6 ozone in the lower stratosphere is improved over that found for LIMS V5, as indicated by several LIMS comparisons with ECC ozonesonde profiles. The LIMS V6 ozone is considered especially suitable for detailed studies of large-scale stratospheric processes above the 100-hPa level. Comparison of diurnal, photochemical model calculations with the monthly-averaged, upper stratospheric ozone observed from LIMS V6 indicates only a slight ozone deficit for the model at about 2 hPa. However, that deficit exhibits little to no seasonal variation and is in good agreement with similar model comparisons for a seasonal time series of ozone obtained with ground-based microwave instruments. Because the LIMS V6 ozone in the lower stratosphere has improved accuracy and sampling versus that of V5, it should now be possible to conduct quantitative studies of ozone transport and chemistry for the northern hemisphere, polar stratospheric winter of 1978/79 a time period when the catalytic loss of ozone due to reactive chlorine should not have been a major factor for the Arctic region.

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.

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.

Challenges in Small Screening Laboratories: SaaS to the rescue

PubMed Central

Lemmon, Vance P.; Jia, Yuanyuan; Shi, Yan; Holbrook, S. Douglas; Bixby, John L; Buchser, William

2012-01-01

The Miami Project to Cure Paralysis, part of the University of Miami Miller School of Medicine, includes a laboratory devoted to High Content Analysis (HCA) of neurons. The goal of the laboratory is to uncover signalling pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCA permits the quantification of neuronal morphology, including the lengths and numbers of axons. HCA screening of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. HCA itself produces vast amounts of information including images, well-based data and cell-based phenotypic measures. Managing experimental workflow and library data, along with the extensive amount of experimental results is challenging. For academic laboratories generating large data sets from experiments using thousands of perturbagens, a laboratory information management system (LIMS) is the data tracking solution of choice. With both productivity and efficiency as driving rationales, the Miami Project has equipped its HCA laboratory with a Software As A Service (SAAS) LIMS to ensure the quality of its experiments and workflows. The article discusses this application in detail, and how the system was selected and integrated into the laboratory. The advantages of SaaS are described. PMID:21631415

Implementation of a configurable laboratory information management system for use in cellular process development and manufacturing.

PubMed

Russom, Diana; Ahmed, Amira; Gonzalez, Nancy; Alvarnas, Joseph; DiGiusto, David

2012-01-01

Regulatory requirements for the manufacturing of cell products for clinical investigation require a significant level of record-keeping, starting early in process development and continuing through to the execution and requisite follow-up of patients on clinical trials. Central to record-keeping is the management of documentation related to patients, raw materials, processes, assays and facilities. To support these requirements, we evaluated several laboratory information management systems (LIMS), including their cost, flexibility, regulatory compliance, ongoing programming requirements and ability to integrate with laboratory equipment. After selecting a system, we performed a pilot study to develop a user-configurable LIMS for our laboratory in support of our pre-clinical and clinical cell-production activities. We report here on the design and utilization of this system to manage accrual with a healthy blood-donor protocol, as well as manufacturing operations for the production of a master cell bank and several patient-specific stem cell products. The system was used successfully to manage blood donor eligibility, recruiting, appointments, billing and serology, and to provide annual accrual reports. Quality management reporting features of the system were used to capture, report and investigate process and equipment deviations that occurred during the production of a master cell bank and patient products. Overall the system has served to support the compliance requirements of process development and phase I/II clinical trial activities for our laboratory and can be easily modified to meet the needs of similar laboratories.

Laboratory Information Management Systems for Forensic Laboratories: A White Paper for Directors and Decision Makers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anthony Hendrickson; Brian Mennecke; Kevin Scheibe

2005-10-01

Modern, forensics laboratories need Laboratory Information Management Systems (LIMS) implementations that allow the lab to track evidentiary items through their examination lifecycle and also serve all pertinent laboratory personnel. The research presented here presents LIMS core requirements as viewed by respondents serving in different forensic laboratory capacities as well as different forensic laboratory environments. A product-development methodology was employed to evaluate the relative value of the key features that constitute a LIMS, in order to develop a set of relative values for these features and the specifics of their implementation. In addition to the results of the product development analysis,more » this paper also provides an extensive review of LIMS and provides an overview of the preparation and planning process for the successful upgrade or implementation of a LIMS. Analysis of the data indicate that the relative value of LIMS components are viewed differently depending upon respondents' job roles (i.e., evidence technicians, scientists, and lab management), as well as by laboratory size. Specifically, the data show that: (1) Evidence technicians place the most value on chain of evidence capabilities and on chain of custody tracking; (2) Scientists generally place greatest value on report writing and generation, and on tracking daughter evidence that develops during their analyses; (3) Lab. Managers place the greatest value on chain of custody, daughter evidence, and not surprisingly, management reporting capabilities; and (4) Lab size affects LIMS preference in that, while all labs place daughter evidence tracking, chain of custody, and management and analyst report generation as their top three priorities, the order of this prioritization is size dependent.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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.

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.

Model-Based Assessment of the CO2 Sequestration Potential of Coastal Ocean Alkalinization

NASA Astrophysics Data System (ADS)

Feng, E. Y.; Koeve, W.; Keller, D. P.; Oschlies, A.

2017-12-01

The potential of coastal ocean alkalinization (COA), a carbon dioxide removal (CDR) climate engineering strategy that chemically increases ocean carbon uptake and storage, is investigated with an Earth system model of intermediate complexity. The CDR potential and possible environmental side effects are estimated for various COA deployment scenarios, assuming olivine as the alkalinity source in ice-free coastal waters (about 8.6% of the global ocean's surface area), with dissolution rates being a function of grain size, ambient seawater temperature, and pH. Our results indicate that for a large-enough olivine deployment of small-enough grain sizes (10 µm), atmospheric CO2 could be reduced by more than 800 GtC by the year 2100. However, COA with coarse olivine grains (1000 µm) has little CO2 sequestration potential on this time scale. Ambitious CDR with fine olivine grains would increase coastal aragonite saturation Ω to levels well beyond those that are currently observed. When imposing upper limits for aragonite saturation levels (Ωlim) in the grid boxes subject to COA (Ωlim = 3.4 and 9 chosen as examples), COA still has the potential to reduce atmospheric CO2 by 265 GtC (Ωlim = 3.4) to 790 GtC (Ωlim = 9) and increase ocean carbon storage by 290 Gt (Ωlim = 3.4) to 913 Gt (Ωlim = 9) by year 2100.

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.

Essential attributes identified in the design of a Laboratory Information Management System for a high throughput siRNA screening laboratory.

PubMed

Grandjean, Geoffrey; Graham, Ryan; Bartholomeusz, Geoffrey

2011-11-01

In recent years high throughput screening operations have become a critical application in functional and translational research. Although a seemingly unmanageable amount of data is generated by these high-throughput, large-scale techniques, through careful planning, an effective Laboratory Information Management System (LIMS) can be developed and implemented in order to streamline all phases of a workflow. Just as important as data mining and analysis procedures at the end of complex processes is the tracking of individual steps of applications that generate such data. Ultimately, the use of a customized LIMS will enable users to extract meaningful results from large datasets while trusting the robustness of their assays. To illustrate the design of a custom LIMS, this practical example is provided to highlight the important aspects of the design of a LIMS to effectively modulate all aspects of an siRNA screening service. This system incorporates inventory management, control of workflow, data handling and interaction with investigators, statisticians and administrators. All these modules are regulated in a synchronous manner within the LIMS. © 2011 Bentham Science Publishers

5-hydroxytryptamine level and 5-HT2A receptor mRNA expression in the guinea pigs eyes with spectacle lens-induced myopia

PubMed Central

Yang, Ji-Wen; Xu, Yan-Chun; Sun, Lin; Tian, Xiao-Dan

2010-01-01

AIM To investigate 5-hydroxytryptamine (5-HT) function and 5-HT receptor 2A (5-HT2A) mRNA expression in the formation of lens-induced myopia (LIM). METHODS Lens-induced myopia construction method was applied to generate myopia on guinea pig right eye (LIM eye). RESULTS LIM eyes formed significant myopia with longer axial length. 5-HT level in retina, choroids and sclera from LIM eyes was significantly higher than that in control group. 5-HT2A mRNA expression was also significantly up-regulated. CONCLUSION Refraction lens could induce myopia in guinea pig and 5-HT may play an important role in the formation of myopia by binding with 5-HT2A receptor. PMID:22553578

Compact and Thermosensitive Nature-inspired Micropump

PubMed Central

Kim, Hyejeong; Kim, Kiwoong; Lee, Sang Joon

2016-01-01

Liquid transportation without employing a bulky power source, often observed in nature, has been an essential prerequisite for smart applications of microfluidic devices. In this report, a leaf-inspired micropump (LIM) which is composed of thermo-responsive stomata-inspired membrane (SIM) and mesophyll-inspired agarose cryogel (MAC) is proposed. The LIM provides a durable flow rate of 30 μl/h · cm2 for more than 30 h at room temperature without external mechanical power source. By adapting a thermo-responsive polymer, the LIM can smartly adjust the delivery rate of a therapeutic liquid in response to temperature changes. In addition, as the LIM is compact, portable, and easily integrated into any liquid, it might be utilized as an essential component in advanced hand-held drug delivery devices. PMID:27796357

Analysis of chirality by femtosecond laser ionization mass spectrometry.

PubMed

Horsch, Philipp; Urbasch, Gunter; Weitzel, Karl-Michael

2012-09-01

Recent progress in the field of chirality analysis employing laser ionization mass spectrometry is reviewed. Emphasis is given to femtosecond (fs) laser ionization work from the author's group. We begin by reviewing fundamental aspects of determining circular dichroism (CD) in fs-laser ionization mass spectrometry (fs-LIMS) discussing an example from the literature (resonant fs-LIMS of 3-methylcyclopentanone). Second, we present new data indicating CD in non-resonant fs-LIMS of propylene oxide. Copyright © 2012 Wiley Periodicals, Inc., A Wiley Company.

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.

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

Automatic learning of rules. A practical example of using artificial intelligence to improve computer-based detection of myocardial infarction and left ventricular hypertrophy in the 12-lead ECG.

PubMed

Kaiser, W; Faber, T S; Findeis, M

1996-01-01

The authors developed a computer program that detects myocardial infarction (MI) and left ventricular hypertrophy (LVH) in two steps: (1) by extracting parameter values from a 10-second, 12-lead electrocardiogram, and (2) by classifying the extracted parameter values with rule sets. Every disease has its dedicated set of rules. Hence, there are separate rule sets for anterior MI, inferior MI, and LVH. If at least one rule is satisfied, the disease is said to be detected. The computer program automatically develops these rule sets. A database (learning set) of healthy subjects and patients with MI, LVH, and mixed MI+LVH was used. After defining the rule type, initial limits, and expected quality of the rules (positive predictive value, minimum number of patients), the program creates a set of rules by varying the limits. The general rule type is defined as: disease = lim1l < p1 < or = lim1u and lim2l < p2 < or = lim2u and ... limnl < pn < or = limnu. When defining the rule types, only the parameters (p1 ... pn) that are known as clinical electrocardiographic criteria (amplitudes [mV] of Q, R, and T waves and ST-segment; duration [ms] of Q wave; frontal angle [degrees]) were used. This allowed for submitting the learned rule sets to an independent investigator for medical verification. It also allowed the creation of explanatory texts with the rules. These advantages are not offered by the neurons of a neural network. The learned rules were checked against a test set and the following results were obtained: MI: sensitivity 76.2%, positive predictive value 98.6%; LVH: sensitivity 72.3%, positive predictive value 90.9%. The specificity ratings for MI are better than 98%; for LVH, better than 90%.

The model of self-compensation and pinning of the Fermi level in irradiated semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brudnyi, V. N.; Kolin, N. G.; Smirnov, L. S.

2007-09-15

A model is developed to analyze numerically the electrical properties and the steady-state (limiting) position of the Fermi level (F{sub lim}) in tetrahedral semiconductors irradiated with high-energy particles. It is shown that an irradiated semiconductor represents a highly compensated material, in which F{sub lim} is identical to /2, where is the average energy gap between the conduction band and valence band within the entire Brillouin zone of the crystal. The experimental values of F{sub lim}, the calculated values of /2, and the data on the electrical properties of irradiated semiconductors are presented. The chemical trends controllingmore » the variation in the quantity F{sub lim} in groups of semiconductors with the similar types of chemical bonding are analyzed.« less

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

Effects of Gender Difference and Caffeine Supplementation on Anaerobic Muscle Performance.

PubMed

Chen, H-Y; Wang, H-S; Tung, K; Chao, H-H

2015-11-01

The primary purpose of this study was to investigate the effects of gender difference and caffeine supplementation to maximal voluntary isometric contractions (MVIC) and submaximal voluntary isometric contractions (T(lim)). 10 male (age: 20.10 ± 2.18 years, BMI: 22.23±1.96 kg/m(2)) and 10 female (age: 19.90±0.99 years, BMI: 21.76±2.65 kg/m(2)) elite collegiate athletes were recruited. Subjects ingested caffeine (6 mg/kg) or a placebo in a randomized, double-blind, placebo-control, and counter-balanced fashion. MVIC and T(lim) were measured after supplementations. T(lim) result was calculated based on the time to exhaustion of isometric contraction with 50% MVIC. Fatigue index (FI%) referred to the MVIC tested 20 s after the cessation of T(lim) test, and was indexed by the percentage of MVIC decline. No significant interaction effect was found between the gender factor and the supplementation factor for all dependent variables. Compared to the placebo, caffeine supplementation significantly increased MVIC (5.9%) and T(lim) (15.5%) (p<0.05) whereas it had no significant effect on FI%. This study demonstrates that caffeine supplementation at a 6 mg/kg dosage facilitates performances in MVIC and T(lim). The ergogenic effect of caffeine on muscle power and muscle endurance does not show a gender bias. © Georg Thieme Verlag KG Stuttgart · New York.

Next generation tools for genomic data generation, distribution, and visualization

PubMed Central

2010-01-01

Background With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data. Results Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser. Conclusions These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See http://sourceforge.net/projects/gnomex/, http://sourceforge.net/projects/genoviz/, and http://sourceforge.net/projects/useq. PMID:20828407

Reconstructing paleoclimate fields using online data assimilation with a linear inverse model

NASA Astrophysics Data System (ADS)

Perkins, Walter A.; Hakim, Gregory J.

2017-05-01

We examine the skill of a new approach to climate field reconstructions (CFRs) using an online paleoclimate data assimilation (PDA) method. Several recent studies have foregone climate model forecasts during assimilation due to the computational expense of running coupled global climate models (CGCMs) and the relatively low skill of these forecasts on longer timescales. Here we greatly diminish the computational cost by employing an empirical forecast model (linear inverse model, LIM), which has been shown to have skill comparable to CGCMs for forecasting annual-to-decadal surface temperature anomalies. We reconstruct annual-average 2 m air temperature over the instrumental period (1850-2000) using proxy records from the PAGES 2k Consortium Phase 1 database; proxy models for estimating proxy observations are calibrated on GISTEMP surface temperature analyses. We compare results for LIMs calibrated using observational (Berkeley Earth), reanalysis (20th Century Reanalysis), and CMIP5 climate model (CCSM4 and MPI) data relative to a control offline reconstruction method. Generally, we find that the usage of LIM forecasts for online PDA increases reconstruction agreement with the instrumental record for both spatial fields and global mean temperature (GMT). Specifically, the coefficient of efficiency (CE) skill metric for detrended GMT increases by an average of 57 % over the offline benchmark. LIM experiments display a common pattern of skill improvement in the spatial fields over Northern Hemisphere land areas and in the high-latitude North Atlantic-Barents Sea corridor. Experiments for non-CGCM-calibrated LIMs reveal region-specific reductions in spatial skill compared to the offline control, likely due to aspects of the LIM calibration process. Overall, the CGCM-calibrated LIMs have the best performance when considering both spatial fields and GMT. A comparison with the persistence forecast experiment suggests that improvements are associated with the linear dynamical constraints of the forecast and not simply persistence of temperature anomalies.

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 incorporation into an electronic submission. This environment permits the management of online analytical processing via a single administrator once the data model and warehouse configuration have been designed. The expansion of the current environment will eventually connect data from all phases of research and development ensuring the return on investment and hopefully efficiencies in data processing unforeseen with earlier legacy systems.

Notch-dependent epithelial fold determines boundary formation between developmental fields in the Drosophila antenna.

PubMed

Ku, Hui-Yu; Sun, Y Henry

2017-07-01

Compartment boundary formation plays an important role in development by separating adjacent developmental fields. Drosophila imaginal discs have proven valuable for studying the mechanisms of boundary formation. We studied the boundary separating the proximal A1 segment and the distal segments, defined respectively by Lim1 and Dll expression in the eye-antenna disc. Sharp segregation of the Lim1 and Dll expression domains precedes activation of Notch at the Dll/Lim1 interface. By repressing bantam miRNA and elevating the actin regulator Enable, Notch signaling then induces actomyosin-dependent apical constriction and epithelial fold. Disruption of Notch signaling or the actomyosin network reduces apical constriction and epithelial fold, so that Dll and Lim1 cells become intermingled. Our results demonstrate a new mechanism of boundary formation by actomyosin-dependent tissue folding, which provides a physical barrier to prevent mixing of cells from adjacent developmental fields.

Notch-dependent epithelial fold determines boundary formation between developmental fields in the Drosophila antenna

PubMed Central

2017-01-01

Compartment boundary formation plays an important role in development by separating adjacent developmental fields. Drosophila imaginal discs have proven valuable for studying the mechanisms of boundary formation. We studied the boundary separating the proximal A1 segment and the distal segments, defined respectively by Lim1 and Dll expression in the eye-antenna disc. Sharp segregation of the Lim1 and Dll expression domains precedes activation of Notch at the Dll/Lim1 interface. By repressing bantam miRNA and elevating the actin regulator Enable, Notch signaling then induces actomyosin-dependent apical constriction and epithelial fold. Disruption of Notch signaling or the actomyosin network reduces apical constriction and epithelial fold, so that Dll and Lim1 cells become intermingled. Our results demonstrate a new mechanism of boundary formation by actomyosin-dependent tissue folding, which provides a physical barrier to prevent mixing of cells from adjacent developmental fields. PMID:28708823

Posttranscriptional Regulation of the Neurofibromatosis 2 Gene

DTIC Science & Technology

2006-07-01

clinical presenta- tion would be severe and consistent with the con- ventional form of NF2. Schwannomatosis , a recently defined form of neu...rofibromatosis, is characterized by multiple sch- wannomas without any NF2-associated vestibular schwannomas. Patients with schwannomatosis fre- quently...that approximately one-third of patients with schwannomatosis had tumors in an anatomically lim- ited distribution, such as a single limb, several con

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

Computer-aided design studies of the homopolar linear synchronous motor

NASA Astrophysics Data System (ADS)

Dawson, G. E.; Eastham, A. R.; Ong, R.

1984-09-01

The linear induction motor (LIM), as an urban transit drive, can provide good grade-climbing capabilities and propulsion/braking performance that is independent of steel wheel-rail adhesion. In view of its 10-12 mm airgap, the LIM is characterized by a low power factor-efficiency product of order 0.4. A synchronous machine offers high efficiency and controllable power factor. An assessment of the linear homopolar configuration of this machine is presented as an alternative to the LIM. Computer-aided design studies using the finite element technique have been conducted to identify a suitable machine design for urban transit propulsion.

A logical approach to semantic interoperability in healthcare.

PubMed

Bird, Linda; Brooks, Colleen; Cheong, Yu Chye; Tun, Nwe Ni

2011-01-01

Singapore is in the process of rolling out a number of national e-health initiatives, including the National Electronic Health Record (NEHR). A critical enabler in the journey towards semantic interoperability is a Logical Information Model (LIM) that harmonises the semantics of the information structure with the terminology. The Singapore LIM uses a combination of international standards, including ISO 13606-1 (a reference model for electronic health record communication), ISO 21090 (healthcare datatypes), and SNOMED CT (healthcare terminology). The LIM is accompanied by a logical design approach, used to generate interoperability artifacts, and incorporates mechanisms for achieving unidirectional and bidirectional semantic interoperability.

The accuracy of temperature distributions used to derive the net transport for a zonally averaged model

NASA Technical Reports Server (NTRS)

Remsberg, Ellis E.; Bhatt, Praful P.

1994-01-01

Comparisons of satellite-derived temperatures with correlative temperatures indicate that the LIMS temperatures are accurate and contain more of the needed vertical resolution for calculating a residual mean circulation for transporting tracer-like species. Generally, the LIMS temperatures are accurate to at least 2 K. Other satellite data sets are comprised of temperatures with coarser vertical resolution, leading to biases that occur with an error pattern that is characteristic of their resolution. Their biases exceed 2 K at some altitudes. Retrievals of species using an infrared limb emission technique are sensitive to any temperature bias. Generally, the IMS comparisons with other data sets for ozone and water vapor are good to better than 20 percent; this represents an independent confirmation of the quality of LIMS and temperatures. Zonal mean comparisons between LIMS and SAMS temperatures also indicate agreement to better than 2 K from about 7 to 2hPa. Therefore, we are confident that SAMS N2O and CH4 are relatively free of temperature bias in that region. These factors support the generally good agreement in G90 between model N2O transported using a LIMS-derived RMC and the N2O contours from SAMS.

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.

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.

Effects of cholera toxin on human colon carcinoma cell lines.

PubMed

Barkla, D H; Whitehead, R H; Hayward, I P

1992-10-01

This study reports on changes in morphology and membrane transport in 5 human colon carcinoma cell lines treated with cholera toxin (CT). Three of the cell lines that grew as monolayers (LIM 1215, LIM 1899, LIM 2099) and 1 that grew as floating clumps (LIM 2408) did not show morphological changes after CT treatment. However, cell line LIM 1863 that grows as floating "crypt-like" organoids showed rapid and distinctive changes in morphology and membrane transport after CT treatment. At 1 and 6 hrs after CT treatment, light and transmission electron microscopy revealed rapid dilatation of the central lumen of organoids and the appearance of 2 populations of apical vesicular inclusions. The first population was unusual in being non-membrane bound and limited by fuzzy filamentous material. The second population was membrane bound. Scanning electron microscopy at 1-6 hr after CT treatment showed swelling and loss of surface microvilli on some, but not all, cells. At 24 hr after CT treatment the majority of organoids showed evidence of fluid accumulation and small apical vesicles coalesced to form large single vacuoles that obliterated normal cell morphology. By 48 hr, continued swelling produced extreme attenuation of the plasma membrane with cells taking on an "endothelial cell-like" appearance. The response to CT was dose-dependent. Uptake studies using 86Rubidium and blocking studies using ouabain and amiloride indicated that CT is acting on the Na+/K+ ATPase membrane pump to cause the increased fluid uptake by LIM 1863 cells. This study is the first to report specific morphological changes in intestine-derived cells in response to CT.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Ground-based microwave observations of ozone in the upper stratosphere and mesosphere

NASA Technical Reports Server (NTRS)

Connor, Brian J.; Siskind, David E.; Tsou, J. J.; Parrish, Alan; Remsberg, Ellis E.

1994-01-01

A 9-month-long series of mesurements of ozone in the upper stratosphere and mesosphere is reported. The measurements are presented as monthly averages of profiles in blocks of roughly 20 min local time and as night-to-day ratios. An error analysis predicts accuracies of 5-26% for the monthly profiles and 2.5-9% for the ratios. The data are compared to historical data from Solar Mesosphere Explorer (SME) and limb infrared monitor of the stratosphere (LIMS), and it is shown how to remove the effect of different vertical resolution from the comparisons. The microwave data typically agree to better than 10% with SMF and nighttime LIMS ozone at all altitudes below the 0.1-mbar surface. Comparison of the microwave night-to-day ratio with the corresponding ratio from LIMS suggests that nonlocal thermodynamic equilibrium effects in the LIMS daytime data exceed 10% at all pressures less than or equal to 1 mbar.

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.

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.

LASER BIOLOGY: Peculiarities of studying an isolated neuron by the method of laser interference microscopy

NASA Astrophysics Data System (ADS)

Yusipovich, Alexander I.; Novikov, Sergey M.; Kazakova, Tatiana A.; Erokhova, Liudmila A.; Brazhe, Nadezda A.; Lazarev, Grigory L.; Maksimov, Georgy V.

2006-09-01

Actual aspects of using a new method of laser interference microscopy (LIM) for studying nerve cells are discussed. The peculiarities of the LIM display of neurons are demonstrated by the example of isolated neurons of a pond snail Lymnaea stagnalis. A comparative analysis of the images of the cell and subcellular structures of a neuron obtained by the methods of interference microscopy, optical transmission microscopy, and confocal microscopy is performed. Various aspects of the application of LIM for studying the lateral dimensions and internal structure of the cytoplasm and organelles of a neuron in cytology and cell physiology are discussed.

Peculiarities of studying an isolated neuron by the method of laser interference microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yusipovich, Alexander I; Kazakova, Tatiana A; Erokhova, Liudmila A

2006-09-30

Actual aspects of using a new method of laser interference microscopy (LIM) for studying nerve cells are discussed. The peculiarities of the LIM display of neurons are demonstrated by the example of isolated neurons of a pond snail Lymnaea stagnalis. A comparative analysis of the images of the cell and subcellular structures of a neuron obtained by the methods of interference microscopy, optical transmission microscopy, and confocal microscopy is performed. Various aspects of the application of LIM for studying the lateral dimensions and internal structure of the cytoplasm and organelles of a neuron in cytology and cell physiology are discussed.more » (laser biology)« less

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.

At Periscope Depth: Exploring Submarine Proliferation In Southeast Asia

DTIC Science & Technology

2015-09-01

Regional Security Organization,” Contemporary Southeast Asia 27, no. 1 (2005): 5. 74 Mohd Nizam Basiron and Lim Chee Kia , “The Modernisation of the...2C11059%2C8 411&secondRedirectIndicator=true. Basiron, Mohd Nizam, and Lim Chee Kia . “The Modernisation of the Royal Malaysian Navy: Challenges, Trends

Discriminant Validity of the WISC-IV Culture-Language Interpretive Matrix

ERIC Educational Resources Information Center

Styck, Kara M.; Watkins, Marley W.

2014-01-01

The Culture-Language Interpretive Matrix (C-LIM) was developed to help practitioners determine the validity of test scores obtained from students who are culturally and linguistically different from the normative group of a test. The present study used an idiographic approach to investigate the diagnostic utility of the C-LIM for the Wechsler…

A concerted action of a paired-type homeobox gene, aristaless, and a homolog of Hox11/tlx homeobox gene, clawless, is essential for the distal tip development of the Drosophila leg.

PubMed

Kojima, Tetsuya; Tsuji, Takuya; Saigo, Kaoru

2005-03-15

The subdivision of the developing field by region-specific expression of genes encoding transcription factors is an essential step during appendage development in arthropod and vertebrates. In Drosophila leg development, the distal-most region (pretarsus) is specified by the expression of homeobox genes, aristaless and Lim1, and its immediate neighbor (distal tarsus) is specified by the expression of a pair of Bar homeobox genes. Here, we show that one additional gene, clawless, which is a homolog of vertebrate Hox11/tlx homeobox gene family and formerly known as C15, is specifically expressed in the pretarsus and cooperatively acts with aristaless to repress Bar and possibly to activate Lim1. Similar to aristaless, the maximal expression of clawless requires Lim1 and its co-factor, Chip. Bar attenuates aristaless and clawless expression through Lim1 repression. Aristaless and Clawless proteins form a complex capable of binding to specific DNA targets, which cannot be well recognized solely by Aristaless or Clawless.

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.

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.

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

Remote and Local Influences in Forecasting Pacific SST: a Linear Inverse Model and a Multimodel Ensemble Study

NASA Astrophysics Data System (ADS)

Faggiani Dias, D.; Subramanian, A. C.; Zanna, L.; Miller, A. J.

2017-12-01

Sea surface temperature (SST) in the Pacific sector is well known to vary on time scales from seasonal to decadal, and the ability to predict these SST fluctuations has many societal and economical benefits. Therefore, we use a suite of statistical linear inverse models (LIMs) to understand the remote and local SST variability that influences SST predictions over the North Pacific region and further improve our understanding on how the long-observed SST record can help better guide multi-model ensemble forecasts. Observed monthly SST anomalies in the Pacific sector (between 15oS and 60oN) are used to construct different regional LIMs for seasonal to decadal prediction. The forecast skills of the LIMs are compared to that from two operational forecast systems in the North American Multi-Model Ensemble (NMME) revealing that the LIM has better skill in the Northeastern Pacific than NMME models. The LIM is also found to have comparable forecast skill for SST in the Tropical Pacific with NMME models. This skill, however, is highly dependent on the initialization month, with forecasts initialized during the summer having better skill than those initialized during the winter. The forecast skill with LIM is also influenced by the verification period utilized to make the predictions, likely due to the changing character of El Niño in the 20th century. The North Pacific seems to be a source of predictability for the Tropics on seasonal to interannual time scales, while the Tropics act to worsen the skill for the forecast in the North Pacific. The data were also bandpassed into seasonal, interannual and decadal time scales to identify the relationships between time scales using the structure of the propagator matrix. For the decadal component, this coupling occurs the other way around: Tropics seem to be a source of predictability for the Extratropics, but the Extratropics don't improve the predictability for the Tropics. These results indicate the importance of temporal scale interactions in improving predictability on decadal timescales. Hence, we show that LIMs are not only useful as benchmarks for estimates of statistical skill, but also to isolate contributions to the forecast skills from different timescales, spatial scales or even model components.

Non-invasive ventilation (NIV) as an aid to rehabilitation in acute respiratory disease.

PubMed

Dyer, Fran; Flude, Lizzie; Bazari, Farid; Jolley, Caroline; Englebretsen, Catherine; Lai, Dilys; Polkey, Michael I; Hopkinson, Nicholas S

2011-12-16

Non-invasive ventilation (NIV) can increase exercise tolerance, reduce exercise induced desaturation and improve the outcome of pulmonary rehabilitation in patients with chronic respiratory disease. It is not known whether it can be applied to increase exercise capacity in patients admitted with non-hypercapnic acute exacerbations of COPD (AECOPD). We investigated the acceptability and feasibility of using NIV for this purpose. On a single occasion, patients admitted with an acute exacerbation of chronic respiratory disease who were unable to cycle for five minutes at 20 watts attempted to cycle using NIV and their endurance time (T(lim)) was recorded. To determine feasibility of this approach in clinical practice patients admitted with AECOPD were screened for participation in a trial of regular NIV assisted rehabilitation during their hospital admission. In 12 patients tested on a single occasion NIV increased T(lim) from 184(65) seconds to 331(229) seconds (p = 0.04) and patients desaturated less (median difference = 3.5%, p = 0.029). In the second study, 60 patients were admitted to hospital during a three month period of whom only 18(30)% were eligible to participate and of these patients, only four (7%) consented to participate. NIV improves exercise tolerance in patients with acute exacerbations of chronic respiratory disease but the applicability of this approach in routine clinical practice may be limited. http://www.controlled-trials.com/ISRCTN35692743.

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…

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…

A Positive Approach to Change: The Role of Appreciative Inquiry in Library and Information Organisations

ERIC Educational Resources Information Center

Kelly, Tricia

2010-01-01

Library and information management (LIM) organisations are on an almost continual path of change driven by changes in technology, service models, staffing structures, and financial allocations. The way in which LIM organisations approach change varies, as does the success rate of change management procedures undertaken. One particular approach to…

Development of an Excel-based laboratory information management system for improving workflow efficiencies in early ADME screening.

PubMed

Lu, Xinyan

2016-01-01

There is a clear requirement for enhancing laboratory information management during early absorption, distribution, metabolism and excretion (ADME) screening. The application of a commercial laboratory information management system (LIMS) is limited by complexity, insufficient flexibility, high costs and extended timelines. An improved custom in-house LIMS for ADME screening was developed using Excel. All Excel templates were generated through macros and formulae, and information flow was streamlined as much as possible. This system has been successfully applied in task generation, process control and data management, with a reduction in both labor time and human error rates. An Excel-based LIMS can provide a simple, flexible and cost/time-saving solution for improving workflow efficiencies in early ADME screening.

The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade

PubMed Central

YAN, Fang; JIANG, Ke; WANG, Kai; JIN, Jie-Qiong; SUWANNAPOOM, Chatmongkon; LI, Cheng; Jens, V. VINDUM; Rafe, M. BROWN; CHE, Jing

2016-01-01

In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpine, Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpine form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis. PMID:26828029

76 FR 66361 - Quarterly Publication of Individuals, Who Have Chosen To Expatriate, as Required by Section 6039G

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-26

... THOMAS YUL BAER JULIAN JULIUS BAGGETT SUSAN BANKES FLORA JUNE BARBALACO STEPHEN BATES LIAM ROBERT BAXTER... THOMAS GRIMM CHRISTOPH GRIMM KATJA GULINO SAYAN HABIB OK YO HACKETT PAMELA D. J. HALL NATALIE JUDITH HAMI... KEUNG LI LYDIA KWAN LIEBMANN BRAD HUNTER LIM LILLAN YUXIAN LIM VIVIAN YUJING LIN CHARLYN LINCKE THOMAS...

AtDMC1, the Arabidopsis homologue of the yeast DMC1 gene: characterization, transposon-induced allelic variation and meiosis-associated expression.

PubMed

Klimyuk, V I; Jones, J D

1997-01-01

Based on homologies between the yeast DMC1 and the lily LIM15 meiosis-specific genes, degenerate PCR primers were designed that amplified the Arabidopsis DMC1 gene (AtDMC1). AtDMC1 genomic DNA (8 kb) was sequenced, and the transcript was characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) and by 5' and 3' RACE (rapid amplification of cDNA ends). The AtDMC1 gene contains 15 exons and 14 introns. RNA in situ hybridization analysis showed that expression of the AtDMC1 is restricted to pollen mother cells in anthers and to megaspore mother cells in ovules. The AtDMC1 promoter was fused to the GUS reporter gene, and conferred meiosis-associated expression in both male and female floral lineages. Comparison of AtDMC1 isolated from Landsberg erecta ecotype to its Columbia allele ArLIM15, revealed the presence of a 1874 bp transposon-like element within the promoter region of ArLIM15. RT-PCR analysis showed that the expression levels of AtDMC1 and ArLIM15 are similar. Possible uses for the AtDMC1 promoter are discussed.

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.

Clinical and Molecular Consequences of NF1 Microdeletion

DTIC Science & Technology

2009-08-01

sheath tumors from patients with Recklinghausen’s disease. Cancer Lett. 2000, 155, 181–190. 107. Wallace, M.R.; Rasmussen, S.A.; Lim, I.T.; Gray , B.A...indicated. The GRD (exons 21-27a) and a cysteine/serine-rich domain with 3 cysteine pairs suggestive of ATP binding (exons 11-17) are indicated. Gray ...glycoproteins (exons 2-8), the α-helical domain (exons 10-15), and the unique C-terminus (exons 16-17) are shown. Gray boxes indicate alter- natively spliced

Optimal Repairman Allocation Models

DTIC Science & Technology

1976-03-01

state X under policy ir. Then lim {k1’ lC0 (^)I) e.(X,k) - 0 k*0 *’-’ (3.1.1) Proof; The result is proven by induction on |CQ(X...following theorem. Theorem 3.1 D. Under the conditions of theorem 3.1 A, define g1[ 1) (X) - g^U), then lim k- lC0 W l-mle (XHkl00^ Ig*11 (X

Proceedings from the 6th Annual University of Calgary Leaders in Medicine Research Symposium.

PubMed

Roberts, Jodie I; Beatty, Jennifer K; Peplowski, Michael A; Keough, Michael B; Yipp, Bryan G; Hollenberg, Morley D; Beck, Paul L

2015-12-04

On November 14, 2014, the Leaders in Medicine (LIM) program at the Cumming School of Medicine, University of Calgary hosted its 6th Annual Research Symposium. Dr. Danuta Skowronski, Epidemiology Lead for Influenza and Emerging Respiratory Pathogens at the British Columbia Centre for Disease Control (BCCDC), was the keynote speaker and presented a lecture entitled "Rapid response research during emerging public health crises: influenza and reflections from the five year anniversary of the 2009 pandemic". The LIM symposium provides a forum for both LIM and non-LIM medical students to present their research work, either as an oral or poster presentation. There were a total of six oral presentations and 77 posters presented. 
The oral presentations included: Swathi Damaraju, "The role of cell communication and 3D Cell-Matrix environment in a stem cell-based tissue engineering strategy for bone repair"; Menglin Yang, "The proteolytic activity of Nepenthes pitcher fluid as a therapeutic for the treatment of celiac disease"; Amelia Kellar, "Monitoring pediatric inflammatory bowel disease - a retrospective analysis of transabdominal ultrasound"; Monica M. Faria-Crowder, "The design and application of a molecular profiling strategy to identify polymicrobial acute sepsis infections"; Waleed Rahmani, "Hair follicle dermal stem cells regenerate the dermal sheath, repopulate the dermal papilla and modulate hair type"; and, Laura Palmer, "A novel role for amyloid beta protein during hypoxia/ischemia". 
The article on the University of Calgary Leaders in Medicine Program, "A Prescription that Addresses the Decline of Basic Science Education in Medical School," in a previous issue of CIM (2014 37(5):E292) provides more details on the program. Briefly, the LIM Research Symposium has the following objectives: (1) to showcase the impressive variety of projects undertaken by students in the LIM Program as well as University of Calgary medical students; (2) to encourage medical student participation in research and special projects; and, (3) to inform students and faculty about the diversity of opportunities available for research and special projects during medical school and beyond.

The following abstracts were submitted for publication.

GAMMA-RAY BURST HOST GALAXY SURVEYS AT REDSHIFT z {approx}> 4: PROBES OF STAR FORMATION RATE AND COSMIC REIONIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trenti, Michele; Perna, Rosalba; Levesque, Emily M.

2012-04-20

Measuring the star formation rate (SFR) at high redshift is crucial for understanding cosmic reionization and galaxy formation. Two common complementary approaches are Lyman break galaxy (LBG) surveys for large samples and gamma-ray burst (GRB) observations for sensitivity to SFR in small galaxies. The z {approx}> 4 GRB-inferred SFR is higher than the LBG rate, but this difference is difficult to understand, as both methods rely on several modeling assumptions. Using a physically motivated galaxy luminosity function model, with star formation in dark matter halos with virial temperature T{sub vir} {approx}> 2 Multiplication-Sign 10{sup 4} K (M{sub DM} {approx}> 2more » Multiplication-Sign 10{sup 8} M{sub Sun }), we show that GRB- and LBG-derived SFRs are consistent if GRBs extend to faint galaxies (M{sub AB} {approx}< -11). To test star formation below the detection limit L{sub lim} {approx} 0.05L*{sub z=3} of LBG surveys, we propose to measure the fraction f{sub det}(L > L{sub lim}, z) of GRB hosts with L > L{sub lim}. This fraction quantifies the missing star formation fraction in LBG surveys, constraining the mass-suppression scale for galaxy formation, with weak dependence on modeling assumptions. Because f{sub det}(L > L{sub lim}, z) corresponds to the ratio of SFRs derived from LBG and GRB surveys, if these estimators are unbiased, measuring f{sub det}(L > L{sub lim}, z) also constrains the redshift evolution of the GRB production rate per unit mass of star formation. Our analysis predicts significant success for GRB host detections at z {approx} 5 with f{sub det}(L > L{sub lim}, z) {approx} 0.4, but rarer detections at z > 6. By analyzing the upper limits on host galaxy luminosities of six z > 5 GRBs from literature data, we infer that galaxies with M{sub AB} > -15 were present at z > 5 at 95% confidence, demonstrating the key role played by very faint galaxies during reionization.« less

Which functional unit to identify sustainable foods?

PubMed

Masset, Gabriel; Vieux, Florent; Darmon, Nicole

2015-09-01

In life-cycle assessment, the functional unit defines the unit for calculation of environmental indicators. The objective of the present study was to assess the influence of two functional units, 100 g and 100 kcal (420 kJ), on the associations between three dimensions for identifying sustainable foods, namely environmental impact (via greenhouse gas emissions (GHGE)), nutritional quality (using two distinct nutrient profiling systems) and price. GHGE and price data were collected for individual foods, and were each expressed per 100 g and per 100 kcal. Two nutrient profiling models, SAIN,LIM and UK Ofcom, were used to assess foods' nutritional quality. Spearman correlations were used to assess associations between variables. Sustainable foods were identified as those having more favourable values for all three dimensions. The French Individual and National Dietary Survey (INCA2), 2006-2007. Three hundred and seventy-three foods highly consumed in INCA2, covering 65 % of total energy intake of adult participants. When GHGE and price were expressed per 100 g, low-GHGE foods had a lower price and higher SAIN,LIM and Ofcom scores (r=0·59, -0·34 and -0·43, respectively), suggesting a compatibility between the three dimensions; 101 and 100 sustainable foods were identified with SAIN,LIM and Ofcom, respectively. When GHGE and price were expressed per 100 kcal, low-GHGE foods had a lower price but also lower SAIN,LIM and Ofcom scores (r=0·67, 0·51 and 0·47, respectively), suggesting that more environment-friendly foods were less expensive but also less healthy; thirty-four sustainable foods were identified with both SAIN,LIM and Ofcom. The choice of functional unit strongly influenced the compatibility between the sustainability dimensions and the identification of sustainable foods.

Effect of recovery duration from prior exhaustive exercise on the parameters of the power-duration relationship.

PubMed

Ferguson, C; Rossiter, H B; Whipp, B J; Cathcart, A J; Murgatroyd, S R; Ward, S A

2010-04-01

The physiological equivalents of the curvature constant (W') of the high-intensity power-duration (P-t(LIM)) relationship are poorly understood, although they are presumed to reach maxima/minima at exhaustion. In an attempt to improve our understanding of the determinants of W', we therefore aimed to determine its recovery kinetics following exhaustive exercise (which depletes W') concomitantly with those of O(2) uptake (V(O(2)), a proxy for the kinetics of phosphocreatine replenishment) and blood lactate concentration ([L(-)]). Six men performed cycle-ergometer exercise to t(LIM): a ramp and four constant-load tests, at different work rates, for estimation of lactate threshold, W', critical power (CP), and maximum V(O(2)). Three further exhausting tests were performed at different work rates, each preceded by an exhausting "conditioning" bout, with intervening recoveries of 2, 6, and 15 min. Neither prior exhaustion nor recovery duration altered V(O(2)) or [L(-)] at t(LIM). Postconditioning, the P-t(LIM) relationship remained well characterized by a hyperbola, with CP unchanged. However, W' recovered to 37 +/- 5, 65 +/- 6, and 86 +/- 4% of control following 2, 6, and 15 min of intervening recovery, respectively. The W' recovery was curvilinear [interpolated half time (t(1/2)) = 234 +/- 32 s] and appreciably slower than V(O(2)) recovery (t(1/2) = 74 +/- 2 s) but faster than [L(-)] recovery (t(1/2) = 1,366 +/- 799 s). This suggests that W' determines supra-CP exercise tolerance, its restitution kinetics are not a unique function of phosphocreatine concentration or arterial [L(-)], and it is unlikely to simply reflect a finite energy store that becomes depleted at t(LIM).

Genetic structure of the threatened Hopea chinensis in the Quang Ninh Province, Vietnam.

PubMed

Trang, N T P; Triest, L

2016-04-29

Hopea chinensis Hand-Mazz (synonym H. hongayensis Tardieu), is a wind and insect pollinated species. It is a threatened species known only from two locations: Quang Ninh (Vietnam) and Guangxi (China). As an endemic species, it is worth preserving both for dipterocarp biodiversity, as well as for its medicinal use and economic importance as a fine wood. The genetic diversity and population genetic structure of H. chinensis was investigated, using natural populations distributed throughout the Ba Mun and Cai Lim islands, Quang Ninh Province, Vietnam. A total of 65 alleles were detected. The adult allelic richness was higher than that found in juveniles and seedlings in both populations. Inbreeding was found to be significant in Ba Mun adults (F(ST) = 0.139), as well as in Cai Lim juveniles and seedlings (F(ST) = 0.283 and 0.345, respectively). Evidence of a bottleneck could be detected in the juveniles and seedlings of the Cai Lim population. A Bayesian analysis and F(ST) values suggested high genetic differentiation among the age classes of the Ba Mun and Cai Lim populations. Whereas the adults of the Ba Mun population showed evidence of inbreeding, the next generations showed more potential heterozygotes. In contrast, the adults in the Cai Lim population showed no significant inbreeding, but the observed heterozygosity in the next generation was lower than expected, suggesting significant inbreeding. The H. chinensis populations on islands are developed well and showed re-generation under good condition. Thus, the forestry protector should conserve and protect the natural spatial structure of H. chinensis on each island as their natural habitats and keep them through natural regeneration.

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

Modulation of serpin reaction through stabilization of transient intermediate by ligands bound to alpha-helix F.

PubMed

Komissarov, Andrey A; Zhou, Aiwu; Declerck, Paul J

2007-09-07

Mechanism-based inhibition of proteinases by serpins involves enzyme acylation and fast insertion of the reactive center loop (RCL) into the central beta-sheet of the serpin, resulting in mechanical inactivation of the proteinase. We examined the effects of ligands specific to alpha-helix F (alphaHF) of plasminogen activator inhibitor-1 (PAI-1) on the stoichiometry of inhibition (SI) and limiting rate constant (k(lim)) of RCL insertion for reactions with beta-trypsin, tissue-type plasminogen activator (tPA), and urokinase. The somatomedin B domain of vitronectin (SMBD) did not affect SI for any proteinase or k(lim) for tPA but decreased the k(lim) for beta-trypsin. In contrast to SMBD, monoclonal antibodies MA-55F4C12 and MA-33H1F7, the epitopes of which are located at the opposite side of alphaHF, decreased k(lim) and increased SI for every enzyme. These effects were enhanced in the presence of SMBD. RCL insertion for beta-trypsin and tPA is limited by different subsequent steps of PAI-1 mechanism as follows: enzyme acylation and formation of a loop-displaced acyl complex (LDA), respectively. Stabilization of LDA through the disruption of the exosite interactions between PAI-1 and tPA induced an increase in the k(lim) but did not affect the SI. Thus it is unlikely that LDA contributes significantly to the outcome of the serpin reaction. These results demonstrate that the rate of RCL insertion is not necessarily correlated with SI and indicate that an intermediate, different from LDA, which forms during the late steps of PAI-1 mechanism, and could be stabilized by ligands specific to alphaHF, controls bifurcation between the inhibitory and the substrate pathways.

Kelvin wave-induced trace constituent oscillations in the equatorial stratosphere

NASA Technical Reports Server (NTRS)

Randel, William J.

1990-01-01

Kelvin wave induced oscillations in ozone (O3), water vapor (H2O), nitric acid (HNO3) and nitrogen dioxide (NO2) in the equatorial stratosphere are analyzed using Limb Infrared Monitor of the Stratosphere (LIMS) data. Power and cross-spectrum analyses reveal coherent eastward propagating zonal wave 1 and 2 constituent fluctuations, due to the influence of Kelvin waves previously documented in the LIMS data. Comparison is made between a preliminary and the archival versions of the LIMS data; significant differences are found, demonstrating the sensitivity of constituent retrievals to derived temperature profiles. Because Kelvin waves have vanishing meridional velocity, analysis of tracer transport in the meridional plane is substantially simplified. Kelvin wave vertical advection is demonstrated by coherent, in-phase temperature-tracer oscillations, co-located near regions of strong background vertical gradients.

Identification of high shears and compressive discontinuities in the inner heliosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Greco, A.; Perri, S.

2014-04-01

Two techniques, the Partial Variance of Increments (PVI) and the Local Intermittency Measure (LIM), have been applied and compared using MESSENGER magnetic field data in the solar wind at a heliocentric distance of about 0.3 AU. The spatial properties of the turbulent field at different scales, spanning the whole inertial range of magnetic turbulence down toward the proton scales have been studied. LIM and PVI methodologies allow us to identify portions of an entire time series where magnetic energy is mostly accumulated, and regions of intermittent bursts in the magnetic field vector increments, respectively. A statistical analysis has revealed thatmore » at small time scales and for high level of the threshold, the bursts present in the PVI and the LIM series correspond to regions of high shear stress and high magnetic field compressibility.« less

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

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 oxygenase1 (HO‐1) activity with protoporphyrin IX zinc(II) blocked MLP nuclear accumulation. To examine how mechanosensitivity changes during the transition to heart failure, we studied a guinea‐pig model of angiotensin II infusion (400 ng kg–1 min–1) over 12 weeks. Using subcellular fractionation, we showed that the MLP ratio increased by 88% (n = 4, P < 0.01) during compensated hypertrophy but decreased significantly during heart failure (P < 0.001, n = 4). The MLP ratio correlated significantly with the E/A ratio (r = 0.71, P < 0.01, n = 12), a clinical measure of diastolic function. These data indicate for the first time that myocyte mechanosensitivity as indicated by the MLP ratio is regulated primarily by myocyte contractility via HO‐1 and HDAC signalling. PMID:26847743

Two novel LHX3 mutations in patients with combined pituitary hormone deficiency including cervical rigidity and sensorineural hearing loss.

PubMed

Ramzan, Khushnooda; Bin-Abbas, Bassam; Al-Jomaa, Lolwa; Allam, Rabab; Al-Owain, Mohammed; Imtiaz, Faiqa

2017-03-16

Congenital combined pituitary hormone deficiency (CPHD) is a rare heterogeneous group of conditions. CPHD-type 3 (CPHD3; MIM# 221750) is caused by recessive mutations in LHX3, a LIM-homeodomain transcription factor gene. The isoforms of LHX3 are critical for pituitary gland formation and specification of the anterior pituitary hormone-secreting cell types. They also play distinct roles in the development of neuroendocrine and auditory systems. Here, we summarize the clinical, endocrinological, radiological and molecular features of three patients from two unrelated families. Clinical evaluation revealed severe CPHD coupled with cervical vertebral malformations (rigid neck, scoliosis), mild developmental delay and moderate sensorineural hearing loss (SNHL). The patients were diagnosed with CPHD3 based on the array of hormone deficiencies and other associated syndromic symptoms, suggestive of targeted LHX3 gene sequencing. A novel missense mutation c.437G > T (p. Cys146Phe) and a novel nonsense mutation c.466C > T (p. Arg156Ter), both in homozygous forms, were found. The altered Cys146 resides in the LIM2 domain of the encoded protein and is a phylogenetically conserved residue, which mediates LHX3 transcription factor binding with a zinc cation. The p. Arg156Ter is predicted to result in a severely truncated protein, lacking the DNA binding homeodomain. Considering genotype/phenotype correlation, we suggest that the presence of SNHL and limited neck rotation should be considered in the differential diagnosis of CPHD3 to facilitate molecular diagnosis. This report describes the first LHX3 mutations from Saudi patients and highlights the importance of combining molecular diagnosis with the clinical findings. In addition, it also expands the knowledge of LHX3-related CPHD3 phenotype and the allelic spectrum for this gene.

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…

Using a logical information model-driven design process in healthcare.

PubMed

Cheong, Yu Chye; Bird, Linda; Tun, Nwe Ni; Brooks, Colleen

2011-01-01

A hybrid standards-based approach has been adopted in Singapore to develop a Logical Information Model (LIM) for healthcare information exchange. The Singapore LIM uses a combination of international standards, including ISO13606-1 (a reference model for electronic health record communication), ISO21090 (healthcare datatypes), SNOMED CT (healthcare terminology) and HL7 v2 (healthcare messaging). This logic-based design approach also incorporates mechanisms for achieving bi-directional semantic interoperability.

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.

The eddy transport of nonconserved trace species derived from satellite data

NASA Technical Reports Server (NTRS)

Smith, Anne K.; Lyjak, Lawrence V.; Gille, John C.

1988-01-01

Using the approach of the Garcia and Solomon (1983) model and data obtained by the LIMS instrument on Nimbus 7, the chemical eddy transport matrix for planetary waves was calculated, and the chemical eddy contribution to the components of the matrix obtained from the LIMS satellite observations was computed using specified photochemical damping time scales. The dominant component of the transport matrices for several winter months were obtained for ozone, nitric acid, and quasi-geostrophic potential vorticity (PV), and the parameterized transports of these were compared with the 'exact' transports, computed directly from the eddy LIMS data. The results indicate that the chemical eddy effect can account for most of the observed ozone transport in early winter, decreasing to less than half in late winter. The agreement between the parameterized and observed nitric acid and PV was not as good. Reasons for this are discussed.

Study of Chlamydia trachomatis in Military Women; Prevalence, Risk Factors, and a Cost Benefit Analysis of Early Diagnosis and Treatment

DTIC Science & Technology

1999-09-01

ectopic pregnancy, and infertility represent a large disease burden 1,3. Infection rates for young, sexually active women range from 5-20%. In men...Hospitalizations (PASBA) for PID (ICD9 codes 614 and 615), infertility (ICD9 code 628), and 18 * ectopic pregnancy (ICD9 code 633) in Army enlisted females...trachomatisinfections in women has been lim- flammatory disease, infertility , and ectopic pregnancy. ited by the need for access to a medical clinic and a To design

Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women.

PubMed

El Aila, Nabil A; Tency, Inge; Claeys, Geert; Saerens, Bart; Cools, Piet; Verstraelen, Hans; Temmerman, Marleen; Verhelst, Rita; Vaneechoutte, Mario

2010-09-29

Streptococcus agalactiae (group B streptococcus; GBS) is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics), followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS. A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA), group B streptococcus differential agar (GBSDA) (Granada Medium) and chromID Strepto B agar (CA), with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination. The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100%) was significantly higher than detection on the basis of vaginal sampling (50%), but not significantly higher than for rectal sampling (82%). Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95%) detected more carriers than Lim broth enrichment and subculture onto CNA (77%). One false negative isolate was observed on GBSDA, and three false positives on CA. In conclusion, rectovaginal sampling increased the number GBS positive women detected, compared to vaginal and/or rectal sampling. Direct plating on CA and/or GBSDA provided rapid detection of GBS that was at least as sensitive and specific as the CDC recommended method of Lim broth subcultured onto non chromogenic agar.

Region 7 Laboratory Information Management System

EPA Pesticide Factsheets

This is metadata documentation for the Region 7 Laboratory Information Management System (R7LIMS) which maintains records for the Regional Laboratory. Any Laboratory analytical work performed is stored in this system which replaces LIMS-Lite, and before that LAST. The EPA and its contractors may use this database. The Office of Policy & Management (PLMG) Division at EPA Region 7 is the primary managing entity; contractors can access this database but it is not accessible to the public.

Preliminary Results of the Third Test Series of Nonmetal Material Flammability Evaluation In SKOROST Apparatus on the Space Station Mir

NASA Technical Reports Server (NTRS)

Ivanov, A. V.; Alymov, V. F.; Smirnov, A. B.; Shalayev, S. P.; Ye.Belov, D.; Balashov, Ye.V.; Andreeva, T. V.; Semenov, A. V.; Melikhov, A. S.; Bolodyan, I. A.;

ProteinTracker: an application for managing protein production and purification

PubMed Central

2012-01-01

Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org. PMID:22574679

Genetic variability of six French meat sheep breeds in relation to their genetic management.

PubMed

Huby, Marie; Griffon, Laurent; Moureaux, Sophie; De Rochambeau, Hubert; Danchin-Burge, Coralie; Verrier, Etienne

2003-01-01

Some demographic parameters, the genetic structure and the evolution of the genetic variability of six French meat sheep breeds were analysed in relation with their management. Four of these breeds are submitted to more or less intense selection: the Berrichon du Cher (BCH), Blanc du Massif Central (BMC), Charollais (CHA) and Limousin (LIM); the other two breeds are under conservation: the Roussin de La Hague (RLH) and Solognot (SOL). Genealogical data of the recorded animals born from 1970 to 2000 and of their known ancestors were used. The most balanced contributions of the different flocks to the sire-daughter path was found in the SOL. In the BCH, a single flock provided 43% of the sire-AI sire path, whereas the contributions of the flocks were more balanced in the BMC and LIM (the only other breeds where AI is used to a substantial amount). The distribution of the expected genetic contribution of the founder animals was found to be unbalanced, especially in the BCH and LIM. The effective numbers of ancestors (founders or not) for the ewes born from 1996 to 2000 were equal to 35 (BCH), 144 (BMC), 112 (CHA), 69 (LIM), 40 (RLH) and 49 (SOL). Inbreeding was not analysed in the BMC, due to incomplete pedigree information. From 1980 on, the rates of inbreeding, in percentage points per year, were +0.112 (BCH), +0.045 (CHA), +0.036 (LIM), +0.098 (RLH) and +0.062 (SOL). The implications of the observed trends on genetic variability are discussed in relation to the genetic management of each breed. The need for a larger selection basis in the BCH, the efficiency of the rules applied in the SOL to preserve the genetic variability and the need for a more collective organisation in the CHA and RLH are outlined.

The influence of the sennosides on absorption of glycyrrhetic acid in rats.

PubMed

Mizuhara, Yasuharu; Takizawa, Yukiho; Ishihara, Kazuhisa; Asano, Takayuki; Kushida, Hirotaka; Morota, Takashi; Kase, Yoshio; Takeda, Shuichi; Aburada, Masaki; Nomura, Masaaki; Yokogawa, Koichi

2005-10-01

In the course of our clinical studies of Kampo medicine (traditional Japanese medicines), we observed the pharmacokinetic interactions between two herbs. When Onpito (TJ-8117, Kampo medicine) containing licorice and rhubarb was administered orally to human subjects, we observed that the AUC(0-lim) and Cmax of glycyrrhetic acid (GA) in plasma were lower than those treated with other Kampo medicines containing licorice. In this study, we demonstrate the pharmacokinetic interactions of GA derived from glycyrrhizinic acid (GL) in licorice and anthraquinones derived from rhubarb. To our knowledge, this is the first report to investigate the pharmacokinetic interactions between two herbs. When GL was orally co-administrated to rats with a non-effective dose of sennoside A having purgative activity, the AUC(0-lim) and Cmax of GA decreased. In addition, sennoside A did not affect the metabolism of GL by the intestinal bacteria in vitro. In the examination using an in situ loop of rat colon, the remaining ratio of GA rose drastically by the co-administration of sennoside A, sennidin A and rhein. Observed inhibition activity of these anthraquinones on GA absorption depended on the concentration of the components added. The maximum inhibition ratio was approximately 75% by rhein, 60% by sennoside A and 25% by sennidin A. We conclude that the decrease of the pharmacokinetic parameters of GA in human plasma observed in the clinical study of TJ-8117 is attributable to an interactive action of absorption from the intestinal tract by anthraquinones contained in or derived from rhubarb.

Ittigahat wa Nozom at-Ta lim fi al-Gonhouriyyah al-Arabiyyah al-Mouttahidah wa Makanat at-ta lim at-tougari fiha (Education in the United Arab Republic: Its Structure and Orientation, and the Position of Commercial Studies within the Educational System).

ERIC Educational Resources Information Center

Ministry of Education, Cairo (United Arab Republic).

This document is an English-language abstract (approximately 1,500 words) surveying Egyptian education. Elementary education is compulsory. It begins between the ages of six and eight and lasts six years. The curriculum includes Arabic, religion, social subjects, hygiene, arithmetic, community singing, music, physical education, drawing and…

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 ...

Alterations in Protein Expression in Tree Shrew Sclera during Development of Lens-Induced Myopia and Recovery

PubMed Central

Norton, Thomas T.

2012-01-01

Purpose. During the development of, and recovery from, negative lens-induced myopia there is regulated remodeling of the scleral extracellular matrix (ECM) that controls the extensibility of the sclera. Difference gel electrophoresis (DIGE) was used to identify and categorize proteins whose levels are altered in this process. Methods. Two groups of five tree shrews started monocular lens wear 24 days after eye opening (days of visual experience [VE]). The lens-induced myopia (LIM) group wore a −5 D lens for 4 days. The recovery (REC) group wore a −5 D lens for 11 days and then recovered for 4 days. Two normal groups (28 and 39 days of VE; n = 5 each) were also examined, age-matched to each of the treatment groups. Refractive and A-scan measures confirmed the effect of the treatments. Scleral proteins were isolated and resolved by DIGE. Proteins that differed in abundance were identified by mass spectrometry. Ingenuity pathway analysis was used to investigate potential biological pathway interactions. Results. During normal development (28–39 days of VE), eight proteins decreased and one protein increased in relative abundance. LIM-treated eyes were myopic and longer than control eyes; LIM-control eyes were slightly myopic compared with 28N eyes, indicating a yoking effect. In both the LIM-treated and the LIM-control eyes, there was a general downregulation from normal of proteins involved in transcription, cell adhesion, and protein synthesis. Additional proteins involved in cell adhesion, actin cytoskeleton, transcriptional regulation, and ECM structural proteins differed in the LIM-treated eyes versus normal but did not differ in the control eyes versus normal. REC-treated eyes were recovering from the induced myopia. REC-control eye refractions were not significantly different from the 39N eyes, and few proteins differed from age-matched normal eyes. The balance of protein expression in the REC-treated eyes, compared with normal eyes and REC-control eyes, shifted toward upregulation or a return to normal levels of proteins involved in cell adhesion, cell division, cytoskeleton, and ECM structural proteins, including upregulation of several cytoskeleton-related proteins not affected during myopia development. Conclusions. The DIGE procedure revealed new proteins whose abundance is altered during myopia development and recovery. Many of these are involved in cell-matrix adhesions, cytoskeleton, and transcriptional regulation and extend our understanding of the remodeling that controls the extensibility of the sclera. Reductions in these proteins during minus lens wear may produce the increased scleral viscoelasticity that results in faster axial elongation. Recovery is not a mirror image of lens-induced myopia—many protein levels, decreased during LIM, returned to normal, or slightly above normal, and additional cytoskeleton proteins were upregulated. However, no single protein or pathway appeared to be responsible for the scleral changes during myopia development or recovery. PMID:22039233

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.

Conserved regulation of mesenchymal gene expression by Fgf-8 in face and limb development.

PubMed

Tucker, A S; Al Khamis, A; Ferguson, C A; Bach, I; Rosenfeld, M G; Sharpe, P T

1999-01-01

Clim-2 (NLI, Lbd1) is one of two related mouse proteins that interact with Lim-domain homeoproteins. In the mouse, embryonic expression of Clim-2 is particularly pronounced in facial ectomesenchyme and limb bud mesenchyme in association with Lim genes, Lhx-6 and Lmx-1 respectively. We show that in common with both these Lim genes, Clim-2 expression is regulated by signals from overlying epithelium. In both the developing face and the limb buds we identify Fgf-8 as the likely candidate signalling molecule that regulates Clim-2 expression. We show that in the mandibular arch, as in the limb, Fgf-8 functions in combination with CD44, a cell surface binding protein, and that blocking CD44 binding results in inhibition of Fgf8-induced expression of Clim-2 and Lhx-6. Regulation of gene expression by Fgf8 in association with CD44 is thus conserved between limb and mandibular arch development.

Tes, a specific Mena interacting partner, breaks the rules for EVH1 binding.

PubMed

Boëda, Batiste; Briggs, David C; Higgins, Theresa; Garvalov, Boyan K; Fadden, Andrew J; McDonald, Neil Q; Way, Michael

2007-12-28

The intracellular targeting of Ena/VASP family members is achieved via the interaction of their EVH1 domain with FPPPP sequence motifs found in a variety of cytoskeletal proteins, including lamellipodin, vinculin, and zyxin. Here we show that the LIM3 domain of Tes, which lacks the FPPPP motif, binds to the EVH1 domain of Mena, but not to those of VASP or Evl. The structure of the LIM3:EVH1 complex reveals that Tes occludes the FPPPP-binding site and competes with FPPPP-containing proteins for EVH1 binding. Structure-based gain-of-function experiments define the molecular basis for the specificity of the Tes-Mena interaction. Consistent with in vitro observations, the LIM3 domain displaces Mena, but not VASP, from the leading edge and focal adhesions. It also regulates cell migration through a Mena-dependent mechanism. Our observations identify Tes as an atypical EVH1 binding partner and a regulator specific to a single Ena/VASP family member.

Design Considerations and Experimental Verification of a Rail Brake Armature Based on Linear Induction Motor Technology

NASA Astrophysics Data System (ADS)

Sakamoto, Yasuaki; Kashiwagi, Takayuki; Hasegawa, Hitoshi; Sasakawa, Takashi; Fujii, Nobuo

This paper describes the design considerations and experimental verification of an LIM rail brake armature. In order to generate power and maximize the braking force density despite the limited area between the armature and the rail and the limited space available for installation, we studied a design method that is suitable for designing an LIM rail brake armature; we considered adoption of a ring winding structure. To examine the validity of the proposed design method, we developed a prototype ring winding armature for the rail brakes and examined its electromagnetic characteristics in a dynamic test system with roller rigs. By repeating various tests, we confirmed that unnecessary magnetic field components, which were expected to be present under high speed running condition or when a ring winding armature was used, were not present. Further, the necessary magnetic field component and braking force attained the desired values. These studies have helped us to develop a basic design method that is suitable for designing the LIM rail brake armatures.

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 colonization status in pregnant patients near term results in decreased turnaround time for reporting positive results.

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 the production, release, and transmission of retroviruses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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.

Fast detection of toxic industrial compounds by laser ion mobility spectrometry

NASA Astrophysics Data System (ADS)

Oberhuettinger, Carola; Langmeier, Andreas; Oberpriller, Helmut; Kessler, Matthias; Goebel, Johann; Mueller, Gerhard

2009-05-01

Trace detection of toxic industrial compounds has been investigated with the help of a laser ion mobility spectrometer (LIMS). The LIMS was equipped with a tuneable UV laser source for enabling two-photon ionization of the analyte gases and an ion drift tube for the measurement of the ion mobility. Different aromatic and aliphatic hydrocarbons as well as amines were investigated. We find that the first class of molecules can be well ionized due to the delocalization of their valence electron shells and the second due to the presence of non-bonding electrons in lone-pair orbitals. Selectivity of detection is attained on the basis of molecule-specific photo-ionization and drift time spectra. Ion currents were found to scale linearly with the substance concentration over several orders of magnitude down to the detection limits in the ppt range. As besides toxic industrial compounds, similar electron configurations also occur in illicit drugs, toxins and pharmaceutical substances, LIMS can be applied in a variety of fields ranging from environmental analysis, air pollution monitoring, drug detection and chemical process monitoring.

Preparation of Microcellular Epoxy Foams through a Limited-Foaming Process: A Contradiction with the Time-Temperature-Transformation Cure Diagram.

PubMed

Wang, Lijun; Zhang, Chun; Gong, Wei; Ji, Yubi; Qin, Shuhao; He, Li

2018-01-01

3D cross-linking networks are generated through chemical reactions between thermosetting epoxy resin and hardener during curing. The curing degree of epoxy material can be increased by increasing curing temperature and/or time. The epoxy material must then be fully cured through a postcuring process to optimize its material characteristics. Here, a limited-foaming method is introduced for the preparation of microcellular epoxy foams (Lim-foams) with improved cell morphology, high thermal expansion coefficient, and good compressive properties. Lim-foams exhibit a lower glass transition temperature (T g ) and curing degree than epoxy foams fabricated through free-foaming process (Fre-foams). Surprisingly, however, the T g of Lim-foams is unaffected by postcuring temperature and time. This phenomenon, which is related to high gas pressure in the bubbles, contradicts that indicated by the time-temperature-transformation cure diagram. High bubble pressure promotes the movement of molecular chains under heating at low temperature and simultaneously suppresses the etherification cross-linking reaction during post-curing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A way around the Nyquist lag

NASA Astrophysics Data System (ADS)

Penland, C.

2017-12-01

One way to test for the linearity of a multivariate system is to perform Linear Inverse Modeling (LIM) to a multivariate time series. LIM yields an estimated operator by combining a lagged covariance matrix with the contemporaneous covariance matrix. If the underlying dynamics is linear, the resulting dynamical description should not depend on the particular lag at which the lagged covariance matrix is estimated. This test is known as the "tau test." The tau test will be severely compromised if the lag at which the analysis is performed is approximately half the period of an internal oscillation frequency. In this case, the tau test will fail even though the dynamics are actually linear. Thus, until now, the tau test has only been possible for lags smaller than this "Nyquist lag." In this poster, we investigate the use of Hilbert transforms as a way to avoid the problems associated with Nyquist lags. By augmenting the data with dimensions orthogonal to those spanning the original system, information that would be inaccessible to LIM in its original form may be sampled.

Effects of electroacupuncture on the levels of retinal gamma-aminobutyric acid and its receptors in a guinea pig model of lens-induced myopia.

PubMed

Sha, F; Ye, X; Zhao, W; Xu, C-L; Wang, L; Ding, M-H; Bi, A-L; Wu, J-F; Jiang, W-J; Guo, D-D; Guo, J-G; Bi, H-S

2015-02-26

Gamma-aminobutyric acid (GABA) is a major inhibitory neurotransmitter of the retina and affects myopic development. Electroacupuncture (EA) is widely utilized to treat myopia in clinical settings. However, there are few reports on whether EA affects the level of retinal GABA during myopic development. To study this issue, in the present study, we explored the changes of retinal GABA content and the expression of its receptor subtypes, and the effects of EA stimulation on them in a guinea pig model with lens-induced myopia (LIM). Our results showed that the content of GABA and the expression of GABAA and GABAC receptors of retina were up-regulated during the development of myopia, and this up-regulation was inhibited by applying EA to Hegu (LI4) and Taiyang (EX-HN5) acupoints. Moreover, these effects of EA show a positional specificity. While applying EA at a sham acupoint, no apparent change of myopic retinal GABA and its receptor subtypes was observed. Taken together, our findings suggest that LIM is effective to up-regulate the level of retinal GABA, GABAA and GABAC receptors in guinea pigs and the effect may be inhibited by EA stimulation at LI4 and EX-HN5 acupoints. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.

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.

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.

Comparative assessment of three drug eluting stents with different platforms but with the same biodegradable polymer and the drug based on quantitative coronary angiography and optical coherence tomography at 12-month follow-up.

PubMed

Gil, Robert J; Bil, Jacek; Legutko, Jacek; Pawłowski, Tomasz; Gil, Katarzyna E; Dudek, Dariusz; Costa, Ricardo A

2018-03-01

The aim of this study was to compare neointima proliferation in three drug-eluting stents (DES) produced by the same company (Balton, Poland) which are covered with a biodegradable polymer and elute sirolimus (concentration: 1.0 and 1.2 µg/mm 2 ), but have different stent platforms and strut thickness: stainless steel Prolim ® (115 µm) and BiOSS LIM ® (120 µm) and cobalt-chromium Alex ® (70 µm). We analyzed data of patients with quantitative coronary angiography (QCA) and optical coherence tomography (OCT) at 12 months from BiOSS LIM Registry, Prolim Registry and Alex OCT clinical trial. There were 56 patients enrolled, in whom 29 Prolim ® stents were deployed, in 11-BiOSS LIM ® and in 16-Alex stents. The late lumen loss was the smallest in Prolim ® subgroup (0.26 ± 0.17 mm) and did not differ from Alex ® subgroup (0.28 ± 0.47 mm). This parameter was significantly bigger in BiOSS ® subgroup (0.38 ± 0.19 mm; p < 0.05). In OCT analysis there was no statistically significant difference between Prolim ® and Alex ® subgroups in terms of mean neointima burden (24.6 ± 8.6 vs. 19.27 ± 8.11%) and neointima volume (28.16 ± 15.10 vs. 24.51 ± 17.64 mm 3 ). In BiOSS ® group mean neointima burden (30.9 ± 6.2%) and mean neointima volume (44.9 ± 4.9 mm 3 ) were significantly larger. The morphological analysis revealed that in most cases in all groups the neointima was homogenous with plaque presence only around stent struts. In the QCA and OCT analysis regular DES (Prolim ® and Alex ® ) obtained similar results, whereas more pronounced response from the vessel wall was found in the BiOSS ® subgroup.

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.

Islet-1 Controls the Differentiation of Retinal Bipolar and Cholinergic Amacrine Cells

PubMed Central

Elshatory, Yasser; Everhart, Drew; Deng, Min; Xie, Xiaoling; Barlow, Robert B.; Gan, Lin

2010-01-01

Whereas the mammalian retina possesses a repertoire of factors known to establish general retinal cell types, these factors alone cannot explain the vast diversity of neuronal subtypes. In other CNS regions, the differentiation of diverse neuronal pools is governed by coordinately acting LIM-homeodomain proteins including the Islet-class factor Islet-1 (Isl1). We report that deletion of Isl1 profoundly disrupts retinal function as assessed by electroretinograms and vision as assessed by optomotor behavior. These deficits are coupled with marked reductions in mature ON- and OFF-bipolar (>76%), cholinergic amacrine (93%), and ganglion (71%) cells. Mosaic deletion of Isl1 permitted a chimeric analysis of “wild-type” cells in a predominantly Isl1-null environment, demonstrating a cell-autonomous role for Isl1 in rod bipolar and cholinergic amacrine development. Furthermore, the effects on bipolar cell development appear to be dissociable from the preceding retinal ganglion cell loss, because Pou4f2-null mice are devoid of similar defects in bipolar cell marker expression. Expression of the ON- and OFF-bipolar cell differentiation factors Bhlhb4 and Vsx1, respectively, requires the presence of Isl1, whereas the early bipolar cell marker Prox1 initially did not. Thus, Isl1 is required for engaging bipolar differentiation pathways but not for general bipolar cell specification. Spatiotemporal expression analysis of additional LIM-homeobox genes identifies a LIM-homeobox gene network during bipolar cell development that includes Lhx3 and Lhx4. We conclude that Isl1 has an indispensable role in retinal neuron differentiation within restricted cell populations and this function may reflect a broader role for other LIM-homeobox genes in retinal development, and perhaps in establishing neuronal subtypes. PMID:18003851

Evaluation of the Granada agar plate for detection of vaginal and rectal group B streptococci in pregnant women.

PubMed

Gil, E G; Rodríguez, M C; Bartolomé, R; Berjano, B; Cabero, L; Andreu, A

1999-08-01

Granada medium was evaluated for the detection of group B streptococci (GBS) in vaginal and rectal swabs compared with selective Columbia blood agar and selective Lim broth. From May 1996 to March 1998, 702 pregnant women (35 to 37 weeks of gestation) participated in this three-phase study; 103 (14.7%) of these women carried GBS. In the first phase of the experiment (n = 273 women), vaginorectal specimens were collected on the same swab; the sensitivities of Granada tube, selective Columbia blood agar, and Lim broth were 31.4, 94.3, and 74.3%, respectively. In the second and third phases (n = 429 women), vaginal and rectal specimens were collected separately; the sensitivities of Granada plate, selective Columbia blood agar, and Lim broth (subcultured at 4 h on selective Columbia agar in the second phase and at 18 to 24 h in Granada plate in the third phase) were 91.1, 83.9, and 75%, respectively, in the second phase and 88.5, 90.4, and 63.5%, respectively, in the third phase. There were no statistically significant differences in GBS recovery between the Granada agar plate and selective Columbia blood agar, but the Granada plate provided a clear advantage; the characteristic red-orange colonies produced overnight by GBS can be identified by the naked eye and is so specific that further identification is unnecessary. The use of the Granada tube and Lim broth did not result in increased isolation of GBS. In conclusion, the Granada agar plate is highly sensitive for detecting GBS in vaginal and rectal swabs from pregnant women and can provide results in 18 to 24 h.

Identification of Streptococcus agalactiae by fluorescent in situ hybridization compared to culturing and the determination of prevalence of Streptococcus agalactiae colonization among pregnant women in Bushehr, Iran.

PubMed

Tajbakhsh, Saeed; Norouzi Esfahani, Marjan; Emaneini, Mohammad; Motamed, Niloofar; Rahmani, Elham; Gharibi, Somayyeh

2013-09-08

Pregnant women colonized by Streptococcus agalactiae (group B streptococci [GBS]) may transfer this microorganism to their newborns. S. agalactiae is an important cause of pneumonia, sepsis, and meningitis in newborns. Fluorescent in situ hybridization (FISH) is considered as a method of identification in the field of diagnostic microbiology. In this paper, we have designed a study to compare the DNA FISH after 7 h Lim broth enrichment and culturing for the identification of S. agalactiae and to determine the prevalence of vaginal colonization by S. agalactiae among pregnant women in Bushehr, Iran. Vaginal swab specimens were obtained from 285 pregnant women at 35 weeks or more than 35 weeks of gestation. The specimens were inoculated into Lim broth. In order to evaluate the sensitivity and specificity of GBS DNA FISH after 7 h Lim broth enrichment, the specimens were tested using both FISH and conventional culture methods. In addition, the prevalence of GBS colonization was determined. Based on the results of this study, both the sensitivity and specificity of FISH were 100%. S. agalactiae was detected by both culture and FISH in 27 of the 285 pregnant women. Thus, the prevalence of GBS colonization was 9.5%. Since short-term (7 h) Lim broth enrichment followed by FISH using oligonucleotide probes showed a high sensitivity and specificity, this protocol is therefore a highly accurate and relatively rapid method for the detection of S. agalactiae. Our analysis suggests that the use of DNA FISH to screen for S. agalactiae colonization in pregnant women may be considered in the absence of GBS culture availability.

An assessment of satellite temperature distributions used to derive the net diabatic transport for zonally averaged models of the middle atmosphere

NASA Technical Reports Server (NTRS)

Remsberg, Ellis E.; Bhatt, Praful P.; Miles, Thomas

1994-01-01

Determinations of the zonally averaged and diabatically derived residual mean circulation (RMC) are particularly sensitive to the assumed zonal mean temperature distribution used as input. Several different middle atmosphere satellite temperature distributions have been employed in models and are compared here: a 4-year (late 1978 to early 1982) National Meteorological Center (NMC) climatology, the Barnett and Corney (or BC) climatology, and the 7 months of Nimbus 7 limb infrared monitor of the stratosphere (LIMS) temperatures. All three climatologies are generally accurate below the 10 hPa level, but there are systematic differences between them of up to +/-5 K in the upper stratosphere and lower mesosphere. The NMC/LIMS differences are evaluated using time series of rocketsonde and reconstructed satellite temperatures at station locations. Much of those biases can be explained by the differing vertical resolutions for the satellite-derived temperatures; the time series of reconstructed LIMS profiles have higher resolution and are more accurate. Because the LIMS temperatures are limited to just two full seasons, one cannot obtain monthly RMCs from them for an annual model calculation. Two alternate monthly climatologies are examined briefly: the 4-year Nimbus 7 stratospheric and mesospheric sounder (SAMS) temperatures and for the mesosphere the distribution from the Solar Mesosphere Explorer (SME), both of which are limb viewers of medium vertical resolution. There are also differences of the order of +/-5 K for those data sets. It is concluded that a major source of error in the determination of diabatic RMCs is a persistent pattern of temperature bias whose characteristics vary according to the vertical resolution of each individual climatology.

Atmospheric Effects of Energetic Particle Precipitation in the Arctic Winter 1978-1979 Revisited

NASA Technical Reports Server (NTRS)

Holt, L. A.; Randall, C. E.; Harvey, V. L.; Remsberg, E. E.; Stiller, G. P.; Funke, B.; Bernath, P. F.; Walker, K. A.

2012-01-01

The Limb Infrared Monitor of the Stratosphere (LIMS) measured polar stratospheric enhancements of NO2 mixing ratios due to energetic particle precipitation (EPP) in the Arctic winter of 1978-1979. Recently reprocessed LIMS data are compared to more recent measurements from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) and the Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE-FTS) to place the LIMS measurements in the context of current observations. The amount of NOx (NO + NO2) entering the stratosphere that has been created by EPP in the mesosphere and lower thermosphere (EPP-NOx) has been quantified for the 1978-1979 and 2002-2003 through 2008-2009 Arctic winters. The NO2 enhancements in the LIMS data are similar to those in MIPAS and ACE-FTS data in the Arctic winters of 2002-2003, 2004-2005, 2006-2007, and 2007-2008. The largest enhancement by far is in 2003-2004 (approximately 2.2 Gmol at 1500 K), which is attributed to a combination of elevated EPP and unusual dynamics that led to strong descent in the upper stratosphere/lower mesosphere in late winter. The enhancements in 2005-2006 and 2008-2009, during which large stratospheric NOx enhancements were caused by a dynamical situation similar to that in 2003 2004, are larger than in all the other years (except 2003-2004) at 3000 K. However, by 2000 K the enhancements in 2005-2006 (2008-2009) are on the same order of magnitude as (smaller than) all other years. These results highlight the importance of the timing of the descent in determining the potential of EPP-NOx for reaching the middle stratosphere.

Multi-centennial upper-ocean heat content reconstruction using online data assimilation

NASA Astrophysics Data System (ADS)

Perkins, W. A.; Hakim, G. J.

2017-12-01

The Last Millennium Reanalysis (LMR) provides an advanced paleoclimate ensemble data assimilation framework for multi-variate climate field reconstructions over the Common Era. Although reconstructions in this framework with full Earth system models remain prohibitively expensive, recent work has shown improved ensemble reconstruction validation using computationally inexpensive linear inverse models (LIMs). Here we leverage these techniques in pursuit of a new multi-centennial field reconstruction of upper-ocean heat content (OHC), synthesizing model dynamics with observational constraints from proxy records. OHC is an important indicator of internal climate variability and responds to planetary energy imbalances. Therefore, a consistent extension of the OHC record in time will help inform aspects of low-frequency climate variability. We use the Community Climate System Model version 4 (CCSM4) and Max Planck Institute (MPI) last millennium simulations to derive the LIMs, and the PAGES2K v.2.0 proxy database to perform annually resolved reconstructions of upper-OHC, surface air temperature, and wind stress over the last 500 years. Annual OHC reconstructions and uncertainties for both the global mean and regional basins are compared against observational and reanalysis data. We then investigate differences in dynamical behavior at decadal and longer time scales between the reconstruction and simulations in the last-millennium Coupled Model Intercomparison Project version 5 (CMIP5). Preliminary investigation of 1-year forecast skill for an OHC-only LIM shows largely positive spatial grid point local anomaly correlations (LAC) with a global average LAC of 0.37. Compared to 1-year OHC persistence forecast LAC (global average LAC of 0.30), the LIM outperforms the persistence forecasts in the tropical Indo-Pacific region, the equatorial Atlantic, and in certain regions near the Antarctic Circumpolar Current. In other regions, the forecast correlations are less than the persistence case but still positive overall.

Increased actin polymerization reduces the inhibition of serum response factor activity by Yin Yang 1.

PubMed Central

Ellis, Peter D; Martin, Karen M; Rickman, Colin; Metcalfe, James C; Kemp, Paul R

2002-01-01

Recent evidence has implicated CC(A/T(richG))GG (CArG) boxes, binding sites for serum response factor (SRF), in the regulation of expression of a number of genes in response to changes in the actin cytoskeleton. In many cases, the activity of SRF at CArG boxes is modulated by transcription factors binding to overlapping (e.g. Yin Yang 1, YY1) or adjacent (e.g. ets) binding sites. However, the mechanisms by which SRF activity is regulated by the cytoskeleton have not been determined. To investigate these mechanisms, we screened for cells that did or did not increase the activity of a fragment of the promoter for a smooth-muscle (SM)-specific gene SM22alpha, in response to changes in actin cytoskeletal polymerization induced by LIM kinase. These experiments showed that vascular SM cells (VSMCs) and C2C12 cells increased the activity of promoters containing at least one of the SM22alpha CArG boxes (CArG near) in response to LIM kinase, whereas P19 cells did not. Bandshift assays using a probe to CArG near showed that P19 cells lacked detectable YY1 DNA binding to the CArG box in contrast with the other two cell types. Expression of YY1 in P19 cells inhibited SM22alpha promoter activity and conferred responsiveness to LIM kinase. Mutation of the CArG box to inhibit YY1 or SRF binding indicated that both factors were required for the LIM kinase response in VSMCs and C2C12 cells. The data indicate that changes in the actin cytoskeletal organization modify SRF activity at CArG boxes by modulating YY1-dependent inhibition. PMID:12023898

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.

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

PubMed

Camerlengo, Terry; Ozer, Hatice Gulcin; Onti-Srinivasan, Raghuram; Yan, Pearlly; Huang, Tim; Parvin, Jeffrey; Huang, Kun

2012-01-01

Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we designed and implemented a scalable architecture to address the challenges associated with the resource intensive nature of NGS secondary analysis built around Illumina Genome Analyzer II sequencers and Illumina's Gerald data processing pipeline. The software infrastructure includes a distributed computing platform consisting of a LIMS called QUEST (http://bisr.osumc.edu), an Automation Server, a computer cluster for processing NGS pipelines, and a network attached storage device expandable up to 40TB. The system has been architected to scale to multiple sequencers without requiring additional computing or labor resources. This platform provides demonstrates how to manage and automate NGS experiments in an institutional or core facility setting.

Improving the maximum transmission distance of continuous-variable quantum key distribution using a noiseless amplifier

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blandino, Rémi; Etesse, Jean; Grangier, Philippe

2014-12-04

We show that the maximum transmission distance of continuous-variable quantum key distribution in presence of a Gaussian noisy lossy channel can be arbitrarily increased using a heralded noiseless linear amplifier. We explicitly consider a protocol using amplitude and phase modulated coherent states with reverse reconciliation. Assuming that the secret key rate drops to zero for a line transmittance T{sub lim}, we find that a noiseless amplifier with amplitude gain g can improve this value to T{sub lim}/g{sup 2}, corresponding to an increase in distance proportional to log g. We also show that the tolerance against noise is increased.

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.

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

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.

Origin, transport, and losses of energetic He(+) and He(2+) ions in the magnetosphere of the Earth - AMPTE/CCE observations

NASA Technical Reports Server (NTRS)

Kremser, G.; Wilken, B.; Gloeckler, G.; Hamilton, D. C.; Ipavich, F. M.; Kistler, L. M.; Tanskanen, P.

1993-01-01

Data from the ion charge-energy-mass spectrometer CHEM flown on AMPTE/CCE spacecraft are used to investigate the origin, transport, and losses of energetic He(+) and He(2+) ions in the earth's magnetosphere. The L profiles of the average ion phase space density f were determined as a function of the magnetic momentum. It is shown that the L profiles have an inner part, where f increases with L for both He(+) adn He(2+) and where steady-state conditions are fulfilled. The outer boundary L(lim) of this region is located at a distance that depends on the ion species and the geomagnetic activity level. Steady-state conditions continue outside L(lim) for He(+) ions, while the He(2+) ion distribution outside L(lim) is strongly influenced by ion convection causing a lack of steady-state conditions. It is concluded that solar wind is the origin of the He(2+), while a mixed origin is suggested for the He(+) ions, in which the major contribution is from the solar wind via charge exchange production from the He(2+) ions.

Preparation and characterization of intelligent starch/PVA films for simultaneous colorimetric indication and antimicrobial activity for food packaging applications.

PubMed

Liu, Bin; Xu, Han; Zhao, Huiying; Liu, Wei; Zhao, Liyun; Li, Yuan

2017-02-10

We have developed an intelligent starch/poly-vinyl alcohol (PVA) film that is capable of monitoring pH changes and inhibiting undesired microbial growth in foods. Starch and PVA polymers in the film were doubly cross-linked by sodium trimetaphosphate and boric acid to improve their water-resistance and mechanical strength. Anthocyanins (ANT) and limonene (LIM) were used to achieve simultaneous colorimetric indication and antimicrobial activity. Firstly, the characterization of surface morphology using SEM confirmed that the starch-PVA-ANT-LIM film possessed a smooth surface. Secondly, the results of the mechanical strength test showed that starch-PVA-ANT-LIM possesses the highest mechanical strength. Additionally, there was a distinguishable change of colors as the film was immersed in solutions of pH ranging from 1.0 to 14.0. Moreover, the film showed excellent antimicrobial activity for three typical undesired microorganisms in foods, Bacillus subtilis, Aspergillus niger, and Staphylococcus aureus. Finally, the film exhibited good color indication and antimicrobial activity on pasteurized milk. The results suggest that the intelligent film reported here shows good capability for both alerting and inhibiting food spoilage. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Effect of retinoic acid on the tight junctions of the retinal pigment epithelium-choroid complex of guinea pigs with lens-induced myopia in vivo

PubMed Central

WANG, SHA; LIU, SHUANGZHEN; MAO, JUNFENG; WEN, DAN

2014-01-01

Zonula occludens-1 (ZO-1) and occludin are important tight junction (TJ)-associated proteins, which are expressed in the retinal pigment epithelium (RPE)-choroid complex. Retinoic acid (RA) is a regulator of eye growth and may play an important role in forming functional TJs. The aim of this study was to detect the changes that occur in the expression of ZO-1 and occludin in the RPE-choroid complex of guinea pigs with lens-induced myopia (LIM), and to investigate the effect of RA on TJ-associated proteins in vivo. We developed an animal model of myopia by placing a −6.00 D negative lens on the right eyes of 3-week-old guinea pigs. The refractive error and axial length of the eye were measured on days 0, 3, 7 and 14. High-performance liquid chromatography (HPLC) was performed to detect the changes in endogenous RA in the RPE-choroid complex. The expression of ZO-1 and occludin was observed by immunofluorescence and assayed by western blot analysis. Additionally, 2 μl LE540 (2.5 μg/μl), an antagonist of RA receptors (RARs), was injected into the vitreous chamber of the eyes of guinea pigs with LIM and 2 μl phosphate-buffered saline (PBS) (2.5 μg/μl) were injected as a negative control. We observed no obvious change in RA, ZO-1 and occludin expression in the normal control group within 14 days. In the LIM and LIM plus PBS groups, the level of RA and the expression of ZO-1 and occludin in the RPE-choroid complex significantly increased within 14 days along with the development of myopia. However, the level of RA was inhibited and the expression of TJ-associated proteins decreased in the eyes of guinea pigs with LIM following the injection of LE540. Thus, we consider that the expression of ZO-1 and occludin is increased in the RPE-choroid complex during the development of myopia. This change in expression may be regulated by RA, a factor known to be involved in the regulation of eye growth. PMID:24535401

Multivariate Probabilistic Analysis of an Hydrological Model

NASA Astrophysics Data System (ADS)

Franceschini, Samuela; Marani, Marco

2010-05-01

Model predictions derived based on rainfall measurements and hydrological model results are often limited by the systematic error of measuring instruments, by the intrinsic variability of the natural processes and by the uncertainty of the mathematical representation. We propose a means to identify such sources of uncertainty and to quantify their effects based on point-estimate approaches, as a valid alternative to cumbersome Montecarlo methods. We present uncertainty analyses on the hydrologic response to selected meteorological events, in the mountain streamflow-generating portion of the Brenta basin at Bassano del Grappa, Italy. The Brenta river catchment has a relatively uniform morphology and quite a heterogeneous rainfall-pattern. In the present work, we evaluate two sources of uncertainty: data uncertainty (the uncertainty due to data handling and analysis) and model uncertainty (the uncertainty related to the formulation of the model). We thus evaluate the effects of the measurement error of tipping-bucket rain gauges, the uncertainty in estimating spatially-distributed rainfall through block kriging, and the uncertainty associated with estimated model parameters. To this end, we coupled a deterministic model based on the geomorphological theory of the hydrologic response to probabilistic methods. In particular we compare the results of Monte Carlo Simulations (MCS) to the results obtained, in the same conditions, using Li's Point Estimate Method (LiM). The LiM is a probabilistic technique that approximates the continuous probability distribution function of the considered stochastic variables by means of discrete points and associated weights. This allows to satisfactorily reproduce results with only few evaluations of the model function. The comparison between the LiM and MCS results highlights the pros and cons of using an approximating method. LiM is less computationally demanding than MCS, but has limited applicability especially when the model response is highly nonlinear. Higher-order approximations can provide more accurate estimations, but reduce the numerical advantage of the LiM. The results of the uncertainty analysis identify the main sources of uncertainty in the computation of river discharge. In this particular case the spatial variability of rainfall and the model parameters uncertainty are shown to have the greatest impact on discharge evaluation. This, in turn, highlights the need to support any estimated hydrological response with probability information and risk analysis results in order to provide a robust, systematic framework for decision making.

Application of the Speed-Duration Relationship to Normalize the Intensity of High-Intensity Interval Training

PubMed Central

Ferguson, Carrie; Wilson, John; Birch, Karen M.; Kemi, Ole J.

2013-01-01

The tolerable duration of continuous high-intensity exercise is determined by the hyperbolic Speed-tolerable duration (S-tLIM) relationship. However, application of the S-tLIM relationship to normalize the intensity of High-Intensity Interval Training (HIIT) has yet to be considered, with this the aim of present study. Subjects completed a ramp-incremental test, and series of 4 constant-speed tests to determine the S-tLIM relationship. A sub-group of subjects (n = 8) then repeated 4 min bouts of exercise at the speeds predicted to induce intolerance at 4 min (WR4), 6 min (WR6) and 8 min (WR8), interspersed with bouts of 4 min recovery, to the point of exercise intolerance (fixed WR HIIT) on different days, with the aim of establishing the work rate that could be sustained for 960 s (i.e. 4×4 min). A sub-group of subjects (n = 6) also completed 4 bouts of exercise interspersed with 4 min recovery, with each bout continued to the point of exercise intolerance (maximal HIIT) to determine the appropriate protocol for maximizing the amount of high-intensity work that can be completed during 4×4 min HIIT. For fixed WR HIIT tLIM of HIIT sessions was 399±81 s for WR4, 892±181 s for WR6 and 1517±346 s for WR8, with total exercise durations all significantly different from each other (P<0.050). For maximal HIIT, there was no difference in tLIM of each of the 4 bouts (Bout 1: 229±27 s; Bout 2: 262±37 s; Bout 3: 235±49 s; Bout 4: 235±53 s; P>0.050). However, there was significantly less high-intensity work completed during bouts 2 (153.5±40. 9 m), 3 (136.9±38.9 m), and 4 (136.7±39.3 m), compared with bout 1 (264.9±58.7 m; P>0.050). These data establish that WR6 provides the appropriate work rate to normalize the intensity of HIIT between subjects. Maximal HIIT provides a protocol which allows the relative contribution of the work rate profile to physiological adaptations to be considered during alternative intensity-matched HIIT protocols. PMID:24244266

ProCon - PROteomics CONversion tool.

PubMed

Mayer, Gerhard; Stephan, Christian; Meyer, Helmut E; Kohl, Michael; Marcus, Katrin; Eisenacher, Martin

2015-11-03

With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest™/Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015. Published by Elsevier B.V.

Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder.

PubMed

Frints, Suzanna G M; Ozanturk, Aysegul; Rodríguez Criado, Germán; Grasshoff, Ute; de Hoon, Bas; Field, Michael; Manouvrier-Hanu, Sylvie; E Hickey, Scott; Kammoun, Molka; Gripp, Karen W; Bauer, Claudia; Schroeder, Christopher; Toutain, Annick; Mihalic Mosher, Theresa; Kelly, Benjamin J; White, Peter; Dufke, Andreas; Rentmeester, Eveline; Moon, Sungjin; Koboldt, Daniel C; van Roozendaal, Kees E P; Hu, Hao; Haas, Stefan A; Ropers, Hans-Hilger; Murray, Lucinda; Haan, Eric; Shaw, Marie; Carroll, Renee; Friend, Kathryn; Liebelt, Jan; Hobson, Lynne; De Rademaeker, Marjan; Geraedts, Joep; Fryns, Jean-Pierre; Vermeesch, Joris; Raynaud, Martine; Riess, Olaf; Gribnau, Joost; Katsanis, Nicholas; Devriendt, Koen; Bauer, Peter; Gecz, Jozef; Golzio, Christelle; Gontan, Cristina; Kalscheuer, Vera M

2018-05-04

RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.

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. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

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 Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Intercomparison of stratospheric water vapor observed by satellite experiments - Stratospheric Aerosol and Gas Experiment II versus Limb Infrared Monitor of the Stratosphere and Atmospheric Trace Molecule Spectroscopy

NASA Technical Reports Server (NTRS)

Chiou, E. W.; Mccormick, M. P.; Mcmaster, L. R.; Chu, W. P.; Larsen, J. C.; Rind, D.; Oltmans, S.

1993-01-01

A comparison is made of the stratospheric water vapor measurements made by the satellite sensors of the Stratospheric Aerosol and Gas Experiment II (SAGE II), the Nimbus-7 LIMS, and the Spacelab 3 Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment. It was found that, despite differences in the measurement techniques, sampling bias, and observational periods, the three experiments have disclosed a generally consistent pattern of stratospheric water vapor distribution. The only significant difference occurs at high southern altitudes in May below 18 km, where LIMS measurements were 2-3 ppmv greater than those of SAGE II and ATMOS.

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.

The Use of Color in the Output Analysis of Statistical Simulations, and Analysis of Estimators of Serial Correlation

DTIC Science & Technology

1988-09-01

0.762 4.4w SAW4 L. 75-41 LIM7041 UW.3334 .50541 LIM3-01 0.53-ft 0.711 0.7141141 LOS1 0.1A354 1 t&1 4tSI *.&439 0.764 0.141 0.91 O.662 0.11 11 0. 1441...0504 .114 0464 .w .. 454 0.504 LOS1 0.&" -. 4.46 L M41 0.43 0.W1 L6 It36" 0!.0.37111 0.0311 .60 0.0354L.314 0.1(4 0.104 L.474 LIS1 0.6647 &:KM2 0.508

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.

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

Fast and accurate computation of system matrix for area integral model-based algebraic reconstruction technique

NASA Astrophysics Data System (ADS)

Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua

2014-11-01

Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.

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.

SPECTRAL LINE DE-CONFUSION IN AN INTENSITY MAPPING SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Yun-Ting; Bock, James; Bradford, C. Matt

2016-12-01

Spectral line intensity mapping (LIM) has been proposed as a promising tool to efficiently probe the cosmic reionization and the large-scale structure. Without detecting individual sources, LIM makes use of all available photons and measures the integrated light in the source confusion limit to efficiently map the three-dimensional matter distribution on large scales as traced by a given emission line. One particular challenge is the separation of desired signals from astrophysical continuum foregrounds and line interlopers. Here we present a technique to extract large-scale structure information traced by emission lines from different redshifts, embedded in a three-dimensional intensity mapping data cube.more » The line redshifts are distinguished by the anisotropic shape of the power spectra when projected onto a common coordinate frame. We consider the case where high-redshift [C ii] lines are confused with multiple low-redshift CO rotational lines. We present a semi-analytic model for [C ii] and CO line estimates based on the cosmic infrared background measurements, and show that with a modest instrumental noise level and survey geometry, the large-scale [C ii] and CO power spectrum amplitudes can be successfully extracted from a confusion-limited data set, without external information. We discuss the implications and limits of this technique for possible LIM experiments.« less

LIMS for Lasers 2015 for achieving long-term accuracy and precision of δ2H, δ17O, and δ18O of waters using laser absorption spectrometry

USGS Publications Warehouse

Coplen, Tyler B.; Wassenaar, Leonard I

2015-01-01

Although laser absorption spectrometry (LAS) instrumentation is easy to use, its incorporation into laboratory operations is not easy, owing to extensive offline manipulation of comma-separated-values files for outlier detection, between-sample memory correction, nonlinearity (δ-variation with water amount) correction, drift correction, normalization to VSMOW-SLAP scales, and difficulty in performing long-term QA/QC audits. METHODS: A Microsoft Access relational-database application, LIMS (Laboratory Information Management System) for Lasers 2015, was developed. It automates LAS data corrections and manages clients, projects, samples, instrument-sample lists, and triple-isotope (δ(17) O, δ(18) O, and δ(2) H values) instrumental data for liquid-water samples. It enables users to (1) graphically evaluate sample injections for variable water yields and high isotope-delta variance; (2) correct for between-sample carryover, instrumental drift, and δ nonlinearity; and (3) normalize final results to VSMOW-SLAP scales. RESULTS: Cost-free LIMS for Lasers 2015 enables users to obtain improved δ(17) O, δ(18) O, and δ(2) H values with liquid-water LAS instruments, even those with under-performing syringes. For example, LAS δ(2) HVSMOW measurements of USGS50 Lake Kyoga (Uganda) water using an under-performing syringe having ±10 % variation in water concentration gave +31.7 ± 1.6 ‰ (2-σ standard deviation), compared with the reference value of +32.8 ± 0.4 ‰, after correction for variation in δ value with water concentration, between-sample memory, and normalization to the VSMOW-SLAP scale. CONCLUSIONS: LIMS for Lasers 2015 enables users to create systematic, well-founded instrument templates, import δ(2) H, δ(17) O, and δ(18) O results, evaluate performance with automatic graphical plots, correct for δ nonlinearity due to variable water concentration, correct for between-sample memory, adjust for drift, perform VSMOW-SLAP normalization, and perform long-term QA/QC audits easily.

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 etc.) and local governments; planning and control of torrential streams and conservation of land, establishing the monitoring system of environmental parameters and its continuous maintenance.

Effects of gradual-elastic compression stockings on running economy, kinematics, and performance in runners.

PubMed

Varela-Sanz, Adrian; España, Javier; Carr, Natasha; Boullosa, Daniel A; Esteve-Lanao, Jonathan

2011-10-01

We investigated the effect of gradual-elastic compression stockings (GCSs) on running economy (RE), kinematics, and performance in endurance runners. Sixteen endurance trained athletes (age: 34.73 ± 6.27 years; VO2max: 62.83 ± 9.03 ml·kg(-1)·min(-1); 38 minutes in 10 km; 1 hour 24 minutes in half marathon) performed in random order 4 bouts of 6 minutes at a recent half-marathon pace on a treadmill to evaluate RE with or without GCSs. Subsequently, 12 athletes were divided into 2 equal groups matched by their VO2max, and they performed a time limit test (T(lim)) on a treadmill at 105% of a recent 10-km pace with or without GCSs for evaluation of physiological responses and running kinematics. There were no significant differences in the RE test in all of the variables analyzed for the conditions, but a moderate reproducibility for some physiological responses was detected in the condition with GCSs. In the T(lim), the group that wore GCSs reached a lower % of maximum heart rate (HRmax) compared with the control group (96.00 ± 2.94 vs. 99.83 ± 0.40) (p = 0.01). Kinematics did not differ between conditions during the T(lim) (p > 0.05). There were improvement trends for time to fatigue (337 vs. 387 seconds; d = 0.32) and a lower VO2peak (≈53 vs. 62 ml·kg(-1)·min(-1); d = 1.19) that were detected with GCSs during the T(lim). These results indicate that GCSs reduce the % of HRmax reached during a test at competition pace. The lower reproducibility of the condition with GCSs perhaps suggests that athletes may possibly need an accommodation period for systematically experiencing the benefits of this garment, but this hypothesis should be further investigated.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

THE DEARTH OF NEUTRAL HYDROGEN IN GALACTIC DWARF SPHEROIDAL GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spekkens, Kristine; Urbancic, Natasha; Mason, Brian S.

We present new upper limits on the neutral hydrogen (H I) content within the stellar half-light ellipses of 15 Galactic dwarf spheroidal galaxies (dSphs), derived from pointed observations with the Green Bank Telescope (GBT) as well as Arecibo L-band Fast ALFA survey and Galactic All-Sky Survey data. All of the limits M{sub H} {sub I}{sup lim} are more stringent than previously reported values, and those from the GBT improve upon constraints in the literature by a median factor of 23. Normalizing by V-band luminosity L{sub V} and dynamical mass M {sub dyn}, we find M{sub H} {sub I}{sup lim}/L{sub V}∼10{supmore » −3} M{sub ⊙}/L{sub ⊙} and M{sub H} {sub I}{sup lim}/M{sub dyn}∼5×10{sup −5}, irrespective of location in the Galactic halo. Comparing these relative H I contents to those of the Local Group and nearby neighbor dwarfs compiled by McConnachie, we find that the Galactic dSphs are extremely gas-poor. Our H I upper limits therefore provide the clearest picture yet of the environmental dependence of the H I content in Local Volume dwarfs. If ram pressure stripping explains the dearth of H I in these systems, then orbits in a relatively massive Milky Way are favored for the outer halo dSph Leo I, while Leo II and Canes Venatici I have had a pericentric passage in the past. For Draco and Ursa Minor, the interstellar medium mass that should accumulate through stellar mass loss in between pericentric passages exceeds M{sub H} {sub I}{sup lim} by a factor of ∼30. In Ursa Minor, this implies that either this material is not in the atomic phase, or that another mechanism clears the recycled gas on shorter timescales.« less

Demonstration of new PCSD capabilities

NASA Technical Reports Server (NTRS)

Gough, M.

1986-01-01

The new, more flexible and more friendly graphics capabilities to be available in later releases of the Pilot Climate Data System were demonstrated. The LIMS-LAMAT data set was chosen to illustrate these new capabilities. Pseudocolor and animation were used to represent the third and fourth dimensions, expanding the analytical capabilities available through the traditional two-dimensional x-y plot. In the new version, variables for the axes are chosen by scrolling through viable selections. This scrolling feature is a function of the new user interface customization. The new graphics are extremely user friendly and should free the scientist to look at data and converse with it, without doing any programming. The system is designed to rapidly plot any variable versus any other variable and animate by any variable. Any one plot in itself is not extraordinary; however, the fact that a user can generate the plots instead of a programmer distinguishes the graphics capabilities of the PCDS from other software packages. In addition, with the new CDF design, the system will become more generic, and the new graphics will become much more rigorous in the area of correlative studies.

An Integrated Nonlinear Analysis library - (INA) for solar system plasma turbulence

NASA Astrophysics Data System (ADS)

Munteanu, Costel; Kovacs, Peter; Echim, Marius; Koppan, Andras

2014-05-01

We present an integrated software library dedicated to the analysis of time series recorded in space and adapted to investigate turbulence, intermittency and multifractals. The library is written in MATLAB and provides a graphical user interface (GUI) customized for the analysis of space physics data available online like: Coordinated Data Analysis Web (CDAWeb), Automated Multi Dataset Analysis system (AMDA), Planetary Science Archive (PSA), World Data Center Kyoto (WDC), Ulysses Final Archive (UFA) and Cluster Active Archive (CAA). Three main modules are already implemented in INA : the Power Spectral Density (PSD) Analysis, the Wavelet and Intemittency Analysis and the Probability Density Functions (PDF) analysis.The layered structure of the software allows the user to easily switch between different modules/methods while retaining the same time interval for the analysis. The wavelet analysis module includes algorithms to compute and analyse the PSD, the Scalogram, the Local Intermittency Measure (LIM) or the Flatness parameter. The PDF analysis module includes algorithms for computing the PDFs for a range of scales and parameters fully customizable by the user; it also computes the Flatness parameter and enables fast comparison with standard PDF profiles like, for instance, the Gaussian PDF. The library has been already tested on Cluster and Venus Express data and we will show relevant examples. Research supported by the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 313038/STORM, and a grant of the Romanian Ministry of National Education, CNCS UEFISCDI, project number PN-II-ID PCE-2012-4-0418.

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems.

PubMed

Araújo, Luciano V; Malkowski, Simon; Braghetto, Kelly R; Passos-Bueno, Maria R; Zatz, Mayana; Pu, Calton; Ferreira, João E

2011-12-22

Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

PubMed Central

2011-01-01

Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces. PMID:22369688

Non-mix fragrances are top sensitizers in consecutive dermatitis patients - a cross-sectional study of the 26 EU-labelled fragrance allergens.

PubMed

Bennike, Niels H; Zachariae, Claus; Johansen, Jeanne D

2017-11-01

For cosmetics, it is mandatory to label 26 fragrance substances, including all constituents of fragrance mix I (FM I) and fragrance mix II (FM II). Earlier reports have not included oxidized R-limonene [hydroperoxides of R-limonene (Lim-OOH)] and oxidized linalool [hydroperoxides of linalool (Lin-OOH)], and breakdown testing of FM I and FM II has mainly been performed in selected, mix-positive patients. To report the prevalence of sensitization to the 26 fragrances, and to assess concomitant reactivity to FM I and/or FM II. A cross-sectional study on consecutive dermatitis patients patch tested with the 26 fragrances and the European baseline series from 2010 to 2015 at a single university clinic was performed. Of 6004 patients, 940 (15.7%, 95%CI: 14.7-16.6%) were fragrance-sensitized. Regarding the single fragrances, most patients were sensitized to Lin-OOH (3.9%), Evernia furfuracea (3.0%), Lim-OOH (2.5%), and hydroxyisohexyl 3-cyclohexene carboxaldehyde (2.1%). Significantly fewer patients were 'FM I-positive and constituent-positive' than 'FM II-positive and constituent-positive' (32.7% versus 57.0%, p < 0.0001). Additionally, significantly more patients were 'FM II-negative but constituent-positive' than 'FM I-negative but constituent-positive' (12.4% versus 3.2%, p = 0.0008). Non-mix fragrances are the most important single fragrance allergens among consecutive patients. The test concentration of the single FM I constituents should be increased when possible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Ldb1 is essential for development of Nkx2.1 lineage derived GABAergic and cholinergic neurons in the telencephalon.

PubMed

Zhao, Yangu; Flandin, Pierre; Vogt, Daniel; Blood, Alexander; Hermesz, Edit; Westphal, Heiner; Rubenstein, John L R

2014-01-01

The progenitor zones of the embryonic mouse ventral telencephalon give rise to GABAergic and cholinergic neurons. We have shown previously that two LIM-homeodomain (LIM-HD) transcription factors, Lhx6 and Lhx8, that are downstream of Nkx2.1, are critical for the development of telencephalic GABAergic and cholinergic neurons. Here we investigate the role of Ldb1, a nuclear protein that binds directly to all LIM-HD factors, in the development of these ventral telencephalon derived neurons. We show that Ldb1 is expressed in the Nkx2.1 cell lineage during embryonic development and in mature neurons. Conditional deletion of Ldb1 causes defects in the expression of a series of genes in the ventral telencephalon and severe impairment in the tangential migration of cortical interneurons from the ventral telencephalon. Similar to the phenotypes observed in Lhx6 or Lhx8 mutant mice, the Ldb1 conditional mutants show a reduction in the number of both GABAergic and cholinergic neurons in the telencephalon. Furthermore, our analysis reveals defects in the development of the parvalbumin-positive neurons in the globus pallidus and striatum of the Ldb1 mutants. These results provide evidence that Ldb1 plays an essential role as a transcription co-regulator of Lhx6 and Lhx8 in the control of mammalian telencephalon development. © 2013 Published by Elsevier Inc.

Ldb1 is essential for development of Nkx2.1 lineage derived GABAergic and cholinergic neurons in the telencephalon

PubMed Central

Zhao, Yangu; Flandin, Pierre; Vogt, Daniel; Blood, Alexander; Hermesz, Edit; Westphal, Heiner; Rubenstein, John

2013-01-01

The progenitor zones of the embryonic mouse ventral telencephalon give rise to GABAergic and cholinergic neurons. We have shown previously that two LIM-homeodomain (LIM-HD) transcription factors, Lhx6 and Lhx8, that are downstream of Nkx2.1, are critical for the development of telencephalic GABAergic and cholinergic neurons. Here we investigate the role of Ldb1, a nuclear protein that binds directly to all LIM-HD factors, in the development of these ventral telencephalon derived neurons. We show that Ldb1 is expressed in the Nkx2.1 cell lineage during embryonic development and in mature neurons. Conditional deletion of Ldb1 causes defects in the expression of a series of genes in the ventral telencephalon and severe impairment in the tangential migration of cortical interneurons from the ventral telencephalon. Similar to the phenotypes observed in Lhx6 or Lhx8 mutant mice, the Ldb1 conditional mutants show a reduction in the number of both GABAergic and cholinergic neurons in the telencephalon. Furthermore, our analysis reveals defects in the development of the parvalbumin-positive neurons in the globus pallidus and striatum of the Ldb1 mutants. These results provide evidence that Ldb1 plays an essential role as a transcription co-regulator of Lhx6 and Lhx8 in the control of mammalian telencephalon development. PMID:24157949

Evaluating fMRI methods for assessing hemispheric language dominance in healthy subjects.

PubMed

Baciu, Monica; Juphard, Alexandra; Cousin, Emilie; Bas, Jean François Le

2005-08-01

We evaluated two methods for quantifying the hemispheric language dominance in healthy subjects, by using a rhyme detection (deciding whether couple of words rhyme) and a word fluency (generating words starting with a given letter) task. One of methods called "flip method" (FM) was based on the direct statistical comparison between hemispheres' activity. The second one, the classical lateralization indices method (LIM), was based on calculating lateralization indices by taking into account the number of activated pixels within hemispheres. The main difference between methods is the statistical assessment of the inter-hemispheric difference: while FM shows if the difference between hemispheres' activity is statistically significant, LIM shows only that if there is a difference between hemispheres. The robustness of LIM and FM was assessed by calculating correlation coefficients between LIs obtained with each of these methods and manual lateralization indices MLI obtained with Edinburgh inventory. Our results showed significant correlation between LIs provided by each method and the MIL, suggesting that both methods are robust for quantifying hemispheric dominance for language in healthy subjects. In the present study we also evaluated the effect of spatial normalization, smoothing and "clustering" (NSC) on the intra-hemispheric location of activated regions and inter-hemispheric asymmetry of the activation. Our results have shown that NSC did not affect the hemispheric specialization but increased the value of the inter-hemispheric difference.

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

Laboratory information management system for membrane protein structure initiative--from gene to crystal.

PubMed

Troshin, Petr V; Morris, Chris; Prince, Stephen M; Papiz, Miroslav Z

2008-12-01

Membrane Protein Structure Initiative (MPSI) exploits laboratory competencies to work collaboratively and distribute work among the different sites. This is possible as protein structure determination requires a series of steps, starting with target selection, through cloning, expression, purification, crystallization and finally structure determination. Distributed sites create a unique set of challenges for integrating and passing on information on the progress of targets. This role is played by the Protein Information Management System (PIMS), which is a laboratory information management system (LIMS), serving as a hub for MPSI, allowing collaborative structural proteomics to be carried out in a distributed fashion. It holds key information on the progress of cloning, expression, purification and crystallization of proteins. PIMS is employed to track the status of protein targets and to manage constructs, primers, experiments, protocols, sample locations and their detailed histories: thus playing a key role in MPSI data exchange. It also serves as the centre of a federation of interoperable information resources such as local laboratory information systems and international archival resources, like PDB or NCBI. During the challenging task of PIMS integration, within the MPSI, we discovered a number of prerequisites for successful PIMS integration. In this article we share our experiences and provide invaluable insights into the process of LIMS adaptation. This information should be of interest to partners who are thinking about using LIMS as a data centre for their collaborative efforts.

Steenrod homotopy

NASA Astrophysics Data System (ADS)

Melikhov, Sergey A.

2009-06-01

Steenrod homotopy theory is a natural framework for doing algebraic topology on general spaces in terms of algebraic topology of polyhedra; or from a different viewpoint, it studies the topology of the \\lim^1 functor (for inverse sequences of groups). This paper is primarily concerned with the case of compacta, in which Steenrod homotopy coincides with strong shape. An attempt is made to simplify the foundations of the theory and to clarify and improve some of its major results. With geometric tools such as Milnor's telescope compactification, comanifolds (=mock bundles), and the Pontryagin-Thom construction, new simple proofs are obtained for results by Barratt-Milnor, Geoghegan-Krasinkiewicz, Dydak, Dydak-Segal, Krasinkiewicz-Minc, Cathey, Mittag-Leffler-Bourbaki, Fox, Eda-Kawamura, Edwards-Geoghegan, Jussila, and for three unpublished results by Shchepin. An error in Lisitsa's proof of the `Hurewicz theorem in Steenrod homotopy' is corrected. It is shown that over compacta, R.H. Fox's overlayings are equivalent to I.M. James' uniform covering maps. Other results include: \\bullet A morphism between inverse sequences of countable (possibly non-Abelian) groups that induces isomorphisms on \\lim and \\lim^1 is invertible in the pro-category. This implies the `Whitehead theorem in Steenrod homotopy', thereby answering two questions of Koyama. \\bullet If X is an LC_{n-1}-compactum, n\\ge 1, then its n-dimensional Steenrod homotopy classes are representable by maps S^n\\to\

Initiation of secondary ice production in clouds

NASA Astrophysics Data System (ADS)

Sullivan, Sylvia C.; Hoose, Corinna; Kiselev, Alexei; Leisner, Thomas; Nenes, Athanasios

2018-02-01

Disparities between the measured concentrations of ice-nucleating particles (INPs) and in-cloud ice crystal number concentrations (ICNCs) have led to the hypothesis that mechanisms other than primary nucleation form ice in the atmosphere. Here, we model three of these secondary production mechanisms - rime splintering, frozen droplet shattering, and ice-ice collisional breakup - with a six-hydrometeor-class parcel model. We perform three sets of simulations to understand temporal evolution of ice hydrometeor number (Nice), thermodynamic limitations, and the impact of parametric uncertainty when secondary production is active. Output is assessed in terms of the number of primarily nucleated ice crystals that must exist before secondary production initiates (NINP(lim)) as well as the ICNC enhancement from secondary production and the timing of a 100-fold enhancement. Nice evolution can be understood in terms of collision-based nonlinearity and the phasedness of the process, i.e., whether it involves ice hydrometeors, liquid ones, or both. Ice-ice collisional breakup is the only process for which a meaningful NINP(lim) exists (0.002 up to 0.15 L-1). For droplet shattering and rime splintering, a warm enough cloud base temperature and modest updraft are the more important criteria for initiation. The low values of NINP(lim) here suggest that, under appropriate thermodynamic conditions for secondary ice production, perturbations in cloud concentration nuclei concentrations are more influential in mixed-phase partitioning than those in INP concentrations.

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.

Modelling noise propagation using Grid Resources. Progress within GDI-Grid

NASA Astrophysics Data System (ADS)

Kiehle, Christian; Mayer, Christian; Padberg, Alexander; Stapelfeld, Hartmut

2010-05-01

Modelling noise propagation using Grid Resources. Progress within GDI-Grid. GDI-Grid (english: SDI-Grid) is a research project funded by the German Ministry for Science and Education (BMBF). It aims at bridging the gaps between OGC Web Services (OWS) and Grid infrastructures and identifying the potential of utilizing the superior storage capacities and computational power of grid infrastructures for geospatial applications while keeping the well-known service interfaces specified by the OGC. The project considers all major OGC webservice interfaces for Web Mapping (WMS), Feature access (Web Feature Service), Coverage access (Web Coverage Service) and processing (Web Processing Service). The major challenge within GDI-Grid is the harmonization of diverging standards as defined by standardization bodies for Grid computing and spatial information exchange. The project started in 2007 and will continue until June 2010. The concept for the gridification of OWS developed by lat/lon GmbH and the Department of Geography of the University of Bonn is applied to three real-world scenarios in order to check its practicability: a flood simulation, a scenario for emergency routing and a noise propagation simulation. The latter scenario is addressed by the Stapelfeldt Ingenieurgesellschaft mbH located in Dortmund adapting their LimA software to utilize grid resources. Noise mapping of e.g. traffic noise in urban agglomerates and along major trunk roads is a reoccurring demand of the EU Noise Directive. Input data requires road net and traffic, terrain, buildings and noise protection screens as well as population distribution. Noise impact levels are generally calculated in 10 m grid and along relevant building facades. For each receiver position sources within a typical range of 2000 m are split down into small segments, depending on local geometry. For each of the segments propagation analysis includes diffraction effects caused by all obstacles on the path of sound propagation. This immense intensive calculation needs to be performed for a major part of European landscape. A LINUX version of the commercial LimA software for noise mapping analysis has been implemented on a test cluster within the German D-GRID computer network. Results and performance indicators will be presented. The presentation is an extension to last-years presentation "Spatial Data Infrastructures and Grid Computing: the GDI-Grid project" that described the gridification concept developed in the GDI-Grid project and provided an overview of the conceptual gaps between Grid Computing and Spatial Data Infrastructures. Results from the GDI-Grid project are incorporated in the OGC-OGF (Open Grid Forum) collaboration efforts as well as the OGC WPS 2.0 standards working group developing the next major version of the WPS specification.

Laboratory information management system: an example of international cooperation in Namibia.

PubMed

Colangeli, Patrizia; Ferrilli, Monica; Quaranta, Fabrizio; Malizia, Elio; Mbulu, Rosa-Stella; Mukete, Esther; Iipumbu, Lukas; Kamhulu, Anna; Tjipura-Zaire, Georgina; Di Francesco, Cesare; Lelli, Rossella; Scacchia, Massimo

2012-01-01

The authors describe the project undertaken by the Istituto G. Caporale to provide a laboratory information management system (LIMS) to the Central Veterinary Laboratory (CVL) in Windhoek, Namibia. This robust laboratory management tool satisfies Namibia's information obligations under international quality standard ISO 17025:2005. The Laboratory Information Management System (LIMS) for Africa was designed to collect and manage all necessary information on samples, tests and test results. The system involves the entry of sample data on arrival, as required by Namibian sampling plans, the tracking of samples through the various sections of the CVL, the collection of test results, generation of test reports and monitoring of outbreaks through data interrogation functions, eliminating multiple registrations of the same data on paper records. It is a fundamental component of the Namibian veterinary information system.

Selecting a Laboratory Information Management System for Biorepositories in Low- and Middle-Income Countries: The H3Africa Experience and Lessons Learned

PubMed Central

Musinguzi, Henry; Lwanga, Newton; Kezimbira, Dafala; Kigozi, Edgar; Katabazi, Fred Ashaba; Wayengera, Misaki; Joloba, Moses Lutaakome; Abayomi, Emmanuel Akin; Swanepoel, Carmen; Croxton, Talishiea; Ozumba, Petronilla; Thankgod, Anazodo; van Zyl, Lizelle; Mayne, Elizabeth Sarah; Kader, Mukthar; Swartz, Garth

2017-01-01

Biorepositories in Africa need significant infrastructural support to meet International Society for Biological and Environmental Repositories (ISBER) Best Practices to support population-based genomics research. ISBER recommends a biorepository information management system which can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative set out to develop regional African biorepositories where Uganda, Nigeria, and South Africa were successfully awarded grants to develop the state-of-the-art biorepositories. The biorepositories carried out an elaborate process to evaluate and choose a laboratory information management system (LIMS) with the aim of integrating the three geographically distinct sites. In this article, we review the processes, African experience, lessons learned, and make recommendations for choosing a biorepository LIMS in the African context.

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.

On the electronic properties of GaSb irradiated with reactor neutrons and its charge neutrality level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiko, V. M.; Brudnii, V. N., E-mail: brudnyi@mail.tsu.ru; Ermakov, V. S.

2015-06-15

The electronic properties and the limiting position of the Fermi level in p-GaSb crystals irradiated with full-spectrum reactor neutrons at up to a fluence of 8.6 × 10{sup 18} cm{sup −2} are studied. It is shown that the irradiation of GaSb with reactor neutrons results in an increase in the concentration of free holes to p{sub lim} = (5−6) × 10{sup 18} cm{sup −3} and in pinning of the Fermi level at the limiting position F{sub lim} close to E{sub V} + 0.02 eV at 300 K. The effect of the annealing of radiation defects in the temperature range 100–550°Cmore » is explored.« less

Studies of small-scale plasma inhomogeneities in the cusp ionosphere using sounding rocket data

NASA Astrophysics Data System (ADS)

Chernyshov, Alexander A.; Spicher, Andres; Ilyasov, Askar A.; Miloch, Wojciech J.; Clausen, Lasse B. N.; Saito, Yoshifumi; Jin, Yaqi; Moen, Jøran I.

2018-04-01

Microprocesses associated with plasma inhomogeneities are studied on the basis of data from the Investigation of Cusp Irregularities (ICI-3) sounding rocket. The ICI-3 rocket is devoted to investigating a reverse flow event in the cusp F region ionosphere. By numerical stability analysis, it is demonstrated that inhomogeneous-energy-density-driven (IEDD) instability can be a mechanism for the excitation of small-scale plasma inhomogeneities. The Local Intermittency Measure (LIM) method also applied the rocket data to analyze irregular structures of the electric field during rocket flight in the cusp. A qualitative agreement between high values of the growth rates of the IEDD instability and the regions with enhanced LIM is observed. This suggests that IEDD instability is connected to turbulent non-Gaussian processes.

A laboratory information management system for DNA barcoding workflows.

PubMed

Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

2012-07-01

This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

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 based on their gridded Level 3 data following the PSC screening. Zonal coefficients of both species are essentially free of effects from PSCs on the 550 K surface, based on their average values along PV contours and in terms of equivalent latitude. Remnants of PSCs are still present in O3 on the 450 K surface during mid-January. It is judged that the LIMS Level 3 data are of good quality for analyzing the larger-scale, stratospheric chemistry and transport processes during the Arctic winter of 1978-1979.

A Virtual Research Environment for a Secondary Ion Mass Spectrometer (SIMS)

NASA Astrophysics Data System (ADS)

Wiedenbeck, M.; Schäfer, L.; Klump, J.; Galkin, A.

2013-12-01

Overview: This poster describes the development of a Virtual Research Environment for the Secondary Ion Mass Spectrometer (SIMS) at GFZ Potsdam. Background: Secondary Ion Mass Spectrometers (SIMS) are extremely sensitive instruments for analyzing the surfaces of solid and thin film samples. These instruments are rare, expensive and experienced operators are very highly sought after. As such, measurement time is a precious commodity, until now only accessible to small numbers of researchers. The challenge: The Virtual SIMS Project aims to set up a Virtual Research Environment for the operation of the CAMECA IMS 1280-HR instrument at the GFZ Potsdam. The objective of the VRE is to provide SIMS access not only to researchers locally present in Potsdam but also to scientists working with SIMS cooperation partners in e.g., South Africa, Brazil or India. The requirements: The system should address the complete spectrum of laboratory procedures - from online application for measurement time, to remote access for data acquisition to data archiving for the subsequent publication and for future reuse. The approach: The targeted Virtual SIMS Environment will consist of a: 1. Web Server running the Virtual SIMS website providing general information about the project, lab access proposal forms and calendar for the timing of project related tasks. 2. LIMS Server, responsible for scheduling procedures, data management and, if applicable, accounting and billing. 3. Remote SIMS Tool, devoted to the operation of the experiment within a remote control environment. 4. Publishing System, which supports the publication of results in cooperation with the GFZ Library services. 5. Training Simulator, which offers the opportunity to rehearse experiments and to prepare for possible events such as a power outages or interruptions to broadband services. First results: The SIMS Virtual Research Environment will be mainly based on open source software, the only exception being the CAMECA IMS 1280-HR SIMS operating under LabView. The Publishing System will be based on eSciDoc, which is already successfully used by the GFZ scientific library. For the LIMS Server we are currently testing various options. The challenge, however, is the successful integration of all the various components and, where necessary, the definition of useful interfaces between the modules.

LIMS for Lasers 2015 for achieving long-term accuracy and precision of δ2H, δ17O, and δ18O of waters using laser absorption spectrometry

USGS Publications Warehouse

Coplen, Tyler B.; Wassenaar, Leonard I

2015-01-01

RationaleAlthough laser absorption spectrometry (LAS) instrumentation is easy to use, its incorporation into laboratory operations is not easy, owing to extensive offline manipulation of comma-separated-values files for outlier detection, between-sample memory correction, nonlinearity (δ-variation with water amount) correction, drift correction, normalization to VSMOW-SLAP scales, and difficulty in performing long-term QA/QC audits.MethodsA Microsoft Access relational-database application, LIMS (Laboratory Information Management System) for Lasers 2015, was developed. It automates LAS data corrections and manages clients, projects, samples, instrument-sample lists, and triple-isotope (δ17O, δ18O, and δ2H values) instrumental data for liquid-water samples. It enables users to (1) graphically evaluate sample injections for variable water yields and high isotope-delta variance; (2) correct for between-sample carryover, instrumental drift, and δ nonlinearity; and (3) normalize final results to VSMOW-SLAP scales.ResultsCost-free LIMS for Lasers 2015 enables users to obtain improved δ17O, δ18O, and δ2H values with liquid-water LAS instruments, even those with under-performing syringes. For example, LAS δ2HVSMOW measurements of USGS50 Lake Kyoga (Uganda) water using an under-performing syringe having ±10 % variation in water concentration gave +31.7 ± 1.6 ‰ (2-σ standard deviation), compared with the reference value of +32.8 ± 0.4 ‰, after correction for variation in δ value with water concentration, between-sample memory, and normalization to the VSMOW-SLAP scale.ConclusionsLIMS for Lasers 2015 enables users to create systematic, well-founded instrument templates, import δ2H, δ17O, and δ18O results, evaluate performance with automatic graphical plots, correct for δ nonlinearity due to variable water concentration, correct for between-sample memory, adjust for drift, perform VSMOW-SLAP normalization, and perform long-term QA/QC audits easily. Published in 2015. This article is a U.S. Government work and is in the public domain in the USA.

Effects of recovery mode (active vs. passive) on performance during a short high-intensity interval training program: a longitudinal study.

PubMed

Ben Abderrahman, Abderraouf; Zouhal, Hassane; Chamari, Karim; Thevenet, Delphine; de Mullenheim, Pierre-Yves; Gastinger, Steven; Tabka, Zouhair; Prioux, Jacques

2013-06-01

The aim of this longitudinal study was to compare two recovery modes (active vs. passive) during a seven-week high-intensity interval training program (SWHITP) aimed to improve maximal oxygen uptake ([Formula: see text]), maximal aerobic velocity (MAV), time to exhaustion (t lim) and time spent at a high percentage of [Formula: see text], i.e., above 90 % (t90 [Formula: see text]) and 95 % (t95 [Formula: see text]) of [Formula: see text]. Twenty-four adults were randomly assigned to a control group that did not train (CG, n = 6) and two training groups: intermittent exercise (30 s exercise/30 s recovery) with active (IEA, n = 9) or passive recovery (IEP, n = 9). Before and after seven weeks with (IEA and IEP) or without (CG) high-intensity interval training (HIT) program, all subjects performed a maximal graded test to determine their [Formula: see text] and MAV. Subsequently only the subjects of IEA and IEP groups carried out an intermittent exercise test consisting of repeating as long as possible 30 s intensive runs at 105 % of MAV alternating with 30 s active recovery at 50 % of MAV (IEA) or 30 s passive recovery (IEP). Within IEA and IEP, mean t lim and MAV significantly increased between the onset and the end of the SWHITP and no significant difference was found in t90 VO2max and t95 VO2max. Furthermore, before and after the SWHITP, passive recovery allowed a longer t lim for a similar time spent at a high percentage of VO2max. Finally, within IEA, but not in IEP, mean VO2max increased significantly between the onset and the end of the SWHITP both in absolute (p < 0.01) and relative values (p < 0.05). In conclusion, our results showed a significant increase in VO2max after a SWHITP with active recovery in spite of the fact that t lim was significantly longer (more than twice longer) with respect to passive recovery.

Nck-2, a Novel Src Homology2/3-containing Adaptor Protein That Interacts with the LIM-only Protein PINCH and Components of Growth Factor Receptor Kinase-signaling Pathways

PubMed Central

Tu, Yizeng; Li, Fugang; Wu, Chuanyue

1998-01-01

Many of the protein–protein interactions that are essential for eukaryotic intracellular signal transduction are mediated by protein binding modules including SH2, SH3, and LIM domains. Nck is a SH3- and SH2-containing adaptor protein implicated in coordinating various signaling pathways, including those of growth factor receptors and cell adhesion receptors. We report here the identification, cloning, and characterization of a widely expressed, Nck-related adaptor protein termed Nck-2. Nck-2 comprises primarily three N-terminal SH3 domains and one C-terminal SH2 domain. We show that Nck-2 interacts with PINCH, a LIM-only protein implicated in integrin-linked kinase signaling. The PINCH-Nck-2 interaction is mediated by the fourth LIM domain of PINCH and the third SH3 domain of Nck-2. Furthermore, we show that Nck-2 is capable of recognizing several key components of growth factor receptor kinase-signaling pathways including EGF receptors, PDGF receptor-β, and IRS-1. The association of Nck-2 with EGF receptors was regulated by EGF stimulation and involved largely the SH2 domain of Nck-2, although the SH3 domains of Nck-2 also contributed to the complex formation. The association of Nck-2 with PDGF receptor-β was dependent on PDGF activation and was mediated solely by the SH2 domain of Nck-2. Additionally, we have detected a stable association between Nck-2 and IRS-1 that was mediated primarily via the second and third SH3 domain of Nck-2. Thus, Nck-2 associates with PINCH and components of different growth factor receptor-signaling pathways via distinct mechanisms. Finally, we provide evidence indicating that a fraction of the Nck-2 and/or Nck-1 proteins are associated with the cytoskeleton. These results identify a novel Nck-related SH2- and SH3-domain–containing protein and suggest that it may function as an adaptor protein connecting the growth factor receptor-signaling pathways with the integrin-signaling pathways. PMID:9843575

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

Wesley Jones | NREL

Science.gov Websites

, W.B.; Kim, K. (2009). "A Note on the Virtual Crystal Approach to Alloy Optimization." BioEnergy Science Center Laboratory Information Management System (LIMS); Korytina, D.; Graf, P.A.; King, R

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 dramatically accelerate clinician analysis and interpretation of patient genomic data. We present the first application of usability methods to evaluate software interfaces in the context of exome analysis. Our results highlight how the study of user responses can lead to identification of usability issues and challenges and reveal software reengineering opportunities for improving clinical next-generation sequencing analysis. While the evaluation focused on two distinctive software tools, the results are general and should inform active and future software development for genome analysis software. As large-scale genome analysis becomes increasingly common in healthcare, it is critical that efficient and effective software interfaces are provided to accelerate clinical adoption of the technology. Implications for improved design of such applications are discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Integration of laboratory and process testing data

PubMed Central

Tyszkiewicz, Michael

1995-01-01

The author describes ACS Inc.'s Pro-LIMS system which integrates laboratory and process procedures. The system has been shown to be an important toolfor quality assurance in the process manufacturing industry. PMID:18924782

Geophysical testing of rock and its relationships to physical properties

DOT National Transportation Integrated Search

2011-02-01

Testing techniques were designed to characterize spatial variability in geotechnical engineering physical parameters of : rock formations. Standard methods using seismic waves, which are routinely used for shallow subsurface : investigation, have lim...

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

PubMed Central

Morris, Chris; Pajon, Anne; Griffiths, Susanne L.; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M.; Wilter da Silva, Alan; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S.; Stuart, David I.; Henrick, Kim; Esnouf, Robert M.

2011-01-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service. PMID:21460443

G-sequentially connectedness for topological groups with operations

NASA Astrophysics Data System (ADS)

Mucuk, Osman; Cakalli, Huseyin

2016-08-01

It is a well-known fact that for a Hausdorff topological group X, the limits of convergent sequences in X define a function denoted by lim from the set of all convergent sequences in X to X. This notion has been modified by Connor and Grosse-Erdmann for real functions by replacing lim with an arbitrary linear functional G defined on a linear subspace of the vector space of all real sequences. Recently some authors have extended the concept to the topological group setting and introduced the concepts of G-sequential continuity, G-sequential compactness and G-sequential connectedness. In this work, we present some results about G-sequentially closures, G-sequentially connectedness and fundamental system of G-sequentially open neighbourhoods for topological group with operations which include topological groups, topological rings without identity, R-modules, Lie algebras, Jordan algebras, and many others.

A robust rotation-invariance displacement measurement method for a micro-/nano-positioning system

NASA Astrophysics Data System (ADS)

Zhang, Xiang; Zhang, Xianmin; Wu, Heng; Li, Hai; Gan, Jinqiang

2018-05-01

A robust and high-precision displacement measurement method for a compliant mechanism-based micro-/nano-positioning system is proposed. The method is composed of an integer-pixel and a sub-pixel matching procedure. In the proposed algorithm (Pro-A), an improved ring projection transform (IRPT) and gradient information are used as features for approximating the coarse candidates and fine locations, respectively. Simulations are conducted and the results show that the Pro-A has the ability of rotation-invariance and strong robustness, with a theoretical accuracy of 0.01 pixel. To validate the practical performance, a series of experiments are carried out using a computer micro-vision and laser interferometer system (LIMS). The results demonstrate that both the LIMS and Pro-A can achieve high precision, while the Pro-A has better stability and adaptability.

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

PubMed

Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

2011-04-01

The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

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.

Inhibition of stored Ca2+ release disrupts convergence-related cell movements in the lateral intermediate mesoderm resulting in abnormal positioning and morphology of the pronephric anlagen in intact zebrafish embryos.

PubMed

Lam, Pui Ying; Webb, Sarah E; Leclerc, Catherine; Moreau, Marc; Miller, Andrew L

2009-05-01

Ca(2+) is a highly versatile intra- and intercellular signal that has been reported to regulate a variety of different pattern-forming processes during early development. To investigate the potential role of Ca(2+) signaling in regulating convergence-related cell movements, and the positioning and morphology of the pronephric anlagen, we treated zebrafish embryos from 11.5 h postfertilization (hpf; i.e. just before the pronephric anlagen are morphologically distinguishable in the lateral intermediate mesoderm; LIM) to 16 hpf, with a variety of membrane permeable pharmacological reagents known to modulate [Ca(2+)](i). The effect of these treatments on pronephric anlagen positioning and morphology was determined in both fixed and live embryos via in situ hybridization using the pronephic-specific probes, cdh17, pax2.1 and sim1, and confocal imaging of BODIPY FL C(5)-ceramide-labeled embryos, respectively. We report that Ca(2+) released from intracellular stores via inositol 1,4,5-trisphosphate receptors plays a significant role in the positioning and morphology of the pronephric anlagen, but does not affect the fate determination of the LIM cells that form these primordia. Our data suggest that when Ca(2+) release is inhibited, the resulting effects on the pronephric anlagen are a consequence of the disruption of normal convergence-related movements of LIM cells toward the embryonic midline.

Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

PubMed

O'Farrell, Brian; Haase, Jana K; Velayudhan, Vimalkumar; Murphy, Ronan A; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

Nutrient profiling can help identify foods of good nutritional quality for their price: a validation study with linear programming.

PubMed

Maillot, Matthieu; Ferguson, Elaine L; Drewnowski, Adam; Darmon, Nicole

2008-06-01

Nutrient profiling ranks foods based on their nutrient content. They may help identify foods with a good nutritional quality for their price. This hypothesis was tested using diet modeling with linear programming. Analyses were undertaken using food intake data from the nationally representative French INCA (enquête Individuelle et Nationale sur les Consommations Alimentaires) survey and its associated food composition and price database. For each food, a nutrient profile score was defined as the ratio between the previously published nutrient density score (NDS) and the limited nutrient score (LIM); a nutritional quality for price indicator was developed and calculated from the relationship between its NDS:LIM and energy cost (in euro/100 kcal). We developed linear programming models to design diets that fulfilled increasing levels of nutritional constraints at a minimal cost. The median NDS:LIM values of foods selected in modeled diets increased as the levels of nutritional constraints increased (P = 0.005). In addition, the proportion of foods with a good nutritional quality for price indicator was higher (P < 0.0001) among foods selected (81%) than among foods not selected (39%) in modeled diets. This agreement between the linear programming and the nutrient profiling approaches indicates that nutrient profiling can help identify foods of good nutritional quality for their price. Linear programming is a useful tool for testing nutrient profiling systems and validating the concept of nutrient profiling.

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.

Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains

PubMed Central

Velayudhan, Vimalkumar; Murphy, Ronan A.; Achtman, Mark

2012-01-01

Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost. PMID:23144721

A robust null hypothesis for the potential causes of megadrought in western North America

NASA Astrophysics Data System (ADS)

Ault, T.; St George, S.; Smerdon, J. E.; Coats, S.; Mankin, J. S.; Cruz, C. C.; Cook, B.; Stevenson, S.

2017-12-01

The western United States was affected by several megadroughts during the last 1200 years, most prominently during the Medieval Climate Anomaly (MCA: 800 to 1300 CE). A null hypothesis is developed to test the possibility that, given a sufficiently long period of time, these events are inevitable and occur purely as a consequence of internal climate variability. The null distribution of this hypothesis is populated by a linear inverse model (LIM) constructed from global sea-surface temperature anomalies and self-calibrated Palmer Drought Severity Index data for North America. Despite being trained only on seasonal data from the late 20th century, the LIM produces megadroughts that are comparable in their duration, spatial scale, and magnitude as the most severe events of the last 12 centuries. The null hypothesis therefore cannot be rejected with much confidence when considering these features of megadrought, meaning that similar events are possible today, even without any changes to boundary conditions. In contrast, the observed clustering of megadroughts in the MCA, as well as the change in mean hydroclimate between the MCA and the 1500-2000 period, are more likely to have been caused by either external forcing or by internal climate variability not well sampled during the latter half of the Twentieth Century. Finally, the results demonstrate the LIM is a viable tool for determining whether paleoclimate reconstructions events should be ascribed to external forcings, "out of sample" climate mechanisms, or if they are consistent with the variability observed during the recent period.

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.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

Complete Genome Sequences of Three Moraxella osloensis Strains Isolated from Human Skin.

PubMed

Lim, Jae Yun; Hwang, Ingyu; Ganzorig, Munkhtsatsral; Huang, Shir-Ly; Cho, Gyu-Sung; Franz, Charles M A P; Lee, Kyoung

2018-01-18

Here, we present the complete whole-genome sequences of three Moraxella osloensis strains with octylphenol polyethoxylate-degrading abilities. These strains were isolated from human skin. Copyright © 2018 Lim et al.

MNE Scan: Software for real-time processing of electrophysiological data.

PubMed

Esch, Lorenz; Sun, Limin; Klüber, Viktor; Lew, Seok; Baumgarten, Daniel; Grant, P Ellen; Okada, Yoshio; Haueisen, Jens; Hämäläinen, Matti S; Dinh, Christoph

2018-06-01

Magnetoencephalography (MEG) and Electroencephalography (EEG) are noninvasive techniques to study the electrophysiological activity of the human brain. Thus, they are well suited for real-time monitoring and analysis of neuronal activity. Real-time MEG/EEG data processing allows adjustment of the stimuli to the subject's responses for optimizing the acquired information especially by providing dynamically changing displays to enable neurofeedback. We introduce MNE Scan, an acquisition and real-time analysis software based on the multipurpose software library MNE-CPP. MNE Scan allows the development and application of acquisition and novel real-time processing methods in both research and clinical studies. The MNE Scan development follows a strict software engineering process to enable approvals required for clinical software. We tested the performance of MNE Scan in several device-independent use cases, including, a clinical epilepsy study, real-time source estimation, and Brain Computer Interface (BCI) application. Compared to existing tools we propose a modular software considering clinical software requirements expected by certification authorities. At the same time the software is extendable and freely accessible. We conclude that MNE Scan is the first step in creating a device-independent open-source software to facilitate the transition from basic neuroscience research to both applied sciences and clinical applications. Copyright © 2018 Elsevier B.V. All rights reserved.

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...

A miniaturised laser ablation/ionisation analyser for investigation of elemental/isotopic composition with the sub-ppm detection sensitivity

NASA Astrophysics Data System (ADS)

Tulej, M.; Riedo, A.; Meyer, S.; Iakovleva, M.; Neuland, M.; Wurz, P.

2012-04-01

Detailed knowledge of the elemental and isotopic composition of solar system objects imposes critical constraints on models describing the origin of our solar system and can provide insight to chemical and physical processes taking place during the planetary evolution. So far, the investigation of chemical composition of planetary surfaces could be conducted almost exclusively by remotely controlled spectroscopic instruments from orbiting spacecraft, landers or rovers. With some exceptions, the sensitivity of these techniques is, however, limited and often only abundant elements can be investigated. Nevertheless, the spectroscopic techniques proved to be successful for global chemical mapping of entire planetary objects such as the Moon, Mars and asteroids. A combined afford of the measurements from orbit, landers and rovers can also yield the determination of local mineralogy. New instruments including Laser Induced Breakdown Spectroscopy (LIBS) and Laser Ablation/Ionisation Mass Spectrometer (LIMS), have been recently included for several landed missions. LIBS is thought to improve flexibility of the investigations and offers a well localised chemical probing from distances up to 10-13 m. Since LIMS is a mass spectrometric technique it allows for very sensitive measurements of elements and isotopes. We will demonstrate the results of the current performance tests obtained by application of a miniaturised laser ablation/ionisation mass spectrometer, a LIMS instrument, developed in Bern for the chemical analysis of solids. So far, the only LIMS instrument on a spacecraft is the LAZMA instrument. This spectrometer was a part of the payload for PHOBOS-GRUNT mission and is also currently selected for LUNA-RESURCE and LUNA-GLOB missions to the lunar south poles (Managadze et al., 2011). Our LIMS instrument has the dimensions of 120 x Ø60 mm and with a weight of about 1.5 kg (all electronics included), it is the lightest mass analyser designed for in situ chemical analysis of solid materials on the planetary surfaces (Rohner et al., 2003). Initial laboratory tests that were conducted with an IR laser radiation for the ablation, atomisation and ionisation of the material, indicated a high performance of the instrument in terms of sensitivity, dynamic range and mass resolution (Tulej et al., 2011). After some technical improvements and implementation of a computer-controlled performance optimiser we have achieved further improvements of both, the instrumental sensitivity down to sub-ppm level and reproducibility of the measurements. We will demonstrate the potential of the mass analyser to perform the quantitative elemental analysis of solids with a spatial (vertical, lateral) resolution commensurate with typical grain sizes, and its capabilities for investigation of isotopic patterns with accuracy and precision comparable to that of large analytical laboratory instruments, e.g., TIMS, SIMS, LA-ICP-MS. The results can be of considerable interest for in situ dating or investigation of other fine isotopic fractionation effects including studies of bio-markers.

Recollections of Stanley Mandelstam

NASA Astrophysics Data System (ADS)

Chew, Geoffrey

2017-01-01

This article is based upon the audio recording taken on September 9th 2016 by my children. I thank Chee Hok Lim for writing the first transcript in the World Scientific format and Ling-Lie Chau for comments and footnotes.

78 FR 13342 - Ocean Transportation Intermediary License Applicants

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

... License. Air Sea Land Shipping & Moving Inc. (NVO & OFF), 211 East 43rd Street, Suite 1206, New York, NY...), 11205 S. La Cienega Blvd.,Los Angeles, CA 90045. Officers: Kirk Kim, Secretary (QI), Woo B. Lim...

Out of l'Hopital Clutches: An Example

ERIC Educational Resources Information Center

Dobos, Jozef

2008-01-01

How to establish the limit lim[subscript x[right arrow]0](x minus sin x) divided by (x[superscript 3]) before learning about l'Hopital rule? The aim of this note is to answer this very reasonable question.

The role of molecular hydrogen and methane oxidation in the water vapour budget of the stratosphere

NASA Technical Reports Server (NTRS)

Le Texier, H.; Solomon, S.; Garcia, R. R.

1988-01-01

The detailed photochemistry of methane oxidation has been studied in a coupled chemical/dynamical model of the middle atmosphere. The photochemistry of formaldehyde plays an important role in determining the production of water vapor from methane oxidation. At high latitudes, the production and transport of molecular hydrogen is particularly important in determining the water vapor distribution. It is shown that the ratio of the methane vertical gradient to the water vapor vertical gradient at any particular latitude should not be expected to be precisely 2, due both to photochemical and dynamical effects. Modeled H2O profiles are compared with measurements from the Limb Infrared Monitor of the Stratosphere (LIMS) experiment at various latitudes. Molecular hydrogen is shown to be responsible for the formation of a secondary maximum displayed by the model water vapor profiles in high latitude summer, a feature also found in the LIMS data.

Numerical calculation of primary slot leakage inductance of a Single-sided HTS linear induction motor used for linear metro

NASA Astrophysics Data System (ADS)

Li, Dong; Wen, Yinghong; Li, Weili; Fang, Jin; Cao, Junci; Zhang, Xiaochen; Lv, Gang

2017-03-01

In the paper, the numerical method calculating asymmetric primary slot leakage inductances of Single-sided High-Temperature Superconducting (HTS) Linear Induction Motor (HTS LIM) is presented. The mathematical and geometric models of three-dimensional nonlinear transient electromagnetic field are established and the boundary conditions are also given. The established model is solved by time-stepping Finite Element Method (FEM). Then, the three-phase asymmetric primary slot leakage inductances under different operation conditions are calculated by using the obtained electromagnetic field distribution. The influences of the special effects such as longitudinal end effects, transversal edge effects, etc. on the primary slot leakage inductance are investigated. The presented numerical method is validated by experiments carried out on a 3.5 kW prototype with copper wires which has the same structures with the HTS LIM.

Comparisons between designs for single-sided linear electric motors: Homopolar synchronous and induction

NASA Astrophysics Data System (ADS)

Nondahl, T. A.; Richter, E.

1980-09-01

A design study of two types of single sided (with a passive rail) linear electric machine designs, namely homopolar linear synchronous machines (LSM's) and linear induction machines (LIM's), is described. It is assumed the machines provide tractive effort for several types of light rail vehicles and locomotives. These vehicles are wheel supported and require tractive powers ranging from 200 kW to 3735 kW and top speeds ranging from 112 km/hr to 400 km/hr. All designs are made according to specified magnetic and thermal criteria. The LSM advantages are a higher power factor, much greater restoring forces for track misalignments, and less track heating. The LIM advantages are no need to synchronize the excitation frequency precisely to vehicle speed, simpler machine construction, and a more easily anchored track structure. The relative weights of the two machine types vary with excitation frequency and speed; low frequencies and low speeds favor the LSM.

A regulatory network to segregate the identity of neuronal subtypes.

PubMed

Lee, Seunghee; Lee, Bora; Joshi, Kaumudi; Pfaff, Samuel L; Lee, Jae W; Lee, Soo-Kyung

2008-06-01

Spinal motor neurons (MNs) and V2 interneurons (V2-INs) are specified by two related LIM-complexes, MN-hexamer and V2-tetramer, respectively. Here we show how multiple parallel and complementary feedback loops are integrated to assign these two cell fates accurately. While MN-hexamer response elements (REs) are specific to MN-hexamer, V2-tetramer-REs can bind both LIM-complexes. In embryonic MNs, however, two factors cooperatively suppress the aberrant activation of V2-tetramer-REs. First, LMO4 blocks V2-tetramer assembly. Second, MN-hexamer induces a repressor, Hb9, which binds V2-tetramer-REs and suppresses their activation. V2-INs use a similar approach; V2-tetramer induces a repressor, Chx10, which binds MN-hexamer-REs and blocks their activation. Thus, our study uncovers a regulatory network to segregate related cell fates, which involves reciprocal feedforward gene regulatory loops.

T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

PubMed Central

Monnier, Stéphanie; Cox, David G; Albion, Tim; Canzian, Federico

2005-01-01

Background Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS. PMID:16221298

The effect of cation doping on spinel LiMn 2O 4: a first-principles investigation

NASA Astrophysics Data System (ADS)

Shi, Siqi; Ouyang, Chuying; Wang, Ding-sheng; Chen, Liquan; Huang, Xuejie

2003-05-01

The effect of the cation doping on the electronic structure of spinel LiM yMn 2- yO 4 (M=Cr, Mn, Fe, Co and Ni) has been calculated by first-principles. Our calculation shows that new M-3d bands emerge in the density of states compared with that in LiMn 2O 4. Simultaneously, the new O-2p bands appear accordingly in almost the same energy range around the Fermi energy owing to the M-3d/O-2p interaction. It is found that the appearance of new O-2p bands in the lower energy position results in a higher intercalation voltage. Consequently, the origin of higher intercalation voltage in LiM yMn 2- yO 4 can be ascribed to the lower O-2p level introduced by the doping cation M.

Polar stratospheric clouds inferred from satellite data

NASA Technical Reports Server (NTRS)

Austin, J.; Jones, R. L.; Remsberg, E. E.; Tuck, A. F.

1986-01-01

Anomalously high radiances from the ozone channel of the Limb Infrared Monitor of the Stratosphere (LIMS) sounding instrument have been observed in the Northern Hemisphere winter lower stratosphere. Such events, thought to be due to polar stratospheric clouds (PSCs), are examined further by computing relative humidities using Stratospheric Sounding Unit temperatures and water vapor measurements from the LIMS Map Archive Tape analyses. Regions identified as PSCs are found to correspond closely to regions of high humidity. While instances of saturation were found, the average humidity at the centers of 39 PSCs was calculated to be 58 percent. Possible reasons for this apparent discrepancy are discussed. Applying a similar approach to the Southern Hemisphere, in 1979, virtually no PSCs are found in the vortex after September 10 at 20 km. This result has important implications for a number of proposed explanations for the Antarctic ozone hole.

The stratified syncytium of the vertebrate lens.

PubMed

Shi, Yanrong; Barton, Kelly; De Maria, Alicia; Petrash, J Mark; Shiels, Alan; Bassnett, Steven

2009-05-15

The fusion of cells to generate syncytial tissues is a crucial event in the development of many organisms. In the lens of the vertebrate eye, proteins and other macromolecules diffuse from cell to cell via the large molecule diffusion pathway (LMDP). We used the tamoxifen-induced expression of GFP to investigate the nature and role of the LMDP in living, intact lenses. Our data indicate that the LMPD preferentially connects cells lying within a stratum of the lens cortex and that formation of the LMPD depends on the expression of Lim2, a claudin-like molecule. The conduits for intercellular protein exchange are most likely regions of partial cellular fusion, which are commonly observed in wild-type lenses but rare or absent in Lim2-deficient lenses. The observation that lens tissue constitutes a stratified syncytium has implications for the transparency, refractive function and pathophysiology of the tissue.

Kinetic-energy release distributions of fragment anions from collisions of potassium atoms with D-Ribose and tetrahydrofuran*

NASA Astrophysics Data System (ADS)

Rebelo, André; Cunha, Tiago; Mendes, Mónica; da Silva, Filipe Ferreira; García, Gustavo; Limão-Vieira, Paulo

2016-06-01

Kinetic-energy release distributions have been obtained from the width and shapes of the time-of-flight (TOF) negative ion mass peaks formed in collisions of fast potassium atoms with D-Ribose (DR) and tetrahydrofuran (THF) molecules. Recent dissociative ion-pair formation experiments yielding anion formation have shown that the dominant fragment from D-Ribose is OH- [D. Almeida, F. Ferreira da Silva, G. García, P. Limão-Vieira, J. Chem. Phys. 139, 114304 (2013)] whereas in the case of THF is O- [D. Almeida, F. Ferreira da Silva, S. Eden, G. García, P. Limão-Vieira, J. Phys. Chem. A 118, 690 (2014)]. The results for DR and THF show an energy distribution profile reminiscent of statistical degradation via vibrational excitation and partly due to direct transformation of the excess energy in translational energy.

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.

Overexpression of Lhx2 suppresses proliferation of human T cell acute lymphoblastic leukemia-derived cells, partly by reducing LMO2 protein levels.

PubMed

Miyashita, Kazuya; Kitajima, Kenji; Goyama, Susumu; Kitamura, Toshio; Hara, Takahiko

2018-01-15

T cell acute lymphoblastic leukemia (T-ALL) is a malignant cancer with poor prognosis. The transcriptional co-factor LIM domain only 2 (LMO2) and its target gene HHEX are essential for self-renewal of T cell precursors and T-ALL etiology. LMO2 directly associates with LDB1 in a large DNA-containing nuclear complex and controls the transcription of T-ALL-related genes. Recently, we reported that overexpression of the LIM-homeodomain transcription factor, Lhx2, results in liberation of the Lmo2 protein from the Lmo2-Ldb1 complex, followed by ubiquitin proteasome mediated degradation. Here, we found that proliferation of five human T-ALL-derived cell lines, including CCRF-CEM, was significantly suppressed by retroviral overexpression of Lhx2. The majority of Lhx2-transduced CCRF-CEM cells arrested in G 0 phase and subsequently underwent apoptosis. Expression of LMO2 protein as well as HHEX, ERG, HES1 and MYC genes was repressed in CCRF-CEM cells by transduction with Lhx2. Lhx2-mediated growth inhibition was partially rescued by simultaneous overexpression of Lmo2; however, both the C-terminal LIM domain and the homeodomain of Lhx2 were required for its growth-suppressive activity. These data indicate that Lhx2 is capable of blocking proliferation of T-ALL-derived cells by both LMO2-dependent and -independent means. We propose Lhx2 as a new molecular tool for anti-T-ALL drug development. Copyright © 2017 Elsevier Inc. All rights reserved.

Water-Soluble Lignins from Different Bioenergy Crops Stimulate the Early Development of Maize (Zea mays, L.).

PubMed

Savy, Davide; Cozzolino, Vincenza; Vinci, Giovanni; Nebbioso, Antonio; Piccolo, Alessandro

2015-11-05

The molecular composition of water-soluble lignins isolated from four non-food bioenergy crops (cardoon CAR, eucalyptus EUC, and two black poplars RIP and LIM) was characterized in detail, and their potential bioactivity towards maize germination and early growth evaluated. Lignins were found to not affect seed germination rates, but stimulated the maize seedling development, though to a different extent. RIP promoted root elongation, while CAR only stimulated the length of lateral seminal roots and coleoptile, and LIM improved only the coleoptile development. The most significant bioactivity of CAR was related to its large content of aliphatic OH groups, C-O carbons and lowest hydrophobicity, as assessed by (31)P-NMR and (13)C-CPMAS-NMR spectroscopies. Less bioactive RIP and LIM lignins were similar in composition, but their stimulation of maize seedling was different. This was accounted to their diverse content of aliphatic OH groups and S- and G-type molecules. The poorest bioactivity of the EUC lignin was attributed to its smallest content of aliphatic OH groups and largest hydrophobicity. Both these features may be conducive of a EUC conformational structure tight enough to prevent its alteration by organic acids exuded from vegetal tissues. Conversely the more labile conformational arrangements of the other more hydrophilic lignin extracts promoted their bioactivity by releasing biologically active molecules upon the action of exuded organic acids. Our findings indicate that water-soluble lignins from non-food crops may be effectively used as plant biostimulants, thus contributing to increase the economic and ecological liability of bio-based industries.

A New Dimensionless Number for Redox Conditions within the Hyporheic Zone: Morphological and Biogeochemical Controls

NASA Astrophysics Data System (ADS)

Marzadri, A.; Tonina, D.; Bellin, A.

2012-12-01

We introduce a new Damköhler number, Da, to quantify the biogeochemical status of the hyporheic zone and to upscale local hyporheic processes to reach scale. Da is defined as the ratio between the median hyporheic residence time, τup,50, which is a representative time scale of the hyporheic flow, and a representative time scale of biogeochemical reactions, which we define as the time τlim needed to consume dissolved oxygen to a prescribed threshold concentration below which reducing reactions are activated: Da = τup,50/τlim. This approach accounts for streambed topography and surface hydraulics via the hyporheic residence time and biogeochemical reaction via the time limit τlim. Da can readily evaluate the redox status of the hyporheic zone. Values of Da larger than 1 indicate prevailing anaerobic conditions, whereas values smaller than 1 prevailing aerobic conditions. This new Damköhler number can quantify the efficiency of hyporheic zone in transforming dissolved inorganic nitrogen species such as ammonium and nitrate, whose transformation depends on the redox condition of the hyporheic zone. We define a particular value of Da, Das, that indicates when the hyporheic zone is a source or a sink of nitrate. This index depends only on the relative abundance of ammonium and nitrate. The approach can be applied to any hyporheic zone of which the median hyporheic residence time is known. Application to streams with pool-riffle morphology shows that Da increases passing from small to large streams implying that the fraction of the hyporheic zone in anaerobic conditions increases with stream size.

Probability distributions of linear statistics in chaotic cavities and associated phase transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vivo, Pierpaolo; Majumdar, Satya N.; Bohigas, Oriol

2010-03-01

We establish large deviation formulas for linear statistics on the N transmission eigenvalues (T{sub i}) of a chaotic cavity, in the framework of random matrix theory. Given any linear statistics of interest A=SIGMA{sub i=1}{sup N}a(T{sub i}), the probability distribution P{sub A}(A,N) of A generically satisfies the large deviation formula lim{sub N-}>{sub i}nfinity[-2 log P{sub A}(Nx,N)/betaN{sup 2}]=PSI{sub A}(x), where PSI{sub A}(x) is a rate function that we compute explicitly in many cases (conductance, shot noise, and moments) and beta corresponds to different symmetry classes. Using these large deviation expressions, it is possible to recover easily known results and to produce newmore » formulas, such as a closed form expression for v(n)=lim{sub N-}>{sub i}nfinity var(T{sub n}) (where T{sub n}=SIGMA{sub i}T{sub i}{sup n}) for arbitrary integer n. The universal limit v*=lim{sub n-}>{sub i}nfinity v(n)=1/2pibeta is also computed exactly. The distributions display a central Gaussian region flanked on both sides by non-Gaussian tails. At the junction of the two regimes, weakly nonanalytical points appear, a direct consequence of phase transitions in an associated Coulomb gas problem. Numerical checks are also provided, which are in full agreement with our asymptotic results in both real and Laplace space even for moderately small N. Part of the results have been announced by Vivo et al. [Phys. Rev. Lett. 101, 216809 (2008)].« less

Interannual to Decadal SST Variability in the Tropical Indian Ocean

NASA Astrophysics Data System (ADS)

Wang, G.; Newman, M.; Han, W.

2017-12-01

The Indian Ocean has received increasing attention in recent years for its large impacts on regional and global climate. However, due mainly to the close interdependence of the climate variation within the Tropical Pacific and the Indian Ocean, the internal sea surface temperature (SST) variability within the Indian Ocean has not been studied extensively on longer time scales. In this presentation we will show analysis of the interannual to decadal SST variability in the Tropical Indian Ocean in observations and Linear Inverse Model (LIM) results. We also compare the decoupled Indian Ocean SST variability from the Pacific against fully coupled one based on LIM integrations, to test the factors influence the features of the leading SST modes in the Indian Ocean. The result shows the Indian Ocean Basin (IOB) mode, which is strongly related to global averaged SST variability, passively responses to the Pacific variation. Without tropical Indo-Pacific coupling interaction, the intensity of IOB significantly decreases by 80%. The Indian Ocean Dipole (IOD) mode demonstrates its independence from the Pacific SST variability since the IOD does not change its long-term characteristics at all without inter-basin interactions. The overall SSTA variance decreases significantly in the Tropical Indian Ocean in the coupling restricted LIM runs, especially when the one-way impact from the Pacific to the Indian Ocean is turned off, suggesting that most of the variability in the Indian Ocean comes from the Pacific influence. On the other hand, the Indian Ocean could also transport anomalies to the Pacific, making the interaction a complete two-way process.

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.

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.

Study of linear induction motor characteristics : the Oberretl model

DOT National Transportation Integrated Search

1975-05-30

The Oberretl theory of the double-sided linear induction motor (LIM) is examined, starting with the idealized model and accompanying assumptions, and ending with relations for predicted thrust, airgap power, and motor efficiency. The effect of varyin...

Gastric Bypass Surgery: Who Is It For?

MedlinePlus

... you, talk with your doctor. Lim RB. Bariatric operations for management of obesity: Indications and preoperative preparation. https://www. ... https://www.niddk.nih.gov/health-information/weight-management/bariatric-surgery. Accessed July 12, 2017. Sogg S, et al. Recommendations ...

Inhaled Corticosteroids (ICSs) and Pregnancy

MedlinePlus

... malformations after the use of inhaled budesonide in early pregnancy. Obstet Gynecol 93(3):392-395. Lim AS, et al. 2011. Management of asthma in pregnant women by general practitioners: A cross sectional survey BMC Family Practice 12:121 Namazy J, et ...

Annual Report 2005

DTIC Science & Technology

2005-01-01

Program Integration PROJECT LEADERS: Bernard Rostker and Laura Miller 20 RAND National Security Research Division The more intensive use of the...Lim, Laura Werber Castaneda, Daniela Golinelli. MG-196-OSD. NOTE: MG stands for monograph; CF for confer- ence proceedings; CT for congressional

Dimensionless Numbers For Morphological, Thermal And Biogeochemical Controls Of Hyporheic Processes

NASA Astrophysics Data System (ADS)

Bellin, Alberto; Marzadri, Alessandra; Tonina, Daniele

2013-04-01

Transport of solutes and heat within the hyporheic zone are interface processes that gained growing attention in the last decade, when several modelling strategies have been proposed, mainly at the local or reach scale. We propose to upscale local hyporheic biogeochemical processes to reach and network scales by means of a Lagrangian modelling framework, which allows to consider the impact of the flow structure on the processes modelled. This analysis shows that geochemical processes can be parametrized through two new Damköhler numbers, DaO, and DaT. DaO = ?up,50-?lim is defined as the ratio between the median hyporheic residence time, ?up,50 and the time of consuming dissolved oxygen to a prescribed threshold concentration, ?lim, below which reductive reactions are activated. It quantifies the biogeochemical status of the hyporheic zone and could be a metric for upscaling local hyporheic biogeochemical processes to reach and river-network scale processes. In addition, ?up,50 is the time scale of hyporheic advection; while ?lim is the representative time scale of biogeochemical reactions and indicates the distance along the streamline, measured as the time needed to travel that distance, that a particle of water travels before the dissolved oxygen concentration declines to [DO]lim, the value at which denitrification is activated. We show that DaO is representative of the redox status and indicates whether the hyporheic zone is a source or a sink of nitrate. Values of DaO larger than 1 indicate prevailing anaerobic conditions, whereas values smaller than 1 prevailing aerobic conditions. Similarly, DaT quantifies the importance of the temperature daily oscillations of the stream water on the hyporheic environment. It is defined as the ratio between ?up,50, and the time limit at which the ratio between the amplitude of the temperature oscillation within the hyporheic zone (evaluated along the streamline) and in the stream water is smaller than e-1. We show that values of DaT > 1 indicate a thermally stable hyporheic zone, where organism metabolism is not influenced by surface water thermal oscillations and biogeochemical reaction rates depend on the mean daily stream water temperature. Values smaller than 1 suggest that organisms need to adapt to the daily thermal variations and biogeochemical reaction rates will depend on the daily fluctuations induced by stream water.

The nature of the bone-implant interface. The lessons learned from implant retrieval and analysis in man and experimental animal.

PubMed

Boss, J H; Shajrawi, I; Mendes, D G

1994-01-01

The morphological appearances of the interface between the bone and the components of arthroplasties depend on multiple factors. Present-day biomaterials being biocompatible when in bulk form, a host reaction consequent upon untoward effects of the implants as such is not expected. Thus, osseointegration, i.e., the direct apposition of bone to the surface of a foreign material at the light microscopical level, occurs, under favorable biomechanical circumstances, irrespective of the chemical composition of the implant. Osseointegration is a multifaceted phenomenon. First and foremost, it evolves when an initially rigid fixation of the component is surgically attained. Interfacial motions are associated with resorption of the bony bed, macrophagic activation and production of wear particles, the close bone-implant apposition is lost and the formation of an interfacial membrane (IM) ensues. The histological features of the IM coincide with the context of its formation and evolution. The quiescent IM is composed of a thin layer of fibrous tissue and its occurrence is compatible with the biofunctionality of the implant. The aggressive or lytic IM (LIM) develops when tissue-irritating, small, irregularly shaped and edgy breakdown products are deposited at the interface. The thick LIM consists of an inflamed fibrous tissue, scattered within which are myriad granulomas, and its surface facing the implant displays a synovial-like aspect. The mono- and polykaryonic macrophages, constituting the granulomatous response, ingest and abut on the wear particles. Amongst the intermediary substances of inflammation elaborated by the lymphocytes and macrophages of the LIM, factors which stimulate the osteoclasts play the pivotal role in as much as progressive bone resorption is associated with progressive growth of the IM and, hence, with incremental interfacial motion, interfacial deposition of wear particles and inflammatory-granulomatous response. The ensuing vicious circle culminates in aseptic loosening of the arthroplasty. The morphological features of the LIM, though characterized by a stereotypical reaction pattern, are, in their details, closely linked with the nature of the diverse components of the composite joint replacement. The histological appearances of the bone-implant interface of stable and loose arthroplasties, the tissular reactions to polymethylmethacrylate, polyethylene, polyacetal, metals and hydroxyapatite as well as the characteristics of cemented and cementless porous-coated, press-fit and hydroxyapatite-coated prostheses are described.

Beneficial utilization of lime sludge for subgrade stabilization, a pilot study : executive summary report.

DOT National Transportation Integrated Search

2010-06-01

A global chemical stabilization design is recently : adopted by the Ohio Department of Transportation : (ODOT). This produces performance and economic : benefits in providing pavement with a rugged base : supporting. Given the large quantities of lim...

Beneficial Utilization of Lime Sludge for Subgrade Stabilization : a Pilot study : Executive Summary Report

DOT National Transportation Integrated Search

2010-06-01

A global chemical stabilization design is recently : adopted by the Ohio Department of Transportation : (ODOT). This produces performance and economic : benefits in providing pavement with a rugged base : supporting. Given the large quantities of lim...

Infrared heating

USDA-ARS?s Scientific Manuscript database

IR heating was first industrially used in the 1930s for automotive curing applications and rapidly became a widely applied technology in the manufacturing industry. Contrarily, a slower pace in the development of IR technologies for processing foods and agricultural products was observed, due to lim...

Laboratory investigation of hydrated lime as an antistripping additive : final report.

DOT National Transportation Integrated Search

1983-01-01

The purpose of this laboratory study was to determine the effectiveness of hydrated lime as an antistripping additive when used in bituminous mixes incorporating aggregates frequently used in such mixes in Virginia. The application of 1% hydrated lim...

Progress in increasing electronic reporting of laboratory results to public health agencies--United States, 2013.

PubMed

2013-09-27

Electronic reporting of laboratory results to public health agencies can improve public health surveillance for reportable diseases and conditions by making reporting more timely and complete. Since 2010, CDC has provided funding to 57 state, local, and territorial health departments through the Epidemiology and Laboratory Capacity for Infectious Diseases cooperative agreement to assist with improving electronic laboratory reporting (ELR) from clinical and public health laboratories to public health agencies. As part of this agreement, CDC and state and large local health departments are collaborating to monitor ELR implementation in the United States by developing data from each jurisdiction regarding total reporting laboratories, laboratories sending ELR by disease category and message format, and the number of ELR laboratory reports compared with the total number of laboratory reports. At the end of July 2013, 54 of the 57 jurisdictions were receiving at least some laboratory reports through ELR, and approximately 62% of 20 million laboratory reports were being received electronically, compared with 54% in 2012. Continued progress will require collaboration between clinical laboratories, laboratory information management system (LIMS) vendors, and public health agencies.

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics

PubMed Central

Ramirez-Gonzalez, Ricardo H.; Leggett, Richard M.; Waite, Darren; Thanki, Anil; Drou, Nizar; Caccamo, Mario; Davey, Robert

2014-01-01

Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages. PMID:24627795

Evaluation of linear induction motor characteristics : the Yamamura model

DOT National Transportation Integrated Search

1975-04-30

The Yamamura theory of the double-sided linear induction motor (LIM) excited by a constant current source is discussed in some detail. The report begins with a derivation of thrust and airgap power using the method of vector potentials and theorem of...

IFLA General Conference, 1986. Bibliographic Control Division. Section: Bibliography. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations and Institutions, The Hague (Netherlands).

Papers on bibliographic control presented at the 1986 International Federation of Library Associations (IFLA) conference include: (1) "Bibliographic Interchange/Coordination in Southeast Asia (Huck Tee Lim, Malaysia); (2) "Project for 'Chinese National Bibliography' and Its Progress" (Huang Jungui, China); (3) "Subject…

Information Management Systems in the Undergraduate Instrumental Analysis Laboratory.

ERIC Educational Resources Information Center

Merrer, Robert J.

1985-01-01

Discusses two applications of Laboratory Information Management Systems (LIMS) in the undergraduate laboratory. They are the coulometric titration of thiosulfate with electrogenerated triiodide ion and the atomic absorption determination of calcium using both analytical calibration curve and standard addition methods. (JN)

Double bifurcation optimization stent system technique for left main stenosis.

PubMed

Vassilev, D; Mateev, H; Alexandrov, A; Karamfiloff, K; Gil, R J

2014-12-01

We present a first-in-man case with implantation in culottes' fashion of two dedicated coronary bifurcation stents (BiOSS Lim) in distal left main stenosis. The immediate procedural and very short-term result was excellent. © 2014, Wiley Periodicals, Inc.

65 mph speed limit : analysis of fatal accident injury severity

DOT National Transportation Integrated Search

1989-11-01

Several studies of the fatality experience in the 38 states that implemented a65 mph speed : limit on Rural Interstate highways in 1987 concluded that the higher speed limit has : caused fatalities to increase. This relationship between the speed lim...

Secondary organic aerosol formation by limonene ozonolysis: Parameterizing multi-generational chemistry in ozone- and residence time-limited indoor environments

NASA Astrophysics Data System (ADS)

Waring, Michael S.

2016-11-01

Terpene ozonolysis reactions can be a strong source of secondary organic aerosol (SOA) indoors. SOA formation can be parameterized and predicted using the aerosol mass fraction (AMF), also known as the SOA yield, which quantifies the mass ratio of generated SOA to oxidized terpene. Limonene is a monoterpene that is at sufficient concentrations such that it reacts meaningfully with ozone indoors. It has two unsaturated bonds, and the magnitude of the limonene ozonolysis AMF varies by a factor of ∼4 depending on whether one or both of its unsaturated bonds are ozonated, which depends on whether ozone is in excess compared to limonene as well as the available time for reactions indoors. Hence, this study developed a framework to predict the limonene AMF as a function of the ozone [O3] and limonene [lim] concentrations and the air exchange rate (AER, h-1), which is the inverse of the residence time. Empirical AMF data were used to calculate a mixing coefficient, β, that would yield a 'resultant AMF' as the combination of the AMFs due to ozonolysis of one or both of limonene's unsaturated bonds, within the volatility basis set (VBS) organic aerosol framework. Then, β was regressed against predictors of log10([O3]/[lim]) and AER (R2 = 0.74). The β increased as the log10([O3]/[lim]) increased and as AER decreased, having the physical meaning of driving the resultant AMF to the upper AMF condition when both unsaturated bonds of limonene are ozonated. Modeling demonstrates that using the correct resultant AMF to simulate SOA formation owing to limonene ozonolysis is crucial for accurate indoor prediction.

Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption.

PubMed

Hadzic, Ermin; Catillon, Marie; Halavatyi, Aliaksandr; Medves, Sandrine; Van Troys, Marleen; Moes, Michèle; Baird, Michelle A; Davidson, Michael W; Schaffner-Reckinger, Elisabeth; Ampe, Christophe; Friederich, Evelyne

2015-01-01

Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading.

Enigma interacts with adaptor protein with PH and SH2 domains to control insulin-induced actin cytoskeleton remodeling and glucose transporter 4 translocation.

PubMed

Barrès, Romain; Grémeaux, Thierry; Gual, Philippe; Gonzalez, Teresa; Gugenheim, Jean; Tran, Albert; Le Marchand-Brustel, Yannick; Tanti, Jean-François

2006-11-01

APS (adaptor protein with PH and SH2 domains) initiates a phosphatidylinositol 3-kinase-independent pathway involved in insulin-stimulated glucose transport. We recently identified Enigma, a PDZ and LIM domain-containing protein, as a partner of APS and showed that APS-Enigma complex plays a critical role in actin cytoskeleton organization in fibroblastic cells. Because actin rearrangement is important for insulin-induced glucose transporter 4 (Glut 4) translocation, we studied the potential involvement of Enigma in insulin-induced glucose transport in 3T3-L1 adipocytes. Enigma mRNA was expressed in differentiated adipocytes and APS and Enigma were colocalized with cortical actin. Expression of an APS mutant unable to bind Enigma increased the insulin-induced Glut 4 translocation to the plasma membrane. By contrast, overexpression of Enigma inhibited insulin-stimulated glucose transport and Glut 4 translocation without alterations in proximal insulin signaling. This inhibitory effect was prevented with the deletion of the LIM domains of Enigma. Using time-lapse fluorescent microscopy of green fluorescent protein-actin, we demonstrated that the overexpression of Enigma altered insulin-induced actin rearrangements, whereas the expression of Enigma without its LIM domains was without effect. A physiological link between increased expression of Enigma and an alteration in insulin-induced glucose uptake was suggested by the increase in Enigma mRNA expression in adipose tissue of diabetic obese patients. Taken together, these data strongly suggest that the interaction between APS and Enigma is involved in insulin-induced Glut 4 translocation by regulating cortical actin remodeling and raise the possibility that modification of APS/Enigma ratio could participate in the alteration of insulin-induced glucose uptake in adipose tissue.

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

Effects of day-time exposure to different light intensities on light-induced melatonin suppression at night.

PubMed

Kozaki, Tomoaki; Kubokawa, Ayaka; Taketomi, Ryunosuke; Hatae, Keisuke

2015-07-04

Bright nocturnal light has been known to suppress melatonin secretion. However, bright light exposure during the day-time might reduce light-induced melatonin suppression (LIMS) at night. The effective proportion of day-time light to night-time light is unclear; however, only a few studies on accurately controlling both day- and night-time conditions have been conducted. This study aims to evaluate the effect of different day-time light intensities on LIMS. Twelve male subjects between the ages of 19 and 23 years (mean ± S.D., 20.8 ± 1.1) gave informed consent to participate in this study. They were exposed to various light conditions (<10, 100, 300, 900 and 2700 lx) between the hours of 09:00 and 12:00 (day-time light conditions). They were then exposed to bright light (300 lx) again between 01:00 and 02:30 (night-time light exposure). They provided saliva samples before (00:55) and after night-time light exposure (02:30). A one-tailed paired t test yielded significant decrements of melatonin concentration after night-time light exposure under day-time dim, 100- and 300-lx light conditions. No significant differences exist in melatonin concentration between pre- and post-night-time light exposure under day-time 900- and 2700-lx light conditions. Present findings suggest the amount of light exposure needed to prevent LIMS caused by ordinary nocturnal light in individuals who have a general life rhythm (sleep/wake schedule). These findings may be useful in implementing artificial light environments for humans in, for example, hospitals and underground shopping malls.

High and escalating levels of cocaine intake are dissociable from subsequent incentive motivation for the drug in rats.

PubMed

Allain, Florence; Bouayad-Gervais, Karim; Samaha, Anne-Noël

2018-01-01

Taking high and increasing amounts of cocaine is thought to be necessary for the development of addiction. Consequently, a widely used animal model of drug self-administration involves giving animals continuous drug access during long sessions (LgA), as this produces high and escalating levels of intake. However, human cocaine addicts likely use the drug with an intermittent rather than continuous pattern, producing spiking brain cocaine levels. Using an intermittent-access (IntA) cocaine self-administration procedure in rats, we studied the relationship between escalation of cocaine intake and later incentive motivation for the drug, as measured by responding under a progressive ratio schedule of cocaine reinforcement. First, under IntA, rats escalated their cocaine use both within and between sessions. However, escalation did not predict later incentive motivation for the drug. Second, incentive motivation for cocaine was similar in IntA-rats limited to low- and non-escalating levels of drug intake (IntA-Lim) and in IntA-rats that took high and escalating levels of drug. Finally, IntA-Lim rats took much less cocaine than rats given continuous drug access during each self-administration session (LgA-rats). However, IntA-Lim rats later responded more for cocaine under a progressive ratio schedule of reinforcement. Taking large and escalating quantities of cocaine does not appear necessary to increase incentive motivation for the drug. Taking cocaine in an intermittent pattern-even in small amounts-is more effective in producing this addiction-relevant change. Thus, beyond the amount of drug taken, the temporal kinetics of drug use predict change in drug use over time.

Six weeks of aerobic training improves VO2max and MLSS but does not improve the time to fatigue at the MLSS.

PubMed

Mendes, Thiago Teixeira; Fonseca, Tatiana Ramos; Ramos, Guilherme Passos; Wilke, Carolina Franco; Cabido, Christian Emmanuel Torres; De Barros, Cristiano Lino Monteiro; Lima, André Maia; Mortimer, Lucas de Avila Carvalho Fleury; de Carvalho, Moisés Vieira; Teixeira, Mauro Martins; Lima, Nilo Resende Viana; Garcia, Emerson Silami

2013-04-01

The purpose of this study was to investigate the effects of a 6-week aerobic training period on the time to fatigue (t lim) during exercise performed at the maximal lactate steady state (MLSS). Thirteen untrained male subjects (TG; age 22.5 ± 2.4 years, body mass 72.9 ± 6.7 kg and VO2max 44.9 ± 4.8 mL kg(-1) min(-1)) performed a cycle ergometer test until fatigue at the MLSS power output before and after 6 weeks of aerobic training. A group of eight control subjects (CG; age 25.1 ± 2.4 years, body mass 70.1 ± 9.8 kg and VO2max 45.2 ± 4.1 mL kg(-1) min(-1)) also performed the two tests but did not train during the 6-week period. There were no differences between the groups with respect to the VO2max or MLSS power output (MLSSw) before the treatment period. The VO2max and the MLSSw of the TG increased by 11.2 ± 7.2 % (pre-treatment = 44.9 ± 4.8 vs. post-treatment = 49.8 ± 4.5 mL kg(-1) min(-1)) and 14.7 ± 8.9 % (pre-treatment = 150 ± 27 vs. post-treatment = 171 ± 26 W), respectively, after 6 weeks of training. The results of the CG were unchanged. There were no differences in t lim between the groups or within groups before and after training. Six weeks of aerobic training increases MLSSw and VO2max, but it does not alter the t lim at the MLSS.

The effects of two soft drinks on bond strength, bracket microleakage, and adhesive remnant on intact and sealed enamel.

PubMed

Navarro, Raúl; Vicente, Ascensión; Ortiz, Antonio J; Bravo, Luis A

2011-02-01

The purpose of this study was to evaluate the effects of Coca-Cola and Schweppes Limón on bond strength, adhesive remnant, and microleakage beneath brackets. One hundred and twenty upper central incisor brackets were bonded to bovine incisors and divided into three groups: (1) Control, (2) Coca-Cola, and (3) Schweppes Limón. The teeth were submerged in the drinks three times a day for 15 minutes over a 15 day period. Shear bond strength (SBS) was measured with a universal testing machine, and adhesive remnant evaluated using image analysis equipment. Microleakage at the enamel-adhesive and adhesive-bracket interfaces was determined using methylene blue. One hundred and eight teeth were used for scanning electron microscopy to determine the effect of the drinks on intact and sealed enamel. SBS and adhesive remnant data were analysed using the Kruskal-Wallis test (P < 0.05) and microleakage using the Kruskal-Wallis and Mann-Whitney tests applying Bonferroni correction (P < 0.017). No significant differences were found in SBS and adhesive remnant between the groups (P > 0.05). Microleakage at the enamel-adhesive interface for groups 2 and 3 was significantly greater than for group 1 (P < 0.017). At the adhesive-bracket interface, microleakage was significantly greater in group 2 than in group 1 (P < 0.017) while microleakage in group 3 did not differ significantly from either group 1 or 2 (P < 0.017). The drinks produced enamel erosion, loss of adhesive and microleakage. Coca-Cola and Schweppes Limón did not affect the SBS of brackets or the adhesive remnant.

Delineating the Tes Interaction Site in Zyxin and Studying Cellular Effects of Its Disruption

PubMed Central

Hadzic, Ermin; Catillon, Marie; Halavatyi, Aliaksandr; Medves, Sandrine; Van Troys, Marleen; Moes, Michèle; Baird, Michelle A.; Davidson, Michael W.; Schaffner-Reckinger, Elisabeth; Ampe, Christophe; Friederich, Evelyne

2015-01-01

Focal adhesions are integrin-based structures that link the actin cytoskeleton and the extracellular matrix. They play an important role in various cellular functions such as cell signaling, cell motility and cell shape. To ensure and fine tune these different cellular functions, adhesions are regulated by a large number of proteins. The LIM domain protein zyxin localizes to focal adhesions where it participates in the regulation of the actin cytoskeleton. Because of its interactions with a variety of binding partners, zyxin has been proposed to act as a molecular scaffold. Here, we studied the interaction of zyxin with such a partner: Tes. Similar to zyxin, Tes harbors three highly conserved LIM domains of which the LIM1 domain directly interacts with zyxin. Using different zyxin variants in pull-down assays and ectopic recruitment experiments, we identified the Tes binding site in zyxin and showed that four highly conserved amino acids are crucial for its interaction with Tes. Based upon these findings, we used a zyxin mutant defective in Tes-binding to assess the functional consequences of abrogating the zyxin-Tes interaction in focal adhesions. Performing fluorescence recovery after photobleaching, we showed that zyxin recruits Tes to focal adhesions and modulates its turnover in these structures. However, we also provide evidence for zyxin-independent localization of Tes to focal adhesions. Zyxin increases focal adhesion numbers and reduces focal adhesion lifetimes, but does so independent of Tes. Quantitative analysis showed that the loss of interaction between zyxin and Tes affects the process of cell spreading. We conclude that zyxin influences focal adhesion dynamics, that it recruits Tes and that this interaction is functional in regulating cell spreading. PMID:26509500

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann–Mangold organizer

PubMed Central

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-01-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann–Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer. PMID:22492356

Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer.

PubMed

Sudou, Norihiro; Yamamoto, Shinji; Ogino, Hajime; Taira, Masanori

2012-05-01

How multiple developmental cues are integrated on cis-regulatory modules (CRMs) for cell fate decisions remains uncertain. The Spemann-Mangold organizer in Xenopus embryos expresses the transcription factors Lim1/Lhx1, Otx2, Mix1, Siamois (Sia) and VegT. Reporter analyses using sperm nuclear transplantation and DNA injection showed that cerberus (cer) and goosecoid (gsc) are activated by the aforementioned transcription factors through CRMs conserved between X. laevis and X. tropicalis. ChIP-qPCR analysis for the five transcription factors revealed that cer and gsc CRMs are initially bound by both Sia and VegT at the late blastula stage, and subsequently bound by all five factors at the gastrula stage. At the neurula stage, only binding of Lim1 and Otx2 to the gsc CRM, among others, persists, which corresponds to their co-expression in the prechordal plate. Based on these data, together with detailed expression pattern analysis, we propose a new model of stepwise formation of the organizer, in which (1) maternal VegT and Wnt-induced Sia first bind to CRMs at the blastula stage; then (2) Nodal-inducible Lim1, Otx2, Mix1 and zygotic VegT are bound to CRMs in the dorsal endodermal and mesodermal regions where all these genes are co-expressed; and (3) these two regions are combined at the gastrula stage to form the organizer. Thus, the in vivo dynamics of multiple transcription factors highlight their roles in the initiation and maintenance of gene expression, and also reveal the stepwise integration of maternal, Nodal and Wnt signaling on CRMs of organizer genes to generate the organizer.

A distal modular enhancer complex acts to control pituitary- and nervous system-specific expression of the LHX3 regulatory gene.

PubMed

Mullen, Rachel D; Park, Soyoung; Rhodes, Simon J

2012-02-01

Lin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency.

A Distal Modular Enhancer Complex Acts to Control Pituitary- and Nervous System-Specific Expression of the LHX3 Regulatory Gene

PubMed Central

Mullen, Rachel D.; Park, Soyoung

2012-01-01

Lin-11, Isl-1, and Mec-3 (LIM)-homeodomain (HD)-class transcription factors are critical for many aspects of mammalian organogenesis. Of these, LHX3 is essential for pituitary gland and nervous system development. Pediatric patients with mutations in coding regions of the LHX3 gene have complex syndromes, including combined pituitary hormone deficiency and nervous system defects resulting in symptoms such as dwarfism, thyroid insufficiency, infertility, and developmental delay. The pathways underlying early pituitary development are poorly understood, and the mechanisms by which the LHX3 gene is regulated in vivo are not known. Using bioinformatic and transgenic mouse approaches, we show that multiple conserved enhancers downstream of the human LHX3 gene direct expression to the developing pituitary and spinal cord in a pattern consistent with endogenous LHX3 expression. Several transferable cis elements can individually guide nervous system expression. However, a single 180-bp minimal enhancer is sufficient to confer specific expression in the developing pituitary. Within this sequence, tandem binding sites recognized by the islet-1 (ISL1) LIM-HD protein are essential for enhancer activity in the pituitary and spine, and a pituitary homeobox 1 (PITX1) bicoid class HD element is required for spatial patterning in the developing pituitary. This study establishes ISL1 as a novel transcriptional regulator of LHX3 and describes a potential mechanism for regulation by PITX1. Moreover, these studies suggest models for analyses of the transcriptional pathways coordinating the expression of other LIM-HD genes and provide tools for the molecular analysis and genetic counseling of pediatric patients with combined pituitary hormone deficiency. PMID:22194342

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.

[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

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.

Modeling of Spatial and Temporal Dynamics in Biological Olfactory Systems

DTIC Science & Technology

2007-09-21

odorants were anisole, camphor , isoamyle acetate, and ilmonene, denoted by ANI, CAM, ISO, and LIM, respectively. The curve fitting resulted in the...much less dimensional connections to the mitral The investigated odorants were anisole (ANI), camphor (CAM), cells. The glomeruli are also highly

The Limb Infrared Monitor of the Stratosphere (LIMS) experiment

NASA Technical Reports Server (NTRS)

Russell, J. M.; Gille, J. C.

1978-01-01

The Limb Infrared Monitor of the Stratosphere is used to obtain vertical profiles and maps of temperature and the concentration of ozone, water vapor, nitrogen dioxide, and nitric acid for the region of the stratosphere bounded by the upper troposphere and the lower mesosphere.

Effective superelevation for large trucks on sharp curves and steep grades

DOT National Transportation Integrated Search

2002-10-01

This project was undertaken to identify the particular problems faced by trucks on sharp curves on steep grades, such as rebuilt switchback curves on mountainous two-lane, two-way roads and the high speed downgrade curves found on West Virginia's lim...

Conceptions of Islamic Education: Pedagogical Framings. Global Studies in Education. Volume 3

ERIC Educational Resources Information Center

Waghid, Yusef

2011-01-01

"Conceptions of Islamic Education: Pedagogical Framings" argues that "madaris" (Muslim schools) cannot exclusively be held responsible for the cultivation of extremism. Islamic education can most appropriately be framed according to three interrelated concepts: "tarbiyyah" (rearing or nurturing), "ta'lim"…

2D Larkin-Imry-Ma state of deformed ABM phase of superfluid 3He in ``ordered'' aerogel

NASA Astrophysics Data System (ADS)

Dmitriev, Vladimir; Senin, Andrey; Yudin, Alexey

2014-03-01

We report NMR studies of high temperature superfluid phase of 3He in so called ``ordered'' aerogel1 which strands are almost parallel to each other. Previously, it was found that the NMR properties of this phase depend on whether it is obtained on cooling from the normal phase or on warming from the low temperature phase2. These two types of high temperature phase (called as ESP1 and ESP2) correspond to Anderson-Brinkman-Morel (ABM) phase with large polar distortion and with orbital vector being in 2D Larkin-Imry-Ma (LIM) state. Here we present results which show that the observed difference in NMR signatures of the ESP1 and the ESP2 states is due to that the corresponding 2D LIM states can be anisotropic. In the ESP1 phase the anisotropy is absent or small, while in the ESP2 phase the anisotropy is large. NMR data have allowed us to estimate values of these anisotropies.

Morphological Comparison of U3O8 Ore Concentrates from Canada Key Lake and Namibia Sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwartz, Daniel S.; Tandon, Lav; Martinez, Patrick Thomas

Uranium ore concentrates from two different sources were examined using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The ore powders are referred to as Namibia (id. no. 90036, LIMS id. no. 18775) and Canada Key Lake (id. no. 90019, LIMS id. no. 18774). Earlier work identified the ores as the U₃O₈ phase of uranium oxide using x-ray diffraction. Both sets of powders were in the form of dark brown to black powder fines. However, the Canada Key Lake concentrates contained larger chunks of material on the millimeter scale that were easily visible to the unaided eye. The powdersmore » were mounted for SEM examination by hand dispersing a small amount onto conductive sticky tape. Two types of applicators were used and compared: a fine-tipped spatula and a foam-tipped applicator. The sticky tape was on a standard SEM “tee” mount, which was tapped to remove loose contamination before being inserted into the SEM.« less

Energetics of a strongly correlated Fermi gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Shina

2008-12-15

The energy of the two-component Fermi gas with the s-wave contact interaction is a simple linear functional of its momentum distribution: E{sub internal}=h{sup 2}{omega}C/4{pi}am+{sigma}{sub k{sigma}}(h{sup 2}k{sup 2}/2m)(n{sub k{sigma}}= -C/k{sup 4}) where the external potential energy is not included, a is the scattering length, {omega} is the volume, n{sub k{sigma}} is the average number of fermions with wave vector k and spin {sigma}, and C{identical_to}lim{sub k{yields}}{sub {infinity}}k{sup 4}n{sub k{up_arrow}}=lim{sub k{yields}}{sub {infinity}}k{sup 4}n{sub k{down_arrow}}. This result is a universal identity. Its proof is facilitated by a novel mathematical idea, which might be of utility in dealing with ultraviolet divergences in quantum fieldmore » theories. Other properties of this Fermi system, including pair correlations and the dimer-fermion scattering length, are also studied.« less

Device with Functions of Linear Motor and Non-contact Power Collector for Wireless Drive

NASA Astrophysics Data System (ADS)

Fujii, Nobuo; Mizuma, Tsuyoshi

The authors propose a new apparatus with functions of propulsion and non-contact power collection for a future vehicle which can run like an electric vehicle supplied from the onboard battery source in most of the root except near stations. The batteries or power-capacitors are non-contact charged from the winding connected with commercial power on ground in the stations etc. The apparatus has both functions of linear motor and transformer, and the basic configuration is a wound-secondary type linear induction motor (LIM). In the paper, the wound type LIM with the concentrated single-phase winding for the primary member on the ground is dealt from the viewpoint of low cost arrangement. The secondary winding is changed to the single-phase connection for zero thrust in the transformer operation, and the two-phase connection for the linear motor respectively. The change of connection is done by the special converter for charge and linear drive on board. The characteristics are studied analytically.

Matrix mechanics controls FHL2 movement to the nucleus to activate p21 expression

PubMed Central

Nakazawa, Naotaka; Sathe, Aneesh R.; Shivashankar, G. V.; Sheetz, Michael P.

2016-01-01

Substrate rigidity affects many physiological processes through mechanochemical signals from focal adhesion (FA) complexes that subsequently modulate gene expression. We find that shuttling of the LIM domain (domain discovered in the proteins, Lin11, Isl-1, and Mec-3) protein four-and-a-half LIM domains 2 (FHL2) between FAs and the nucleus depends on matrix mechanics. In particular, on soft surfaces or after the loss of force, FHL2 moves from FAs into the nucleus and concentrates at RNA polymerase (Pol) II sites, where it acts as a transcriptional cofactor, causing an increase in p21 gene expression that will inhibit growth on soft surfaces. At the molecular level, shuttling requires a specific tyrosine in FHL2, as well as phosphorylation by active FA kinase (FAK). Thus, we suggest that FHL2 phosphorylation by FAK is a critical, mechanically dependent step in signaling from soft matrices to the nucleus to inhibit cell proliferation by increasing p21 expression. PMID:27742790

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.

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 goniometric methods determines that the proposed software agrees sufficiently to be used interchangeably.

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.

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.

Nonoscillatory solutions for system of neutral dynamic equations on time scales.

PubMed

Chen, Zhanhe; Sun, Taixiang; Wang, Qi; Xi, Hongjian

2014-01-01

We will discuss nonoscillatory solutions to the n-dimensional functional system of neutral type dynamic equations on time scales. We will establish some sufficient conditions for nonoscillatory solutions with the property lim(t → ∞) x(i) (t) = 0, i = 1, 2,…, n.

Water-Soluble Nanodiamond (Postprint)

DTIC Science & Technology

2012-03-01

Lim, D.-S. Tribological behavior of PTFE film with nanodiamond. Surf. Coat. Technol. 2004, 188−189, 534−538. (9) Williams , O. A.; Nesladek, M.; Daenen...properties and applications. Russ. Chem. Rev. 2001, 70, 607−626. (27) Liang, Y.; Meinhardt, T.; Jarre, G.; Ozawa, M.; Vrodijak, P.; Scholl , A

78 FR 56625 - Housing Counseling Program: New Certification Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

... of, and responses to, rental and mortgage delinquency and avoidance of eviction and mortgage default... (including potential economic, environmental, public health, and safety effects, distributive impacts, and.../vol14num3/Cityscape_Nov2012_impact_lim_sellers.pdf , at page 219.) Specific Request for Comment: HUD...

Phospholipase D¿ enhances diacylglycerol flux into triacylglycerol

USDA-ARS?s Scientific Manuscript database

Plant seeds are the primary source of triacylglycerols (TAG) for food, feed, fuel, and industrial applications. As TAG is produced from diacylglycerol (DAG) successful engineering strategies to enhance TAG levels have focused on the conversion of DAG to TAG. However, the production of TAG can be lim...

Development of load and resistance factor design for ultimate and serviceability limit states of transportation structure foundations.

DOT National Transportation Integrated Search

2011-12-01

"Most foundation solutions for transportation structures rely on deep foundations, often on pile foundations : configured in a way most suitable to the problem at hand. Design of pile foundation solutions can best be pursued by clearly : defining lim...

Wiki-based Data Management System for Toxicogenomics

EPA Science Inventory

We are developing a data management system to enable systems-based toxicology at the US EPA. This is built upon the WikiLIMS platform and is capabale of housing not just genomics data but also a wide variety of toxicology data and associated experimental design information. Thi...

Generalizing a Limit Description of the Natural Logarithm

ERIC Educational Resources Information Center

Dobbs, David E.

2010-01-01

If f is a continuous positive-valued function defined on the closed interval from a to x and if k[subscript 0] is greater than 0, then lim[subscript k[right arrow]0[superscript +] [integral][superscript x] [subscript a] f (t)[superscript k-k[subscript 0

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.

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.

Chloroplast 2010: A Database for Large-Scale Phenotypic Screening of Arabidopsis Mutants1[W][OA

PubMed Central

Lu, Yan; Savage, Linda J.; Larson, Matthew D.; Wilkerson, Curtis G.; Last, Robert L.

2011-01-01

Large-scale phenotypic screening presents challenges and opportunities not encountered in typical forward or reverse genetics projects. We describe a modular database and laboratory information management system that was implemented in support of the Chloroplast 2010 Project, an Arabidopsis (Arabidopsis thaliana) reverse genetics phenotypic screen of more than 5,000 mutants (http://bioinfo.bch.msu.edu/2010_LIMS; www.plastid.msu.edu). The software and laboratory work environment were designed to minimize operator error and detect systematic process errors. The database uses Ruby on Rails and Flash technologies to present complex quantitative and qualitative data and pedigree information in a flexible user interface. Examples are presented where the database was used to find opportunities for process changes that improved data quality. We also describe the use of the data-analysis tools to discover mutants defective in enzymes of leucine catabolism (heteromeric mitochondrial 3-methylcrotonyl-coenzyme A carboxylase [At1g03090 and At4g34030] and putative hydroxymethylglutaryl-coenzyme A lyase [At2g26800]) based upon a syndrome of pleiotropic seed amino acid phenotypes that resembles previously described isovaleryl coenzyme A dehydrogenase (At3g45300) mutants. In vitro assay results support the computational annotation of At2g26800 as hydroxymethylglutaryl-coenzyme A lyase. PMID:21224340

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.

A Laboratory-Based System for Managing and Distributing Publically Funded Geochemical Data in a Collaborative Environment

NASA Astrophysics Data System (ADS)

McInnes, B.; Brown, A.; Liffers, M.

2015-12-01

Publically funded laboratories have a responsibility to generate, archive and disseminate analytical data to the research community. Laboratory managers know however, that a long tail of analytical effort never escapes researchers' thumb drives once they leave the lab. This work reports on a research data management project (Digital Mineralogy Library) where integrated hardware and software systems automatically archive and deliver analytical data and metadata to institutional and community data portals. The scientific objective of the DML project was to quantify the modal abundance of heavy minerals extracted from key lithological units in Western Australia. The selected analytical platform was a TESCAN Integrated Mineral Analyser (TIMA) that uses EDS-based mineral classification software to image and quantify mineral abundance and grain size at micron scale resolution. The analytical workflow used a bespoke laboratory information management system (LIMS) to orchestrate: (1) the preparation of grain mounts with embedded QR codes that serve as enduring links between physical samples and analytical data, (2) the assignment of an International Geo Sample Number (IGSN) and Digital Object Identifier (DOI) to each grain mount via the System for Earth Sample Registry (SESAR), (3) the assignment of a DOI to instrument metadata via Research Data Australia, (4) the delivery of TIMA analytical outputs, including spatially registered mineralogy images and mineral abundance data, to an institutionally-based data management server, and (5) the downstream delivery of a final data product via a Google Maps interface such as the AuScope Discovery Portal. The modular design of the system permits the networking of multiple instruments within a single site or multiple collaborating research institutions. Although sharing analytical data does provide new opportunities for the geochemistry community, the creation of an open data network requires: (1) adopting open data reporting standards and conventions, (2) requiring instrument manufacturers and software developers to deliver and process data in formats compatible with open standards, and (3) public funding agencies to incentivise researchers, laboratories and institutions to make their data open and accessible to consumers.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mijnheer, J.

Let (X(t): O{le}t{le}{infinity} be a stable subordinator with {alpha} {element_of}). For increasing sequences t{sub k} we give normalizing constants a{sub k} such that lim inf{sub k{le}{infinity}} a {sup {minus}1}{sub k} X(t{sub k}) is a.s. constant. We also derive a.s. upper bounds.

Education, Training and Contexts: Studies and Essays.

ERIC Educational Resources Information Center

Lauglo, Jon

This volume provides an overview of some of the outstanding features of the work of the Norwegian sociologist and comparative educationist, Jon Lauglo. After an introduction, "'It Ain't Necessarily So!': Theories and Observations in Jon Lauglo's World of Education and Training" (Se-Yung Lim and Klaus Schaack), essays and studies are…

Retrodirective Radar Calibration Nanosatellite

DTIC Science & Technology

2013-07-01

Martin (Student Program Manager); Nicholas G. Fisher (Student Systems Engineer) University of Hawaii JULY 2013 Final Report...Cost-Effective, Rapid Design of a Student-Built Radar Calibration Nanosatellite Larry K. Martin , Nicholas G. Fisher, Toy Lim, John...University of Hawaii Reinventing Space Conference AIAA-RS-2012-3001 Martin 1 AIAA Reinventing Space Conference 2012

78 FR 76598 - Membership of the Performance Review Board

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-18

..., LARRY G. KIM, ROBERT KOEPPEL, DENNIS LABRECK, JANET L. LAKIN, KENNETH CHARLES LHAMON, CATHERINE E. LIM..., SEAN P. CANELLOS, ERNEST C. CARR, PEGGY G. CARTER, DENISE L. CHAVEZ, ANTHONY S. CHISM, MONIQUE M..., LIBIA S. GOMEZ, GABRIELLA GONIPROW, ALEXANDER GRAHAM, DARRELL W. GREWAL, SATYAMDEEP S. HALL, LINDA W...

Photophysical Properties of Aromatic and Antiaromatic Porphyrinoids

DTIC Science & Technology

2011-04-14

possible to control the number of conjugated π-electrons by changing the number of connected pyrrole rings, ii) by providing a comparable set of [4n...Hexaphyrins: Effects of Confusion of Pyrrole Rings and Molecular Shape on Electronic Structures  Jong Min Lim, Jae Seok Lee, Hyun Woo Chung, Hee Won

Asia Section. Regional Activities Division. Paper.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

Two papers on library and information activities in developing nations, particularly in India and other Asian countries, were presented at the 1983 International Federation of Library Associations (IFLA) conference. In "IFLA in Asia: A Review of the Work of the Regional Section for Asia," Edward Lim Huck Tee (Malaysia) describes the low…

Urban infrastructure influences dissolved organic matter quality and bacterial metabolism in an urban stream network

EPA Science Inventory

Urban streams are degraded by a suite of factors, including burial beneath urban infrastructure (i.e., roads, parking lots) that eliminates light and reduces direct organic matter inputs to streams, with likely consequences for organic matter metabolism by microbes and carbon lim...

Spacecraft instrument calibration and stability

NASA Technical Reports Server (NTRS)

Gille, J. C.; Feldman, P.; Hudson, R.; Lean, J.; Madden, R.; Mcmaster, L.; Mount, G.; Rottman, G.; Simon, P. C.

1989-01-01

The following topics are covered: instrument degradation; the Solar Backscatter Ultraviolet (SBUV) Experiment; the Total Ozone Mapping Spectrometer (TOMS); the Stratospheric Aerosol and Gas Experiment 1 (SAGE-1) and SAGE-2 instruments; the Solar Mesosphere Explorer (SME) UV ozone and near infrared airglow instruments; and the Limb Infrared Monitor of the Stratosphere (LIMS).

THE POTENTIAL INFLUENCES OF FACE VELOCITY ON PM ARTIFACT LOSSES FOR EXPOSURE SAMPLERS USING TEFLON FILTER COLLECTION SUBSTRATES

EPA Science Inventory

The influences of artifact formations and losses on Particulate Matter (PM) sampler collection surfaces are well documented, especially for nitrates (Hering and Cass, 1999), and SVOC's (McDow, 1999), and more recently for speciated carbon (Turpin and Lim, 2001). These artifact...

DigitalVHI--a freeware open-source software application to capture the Voice Handicap Index and other questionnaire data in various languages.

PubMed

Herbst, Christian T; Oh, Jinook; Vydrová, Jitka; Švec, Jan G

2015-07-01

In this short report we introduce DigitalVHI, a free open-source software application for obtaining Voice Handicap Index (VHI) and other questionnaire data, which can be put on a computer in clinics and used in clinical practice. The software can simplify performing clinical studies since it makes the VHI scores directly available for analysis in a digital form. It can be downloaded from http://www.christian-herbst.org/DigitalVHI/.

[Development and practice evaluation of blood acid-base imbalance analysis software].

PubMed

Chen, Bo; Huang, Haiying; Zhou, Qiang; Peng, Shan; Jia, Hongyu; Ji, Tianxing

2014-11-01

To develop a blood gas, acid-base imbalance analysis computer software to diagnose systematically, rapidly, accurately and automatically determine acid-base imbalance type, and evaluate the clinical application. Using VBA programming language, a computer aided diagnostic software for the judgment of acid-base balance was developed. The clinical data of 220 patients admitted to the Second Affiliated Hospital of Guangzhou Medical University were retrospectively analyzed. The arterial blood gas [pH value, HCO(3)(-), arterial partial pressure of carbon dioxide (PaCO₂)] and electrolytes included data (Na⁺ and Cl⁻) were collected. Data were entered into the software for acid-base imbalances judgment. At the same time the data generation was calculated manually by H-H compensation formula for determining the type of acid-base imbalance. The consistency of judgment results from software and manual calculation was evaluated, and the judgment time of two methods was compared. The clinical diagnosis of the types of acid-base imbalance for the 220 patients: 65 cases were normal, 90 cases with simple type, mixed type in 41 cases, and triplex type in 24 cases. The accuracy of the judgment results of the normal and triplex types from computer software compared with which were calculated manually was 100%, the accuracy of the simple type judgment was 98.9% and 78.0% for the mixed type, and the total accuracy was 95.5%. The Kappa value of judgment result from software and manual judgment was 0.935, P=0.000. It was demonstrated that the consistency was very good. The time for software to determine acid-base imbalances was significantly shorter than the manual judgment (seconds:18.14 ± 3.80 vs. 43.79 ± 23.86, t=7.466, P=0.000), so the method of software was much faster than the manual method. Software judgment can replace manual judgment with the characteristics of rapid, accurate and convenient, can improve work efficiency and quality of clinical doctors and has great clinical application promotion value.

How Do Multiple-Star Systems Form? VLA Study Reveals "Smoking Gun"

NASA Astrophysics Data System (ADS)

2006-12-01

Astronomers have used the National Science Foundation's Very Large Array (VLA) radio telescope to image a young, multiple-star system with unprecedented detail, yielding important clues about how such systems are formed. Most Sun-sized or larger stars in the Universe are not single, like our Sun, but are members of multiple-star systems. Astronomers have been divided on how such systems can form, producing competing theoretical models for this process. Multiple Star Formation Graphic Proposed Formation Process for L1551 IRS5 CREDIT: Bill Saxton, NRAO/AUI/NSF Click on image for page of graphics and full information The new VLA study produced a "smoking gun" supporting one of the competing models, said Jeremy Lim, of the Institute of Astronomy & Astrophysics, Academia Sinica, in Taipei, Taiwan, whose study, done with Shigehisa Takakuwa of the National Astronomical Observatory of Japan, is published in the December 10 issue of the Astrophysical Journal. Ironically, their discovery of a third, previously-unknown, young star in the system may support a second theoretical model. "There may be more than one way to make a multiple-star system," Lim explained. The astronomers observed an object called L1551 IRS5, young, still-forming protostars enshrouded in a cloud of gas and dust, some 450 light-years from Earth in the direction of the constellation Taurus. Invisible to optical telescopes because of the gas and dust, this object was discovered in 1976 by astronomers using infrared telescopes. A VLA study in 1998 showed two young stars orbiting each other, each surrounded by a disk of dust that may, in time, congeal into a system of planets. Lim and Takakuwa re-examined the system, using improved technical capabilities that greatly boosted the quality of their images. "In the earlier VLA study, only half of the VLA's 27 antennas had receivers that could collect the radio waves, at a frequency of 43 GigaHertz (GHz), coming from the dusty disks. When we re-observed this system, all the antennas could provide data for us. In addition, we improved the level of detail by using the Pie Town, NM, antenna of the Very Long Baseline Array, as part of an expanded system," Lim said. The implementation and improvement of the 43 GHz receiving system was a collaborative program among the German Max Planck Institute, the Mexican National Autonomous University, and the U.S. National Radio Astronomy Observatory. Two popular theoretical models for the formation of multiple-star systems are, first, that the two protostars and their surrounding dusty disks fragment from a larger parent disk, and, second, that the protostars form independently and then one captures the other into a mutual orbit. "Our new study shows that the disks of the two main protostars are aligned with each other, and also are aligned with the larger, surrounding disk. In addition, their orbital motion resembles the rotation of the larger disk. This is a 'smoking gun' supporting the fragmentation model," Lim said. However, the new study also revealed a third young star with a dust disk. "The disk of this one is misaligned with those of the other two, so it may be the result of either fragmentation or capture," Takakuwa said. The misalignment of the third disk could have come through gravitational interactions with the other two, larger, protostars, the scientists said. They plan further observations to try to resolve the question. "We have a very firm indication that two of these protostars and their dust disks formed from the same, larger disk-like cloud, then broke out from it in a fragmentation process. That strongly supports one theoretical model for how multiple-star systems are formed. The misalignment of the third protostar and its disk leaves open the possibility that it could have formed elsewhere and been captured, and we'll continue to work on reconstructing the history of this fascinating system," Lim summarized. The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

Development and prospective evaluation of an automated software system for quality control of quantitative 99mTc-MAG3 renal studies.

PubMed

Folks, Russell D; Garcia, Ernest V; Taylor, Andrew T

2007-03-01

Quantitative nuclear renography has numerous potential sources of error. We previously reported the initial development of a computer software module for comprehensively addressing the issue of quality control (QC) in the analysis of radionuclide renal images. The objective of this study was to prospectively test the QC software. The QC software works in conjunction with standard quantitative renal image analysis using a renal quantification program. The software saves a text file that summarizes QC findings as possible errors in user-entered values, calculated values that may be unreliable because of the patient's clinical condition, and problems relating to acquisition or processing. To test the QC software, a technologist not involved in software development processed 83 consecutive nontransplant clinical studies. The QC findings of the software were then tabulated. QC events were defined as technical (study descriptors that were out of range or were entered and then changed, unusually sized or positioned regions of interest, or missing frames in the dynamic image set) or clinical (calculated functional values judged to be erroneous or unreliable). Technical QC events were identified in 36 (43%) of 83 studies. Clinical QC events were identified in 37 (45%) of 83 studies. Specific QC events included starting the camera after the bolus had reached the kidney, dose infiltration, oversubtraction of background activity, and missing frames in the dynamic image set. QC software has been developed to automatically verify user input, monitor calculation of renal functional parameters, summarize QC findings, and flag potentially unreliable values for the nuclear medicine physician. Incorporation of automated QC features into commercial or local renal software can reduce errors and improve technologist performance and should improve the efficiency and accuracy of image interpretation.

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 technique with established goniometric methods determines that the proposed software agrees sufficiently to be used interchangeably. PMID:29750166

Adapting a Computerized Medical Dictation System to Prepare Academic Papers in Radiology.

PubMed

Sánchez, Yadiel; Prabhakar, Anand M; Uppot, Raul N

2017-09-14

Everyday radiologists use dictation software to compose clinical reports of imaging findings. The dictation software is tailored for medical use and to the speech pattern of each radiologist. Over the past 10 years we have used dictation software to compose academic manuscripts, correspondence letters, and texts of educational exhibits. The advantages of using voice dictation is faster composition of manuscripts. However, use of such software requires preparation. The purpose of this article is to review the steps of adapting a clinical dictation software for dictating academic manuscripts and detail the advantages and limitations of this technique. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Sediment Microbial Enzyme Activity as an Indicator of Nutrient Limitation in the Great Rivers of the Upper Mississippi River Basin

EPA Science Inventory

Three conclusions are evident from our comparison of approaches for estimating nutrient limitation in these large floodplain rivers: 1) water chemistry and enzymes indicate that P-limitation is more prevalent than N-limitation; 2) the Ohio River reaches are more extensively P-lim...

Biased estimation of forest log characteristics using intersect diameters

Treesearch

Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton

2009-01-01

Logs are an important structural feature of forest ecosystems, and their abundance affects many resources and forest processes, including fire regimes, soil productivity, silviculture, carbon cycling, and wildlife habitat. Consequently, logs are often sampled to estimate their frequency, percent cover, volume, and weight. The line-intersect method (LIM) is one of the...

Internet Worm and Virus Protection for Very High-Speed Networks

DTIC Science & Technology

2004-08-20

John Lockwood • Ronald Loui • Jon Turner – Graduate Students • Mike Attig • Sarang Dharmapurikar • David Lim • Jing Lu • Bharath Madhusudan...James Moscola • Chris Neely • David Schuehler • Todd Sproull • David Taylor • Haoyu Song • Chris Zuver • Industry Research Partners – Matthew Kulig

A High-Order Test for Optimality of Bang-Bang Controls.

DTIC Science & Technology

1983-11-01

Systems * Istituto di Matematica Applicata, Universitl di Padova, ITALY. sponsored by the United States Army under Contract No. DAAG29-80-C-0041...the first order variation at the terminal point of the trajectory lim [x(T,u ) - x(TW)]/E (1.1) Istituto di Matematica Applicata, Universitl di Padova

Hybrid striped bass national breeding program: research towards genetic improvement of a non-model species

USDA-ARS?s Scientific Manuscript database

The hybrid striped bass (HSB) farming industry at present relies almost totally on wild broodstock for annual production of larvae and fingerlings, and industry efforts to domesticate the parent species of the HSB (white bass: WB, Morone chrysops; striped bass: SB, M. saxatilis) have been fairly lim...

Workforce Planning in the Intelligence Community: A Retrospective

DTIC Science & Technology

2013-01-01

segments of this work. We also wish to thank Dwayne M. Butler and Nelson Lim from RAND and Robert B. Murrett of the Syracuse University Department of Public...Taylor, Richard Eisenman, William Fedorochko, Clifford M. Graf II, Mark Hoyer, Paul Bracken, Norman T. O’Meara, Jerry M. Sollinger, Judith Larson

Enabling next-gen sequencing and analysis at the USDA-ARS U.S. Meat Animal Research Center with MiniLIMS

USDA-ARS?s Scientific Manuscript database

There is a growing need to combine DNA sequencing technologies to address complex problems in genome biology. These genomic studies routinely generate voluminous image, sequence, and mapping files that should be associated with quality control information (gels, spectra, etc.), and other important ...

Hybrid striped bass National Breeding Program: Research towards genetic improvement of a non-model species

USDA-ARS?s Scientific Manuscript database

The hybrid striped bass (HSB) farming industry at present relies almost totally on wild broodstock for annual production of larvae and fingerlings, and industry efforts to domesticate the parent species of the HSB (white bass: WB, Morone chrysops; striped bass: SB, M. saxatilis) have been fairly lim...

Syntactic Complexity Effects in Sentence Production: A Reply to MacDonald, Montag, and Gennari (2016)

ERIC Educational Resources Information Center

Scontras, Gregory; Badecker, William; Fedorenko, Evelina

2017-01-01

In our article, "Syntactic complexity effects in sentence production" [Scontras, Badecker, Shank, Lim, & Fedorenko, 2015 (EJ1057757)], we reported two elicited production experiments and argued that there is a cost associated with planning and uttering syntactically complex, object-extracted structures that contain a non-local…

U.S. EPA, Pesticide Product Label, , 07/24/1990

EPA Pesticide Factsheets

2011-04-21

... PII'IIlta _ CIIIlta 1Il8I: In. 1I1I1l11eICEIJ: III.' Inl Milia.. II lim .1811 •. ... Ell. • DI ..... 1111 lII.e II Fla. ... aD II-.t fOIn. FII CIIu.:L _let til iECl ... file( IF til EIIII 11M. ...

Command History for 1991 (Naval Personnel Research and Development Center)

DTIC Science & Technology

1992-08-01

years of age. 18 Chronology of 1991Events New Emtlovee Lieutenant Rolando Lim Code 151 Regina G. Bragg Paul J. Carney Library Technician Supply Clerk Code...Awards 35 Years Ben Garcia Gene Stout 30 Years Jim Julius Ramona Mouzon Hal Rosen 32 25 Years Jim Chadbourne Bob Harris Dorothy Martin Jan Reynolds 20

U.S. EPA, Pesticide Product Label, PARATHION EHTYL-METHYL 6-3, 04/21/1972

EPA Pesticide Factsheets

2011-04-21

... ', .. , nIl I' ~~nh~Ii". " .. 1'1. II'" 'flO: T,,, .. fiji[ 10':;\\1';' ""t' I I rAe 1/"'.I ~t~'. ~ ,Nl .. l' .. : Uf.p ... t •• , • 1"" .1('" I.·, l""'iM".'" "r,_ I., .,"II,d, .11'1'1, I,,,.! ...

Cognates Facilitate Switches and Then Confusion: Contrasting Effects of Cascade versus Feedback on Language Selection

ERIC Educational Resources Information Center

Li, Chuchu; Gollan, Tamar H.

2018-01-01

The current study investigated the hypothesis that cognates (i.e., translation equivalents that overlap in form, e.g., "lemon" is "limón" in Spanish) facilitate language switches. Spanish-English bilinguals were cued to switch languages while repeatedly naming pictures with cognate versus noncognate names in separate…

Learning from hackers: open-source clinical trials.

PubMed

Dunn, Adam G; Day, Richard O; Mandl, Kenneth D; Coiera, Enrico

2012-05-02

Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.

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

Evaluation of a new selective enrichment broth for detection of group B streptococci in pregnant women.

PubMed

Heelan, Judith S; Struminsky, Judith; Lauro, Patricia; Sung, C James

2005-02-01

Studies at two Brown Medical School-affiliated hospitals were undertaken to evaluate a new selective broth medium (GBS broth) and to compare it to the LIM broth currently used to culture for group B streptococci. Beta-hemolytic group B streptococci produce a carotenoid pigment that turns GBS broth an orange color. From a total of 580 pregnant women, duplicate vaginal-rectal swabs were collected at 35 to 37 weeks of gestation and cultured for group B streptococci, using either LIM broth (a selective broth containing antibiotics) or GBS broth for enrichment. Specimens were either transported to the laboratory or immediately placed in the respective enrichment broths and delivered to the laboratory. GBS broth medium had sensitivity, specificity, and positive and negative predictive values of 87.8, 100, 100, and 95.1% when planted in the laboratory and 90.3, 100, 100 and 97.6%, respectively, when inoculated at bedside. Use of GBS broth would satisfy Centers for Disease Control and Prevention requirements and would provide faster, more-sensitive, and cost-effective detection of group B streptococci in pregnant women.

Cloning and functional characterization of three terpene synthases from lavender (Lavandula angustifolia).

PubMed

Landmann, Christian; Fink, Barbara; Festner, Maria; Dregus, Márta; Engel, Karl-Heinz; Schwab, Wilfried

2007-09-15

The essential oil of lavender (Lavandula angustifolia) is mainly composed of mono- and sesquiterpenes. Using a homology-based PCR strategy, two monoterpene synthases (LaLIMS and LaLINS) and one sesquiterpene synthase (LaBERS) were cloned from lavender leaves and flowers. LaLIMS catalyzed the formation of (R)-(+)-limonene, terpinolene, (1R,5S)-(+)-camphene, (1R,5R)-(+)-alpha-pinene, beta-myrcene and traces of alpha-phellandrene. The proportions of these products changed significantly when Mn(2+) was supplied as the cofactor instead of Mg(2+). The second enzyme LaLINS produced exclusively (R)-(-)-linalool, the main component of lavender essential oil. LaBERS transformed farnesyl diphosphate and represents the first reported trans-alpha-bergamotene synthase. It accepted geranyl diphosphate with higher affinity than farnesyl diphosphate and also produced monoterpenes, albeit at low rates. LaBERS is probably derived from a parental monoterpene synthase by the loss of the plastidial signal peptide and by broadening its substrate acceptance spectrum. The identification and description of the first terpene synthases from L. angustifolia forms the basis for the biotechnological modification of essential oil composition in lavender.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Novel pathway of 3-hydroxyanthranilic acid formation in limazepine biosynthesis reveals evolutionary relation between phenazines and pyrrolobenzodiazepines.

PubMed

Pavlikova, Magdalena; Kamenik, Zdenek; Janata, Jiri; Kadlcik, Stanislav; Kuzma, Marek; Najmanova, Lucie

2018-05-17

Natural pyrrolobenzodiazepines (PBDs) form a large and structurally diverse group of antitumour microbial metabolites produced through complex pathways, which are encoded within biosynthetic gene clusters. We sequenced the gene cluster of limazepines and proposed their biosynthetic pathway based on comparison with five available gene clusters for the biosynthesis of other PBDs. Furthermore, we tested two recombinant proteins from limazepine biosynthesis, Lim5 and Lim6, with the expected substrates in vitro. The reactions monitored by LC-MS revealed that limazepine biosynthesis involves a new way of 3-hydroxyanthranilic acid formation, which we refer to as the chorismate/DHHA pathway and which represents an alternative to the kynurenine pathway employed for the formation of the same precursor in the biosynthesis of other PBDs. The chorismate/DHHA pathway is presumably also involved in the biosynthesis of PBD tilivalline, several natural products unrelated to PBDs, and its part is shared also with phenazine biosynthesis. The similarities between limazepine and phenazine biosynthesis indicate tight evolutionary links between these groups of compounds.

NASA's EOSDIS: options for data providers

NASA Astrophysics Data System (ADS)

Khalsa, Siri J.; Ujhazy, John E.

1995-12-01

EOSDIS, the data and information system being developed by NASA to support interdisciplinary earth science research into the 21st century, will do more than manage and distribute data from EOS-era satellites. It will also promote the exchange of data, tools, and research results across disciplinary, agency, and national boundaries. This paper describes the options that data providers will have for interacting with the EOSDIS Core System (ECS), the infrastructure of EOSDIS. The options include: using the ECS advertising service to announce the availability of data at the provider's site; submitting a candidate data set to one of the Distributed Active Archive Centers (DAACs); establishing a data server that will make the data accessible via ECS and establishing Local Information Manager (LIM) which would make the data available for multi-site searches. One additional option is through custom gateway interfaces which would provide access to existing data archives. The gateway, data server, and LIM options require the implementation of ECS code at the provider site to insure proper protocols. The advertisement and ingest options require no part of ECS design to reside at the provider site.

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.

Implementation of a software for REmote COMparison of PARticlE and photon treatment plans: ReCompare.

PubMed

Löck, Steffen; Roth, Klaus; Skripcak, Tomas; Worbs, Mario; Helmbrecht, Stephan; Jakobi, Annika; Just, Uwe; Krause, Mechthild; Baumann, Michael; Enghardt, Wolfgang; Lühr, Armin

2015-09-01

To guarantee equal access to optimal radiotherapy, a concept of patient assignment to photon or particle radiotherapy using remote treatment plan exchange and comparison - ReCompare - was proposed. We demonstrate the implementation of this concept and present its clinical applicability. The ReCompare concept was implemented using a client-server based software solution. A clinical workflow for the remote treatment plan exchange and comparison was defined. The steps required by the user and performed by the software for a complete plan transfer were described and an additional module for dose-response modeling was added. The ReCompare software was successfully tested in cooperation with three external partner clinics and worked meeting all required specifications. It was compatible with several standard treatment planning systems, ensured patient data protection, and integrated in the clinical workflow. The ReCompare software can be applied to support non-particle radiotherapy institutions with the patient-specific treatment decision on the optimal irradiation modality by remote treatment plan exchange and comparison. Copyright © 2015. Published by Elsevier GmbH.

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.

The evaluation of hospital laboratory information management systems based on the standards of the American National Standard Institute

PubMed Central

Isfahani, Sakineh Saghaeiannejad; Khajouei, Reza; Jahanbakhsh, Maryan; Mirmohamadi, Mahboubeh

2014-01-01

Introduction: Nowadays, modern laboratories are faced with a huge volume of information. One of the goals of the Laboratory Information Management System (LIMS) is to assist in the management of the information generated in the laboratory. This study intends to evaluate the LIMS based on the standards of the American National Standard Institute (ANSI). Materials and Methods: This research is a descriptive–analytical study, which had been conducted in 2011, on the LIMSs in use, in the teaching and private hospitals in Isfahan. The data collecting instrument was a checklist, which was made by evaluating three groups of information components namely: ‘System capabilities’, ‘work list functions,’ and ‘reporting’ based on LIS8-A. Data were analyzed using the SPSS 20. Data were analyzed using (relative) frequency, percentage. To compare the data the following statistical tests were used: Leven test, t-test, and Analysis of Variance (ANOVA). Results: The results of the study indicated that the LIMS had a low conformity (30%) with LIS8-A (P = 0.001), with no difference between teaching and private hospitals (P = 0.806). The ANOVA revealed that in terms of conformity with the LIS8-A standard, there was a significant difference between the systems produced by different vendors (P = 0.023). According to the results, a Kowsar system with more than %57 conformity in the three groups of information components had a better conformity to the standard, compared to the other systems. Conclusions: This study indicated that none of the LIMSs had a good conformity to the standard. It seems that system providers did not pay sufficient attention to many of the information components required by the standards when designing and developing their systems. It was suggested that standards from certified organizations and institutions be followed in the design and development process of health information systems. PMID:25077154

DOE Office of Scientific and Technical Information (OSTI.GOV)

Srivastava, Mansi; Larroux, Claire; Lu, Daniel R

LIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known. We identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in themore » genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring. The Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In Nematostella, Lhx gene expression is correlated with neural territories in larval and juvenile polyp stages. This pattern is consistent with a possible role in patterning the Nematostella nervous system. We propose a scenario in which Lhx genes play a homologous role in neural patterning across eumetazoans.« less

Potential Predictability and Prediction Skill for Southern Peru Summertime Rainfall

NASA Astrophysics Data System (ADS)

WU, S.; Notaro, M.; Vavrus, S. J.; Mortensen, E.; Block, P. J.; Montgomery, R. J.; De Pierola, J. N.; Sanchez, C.

2016-12-01

The central Andes receive over 50% of annual climatological rainfall during the short period of January-March. This summertime rainfall exhibits strong interannual and decadal variability, including severe drought events that incur devastating societal impacts and cause agricultural communities and mining facilities to compete for limited water resources. An improved seasonal prediction skill of summertime rainfall would aid in water resource planning and allocation across the water-limited southern Peru. While various underlying mechanisms have been proposed by past studies for the drivers of interannual variability in summertime rainfall across southern Peru, such as the El Niño-Southern Oscillation (ENSO), Madden Julian Oscillation (MJO), and extratropical forcings, operational forecasts continue to be largely based on rudimentary ENSO-based indices, such as NINO3.4, justifying further exploration of predictive skill. In order to bridge this gap between the understanding of driving mechanisms and the operational forecast, we performed systematic studies on the predictability and prediction skill of southern Peru summertime rainfall by constructing statistical forecast models using best available weather station and reanalysis datasets. At first, by assuming the first two empirical orthogonal functions (EOFs) of summertime rainfall are predictable, the potential predictability skill was evaluated for southern Peru. Then, we constructed a simple regression model, based on the time series of tropical Pacific sea-surface temperatures (SSTs), and a more advanced Linear Inverse Model (LIM), based on the EOFs of tropical ocean SSTs and large-scale atmosphere variables from reanalysis. Our results show that the LIM model consistently outperforms the more rudimentary regression models on the forecast skill of domain averaged precipitation index and individual station indices. The improvement of forecast correlation skill ranges from 10% to over 200% for different stations. Further analysis shows that this advantage of LIM is likely to arise from its representation of local zonal winds and the position of Intertropical Convergence Zone (ITCZ).

The evaluation of hospital laboratory information management systems based on the standards of the American National Standard Institute.

PubMed

Isfahani, Sakineh Saghaeiannejad; Khajouei, Reza; Jahanbakhsh, Maryan; Mirmohamadi, Mahboubeh

2014-01-01

Nowadays, modern laboratories are faced with a huge volume of information. One of the goals of the Laboratory Information Management System (LIMS) is to assist in the management of the information generated in the laboratory. This study intends to evaluate the LIMS based on the standards of the American National Standard Institute (ANSI). This research is a descriptive-analytical study, which had been conducted in 2011, on the LIMSs in use, in the teaching and private hospitals in Isfahan. The data collecting instrument was a checklist, which was made by evaluating three groups of information components namely: 'System capabilities', 'work list functions,' and 'reporting' based on LIS8-A. Data were analyzed using the SPSS 20. Data were analyzed using (relative) frequency, percentage. To compare the data the following statistical tests were used: Leven test, t-test, and Analysis of Variance (ANOVA). The results of the study indicated that the LIMS had a low conformity (30%) with LIS8-A (P = 0.001), with no difference between teaching and private hospitals (P = 0.806). The ANOVA revealed that in terms of conformity with the LIS8-A standard, there was a significant difference between the systems produced by different vendors (P = 0.023). According to the results, a Kowsar system with more than %57 conformity in the three groups of information components had a better conformity to the standard, compared to the other systems. This study indicated that none of the LIMSs had a good conformity to the standard. It seems that system providers did not pay sufficient attention to many of the information components required by the standards when designing and developing their systems. It was suggested that standards from certified organizations and institutions be followed in the design and development process of health information systems.

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.

The eSMAF: a software for the assessment and follow-up of functional autonomy in geriatrics

PubMed Central

Boissy, Patrick; Brière, Simon; Tousignant, Michel; Rousseau, Eric

2007-01-01

Background Functional status or disability forms the core of most assessment instruments used to identify mix and level of resources and services needed by older adults who possess common characteristics. The Functional Autonomy Measurement System (SMAF) is a 29-item scale measuring functional ability in five different areas. It has been recommended for use for home care, for allocation of chronic beds, for developing care plans in institutional settings and for epidemiological and evaluative studies. The SMAF can also be used with a case-mix classification system (Iso-SMAF) to allocate resources based on patients' functional autonomy characteristics. The objective of this project was to develop a software version of the SMAF to facilitate the evaluation of the functional status of older adults in health services research and to optimize the clinical decision-making process. Results The eSMAF was developed over an 24-month period using a modified waterfall software engineering process. Requirements and functional specifications were determined using focus groups of stakeholders. Different versions of the software were iteratively field-tested in clinical and research environments and software adaptations made accordingly. User documentation and online help were created to assist the deployment of the software. The software is available in French or English versions under a 30-day unregistered demonstration license or a free restricted registered academic license. It can be used locally on a Windows-based PC or over a network to input SMAF data into a database, search and aggregate client data according to clinical and/or administrative criteria, and generate summary or detailed reports of selected data sets for print or export to another database. Conclusion In the last year, the software has been successfully deployed in the clinical workflow of different institutions in research and clinical applications. The software performed relatively well in terms of stability and performance. Barriers to implementation included antiquated computer hardware, low computer literacy and access to IT support. Key factors for the deployment of the software included standardization of the workflow, user training and support. PMID:17298673

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.

An updated view on the role of dopamine in myopia.

PubMed

Feldkaemper, Marita; Schaeffel, Frank

2013-09-01

A large body of data is available to support the hypothesis that dopamine (DA) is one of the retinal neurotransmitters involved in the signaling cascade that controls eye growth by vision. Initially, reduced retinal DA levels were observed in eyes deprived of sharp vision by either diffusers ("deprivation myopia", DM) or negative lenses ("lens induced myopia", LIM). Simulating high retinal DA levels by intravitreal application of a DA agonist can suppress the development of both DM and LIM. Also more recent studies using knock-out mouse models of DA receptors support the idea of an association between decreased DA levels and DM. There seem to be differences in the magnitude of the effects of DA on DM and LIM, with larger changes in DM but the degrees of image degradation by both treatments need to be matched to support this conclusion. Although a number of studies have shown that the inhibitory effects of dopamine agonists on DM and LIM are mediated through stimulation of the D2-receptor, there is also recent evidence that the balance of D2- and D1-receptor activation is important. Inhibition of D2-receptors can also slow the development of spontaneous myopia in albino guinea pigs. Retinal DA content displays a distinct endogenous diurnal, and partially circadian rhythm. In addition, retinal DA is regulated by a number of visual stimuli like retinal illuminance, spatial frequency content of the image, temporal contrast and, in chicks, by the light input from the pineal organ. A close interaction was found between muscarinergic and dopaminergic systems, and between nitric oxide and dopaminergic pathways, and there is evidence for crosstalk between the different pathways, perhaps multiple binding of the ligands to different receptors. It was shown that DA agonists interact with the immediate early signaling molecule ZENK which triggers the first steps in eye growth regulation. However, since long treatment periods were often needed to induce significant changes in retinal dopamine synthesis and release, the role of dopamine in the early steps is unclear. The wide spatial distribution of dopaminergic amacrine cells in the retina and the observation that changes in dopamine levels can be locally induced by local retinal deprivation is in line with the assumption that dopaminergic mechanisms control both central and peripheral eye growth. The protective effect of outdoor activity on myopia development in children seems to be partly mediated by the stimulatory effect of light on retinal dopamine production and release. However, the dose-response function linking light exposure to dopamine and to the suppression of myopia is not known and requires further studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

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

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.

Teaching Mathematics for Spatial Justice: Beyond a Victory Narrative

ERIC Educational Resources Information Center

Rubel, Laurie H.; Hall-Wieckert, Maren; Lim, Vivian Y.

2016-01-01

In this reflective essay, Laurie H. Rubel, Maren Hall-Wieckert, and Vivian Y. Lim present a design heuristic for teaching mathematics for spatial justice (TMSpJ) based on their development of two curricular modules, one about the state lottery and the other about financial services in a city. Spatial tools, including data visualizations on maps…

Resource Rivalry in the Third World,

DTIC Science & Technology

1984-03-31

and specifically includes comparative NATO/Warsaw Pact dependence on critical resources , externally supplied ; determination of the extent, ways and...essential, especially defense-related, industry, the nation thereby becoming significantly dependent on the supplies of such resource from foreign...8217 consequences; 2. lac’. of adequate domestic resources ; 3. lim- ited potential for suitable substitute materials; and 4. lack of alternative sources

How School Leaders Perceive the Leadership Role of Middle Leaders in Singapore Primary Schools?

ERIC Educational Resources Information Center

Koh, Hak Hiang; Gurr, David; Drysdale, Lawrie; Ang, Li Li

2011-01-01

Middle leaders are "recognised as a significant source in ensuring that quality education reaches out to pupils" (Low and Lim "1997", p. 77) for they are "the human link between national education policy as manifested in school-level strategic planning...and the teaching staff whose "field tactics" are used to…

Factors Affecting the Full Use of Library and Information Management Systems by Library Personnel

ERIC Educational Resources Information Center

Skretas, Georgios

2005-01-01

Purpose: To provide a general list of factors that affects and determines the full use of library information management systems (LIMS) by library staff. Design/methodology/approach: The factors, which were identified mainly during participation in the implementation of automation projects in Greece, are listed and briefly analysed in categories…

Durability of Adhesive Bonded Structures Subjected to Acoustic Loads,

DTIC Science & Technology

1981-12-01

Rights Reserved ISBN 92-835-1409-2 Printed by Technical Editing and Reproduction Ltd Ilarford House, 7-9 Charlotte St London, WJP ) HD fi PREFACE At...foematiommstum am[*l, Deopo do Servigo de Mateial Fy.Madhmatik GmibH 4a Porn Awne KeeaoemeiapmtmumRue da Eacols Pollticalca 42 D-7314 UgmunLeopdisafen 2 Lim Atn

Enhancement of innate immunity with granulocyte colony-stimulating factor did not mitigate disease in pigs infected with a highly pathogenic Chinese PRRSV strain

USDA-ARS?s Scientific Manuscript database

Porcine reproductive and respiratory syndrome virus (PRRSV) is responsible for one of the most economically important diseases in swine worldwide. It causes reproductive failure in sows and pneumonia in pigs that predisposes them to secondary bacterial infections. Methods to control PRRSV and/or lim...

Attrition in the Trades. Research Overview. Monograph Series 07/2011

ERIC Educational Resources Information Center

Wilson, Sara

2011-01-01

"Attrition in the trades," by Tom Karmel, Patrick Lim and Josie Misko, analyses whether attrition--the gradual reduction or weakening of a workforce--occurs more amongst tradespeople than professionals, and if this is to the detriment of the supply of tradespeople. The authors use data from the Australian Labour Mobility Survey in 2008…

Test and Evaluation Report of the IMED Volumetric Infusion Pump Model 960A

DTIC Science & Technology

1992-02-01

tested Ambient tempera- ture was out of test lim- its. Windshield anti-ice X Pitot heat X Vent blower X Windshield wiper X Heater X APU X Generator #1 X...Patterson John A. Dellinger, Air Force Base, OH 45433 Southwest Research Institute P. 0. Box 28510 Henry L. Taylor San Antonio, TX 78284 Director

A Framework for Interaction and Cognitive Engagement in Connectivist Learning Contexts

ERIC Educational Resources Information Center

Wang, Zhijun; Chen, Li; Anderson, Terry

2014-01-01

Interaction has always been highly valued in education, especially in distance education (Moore, 1989; Anderson, 2003; Chen, 2004a; Woo & Reeves, 2007; Wang, 2013; Conrad, in press). It has been associated with motivation (Mahle, 2011; Wen-chi, et al., 2011), persistence (Tello, 2007; Joo, Lim, & Kim, 2011), deep learning (Offir, et al.,…

Clinical analysis of genome next-generation sequencing data using the Omicia platform

PubMed Central

Coonrod, Emily M; Margraf, Rebecca L; Russell, Archie; Voelkerding, Karl V; Reese, Martin G

2013-01-01

Aims Next-generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders. The successful implementation of this technology for diagnosing genetic disorders requires a rapid, user-friendly method to annotate variants and generate short lists of clinically relevant variants of interest. This report describes Omicia’s Opal platform, a new software tool designed for variant discovery and interpretation in a clinical laboratory environment. The software allows clinical scientists to process, analyze, interpret and report on personal genome files. Materials & Methods To demonstrate the software, the authors describe the interactive use of the system for the rapid discovery of disease-causing variants using three cases. Results & Conclusion Here, the authors show the features of the Opal system and their use in uncovering variants of clinical significance. PMID:23895124

SEURAT: visual analytics for the integrated analysis of microarray data.

PubMed

Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

2010-06-03

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

Data file of a deep proteome analysis of the prefrontal cortex in aged mice with progranulin deficiency or neuronal overexpression of progranulin.

PubMed

Heidler, Juliana; Hardt, Stefanie; Wittig, Ilka; Tegeder, Irmgard

2016-12-01

Progranulin deficiency is associated with neurodegeneration in humans and in mice. The mechanisms likely involve progranulin-promoted removal of protein waste via autophagy. We performed a deep proteomic screen of the pre-frontal cortex in aged (13-15 months) female progranulin-deficient mice (GRN -/- ) and mice with inducible neuron-specific overexpression of progranulin (SLICK-GRN-OE) versus the respective control mice. Proteins were extracted and analyzed per liquid chromatography/mass spectrometry (LC/MS) on a Thermo Scientific™ Q Exactive Plus equipped with an ultra-high performance liquid chromatography unit and a Nanospray Flex Ion-Source. Full Scan MS-data were acquired using Xcalibur and raw files were analyzed using the proteomics software Max Quant. The mouse reference proteome set from uniprot (June 2015) was used to identify peptides and proteins. The DiB data file is a reduced MaxQuant output and includes peptide and protein identification, accession numbers, protein and gene names, sequence coverage and label free quantification (LFQ) values of each sample. Differences in protein expression in genotypes are presented in "Progranulin overexpression in sensory neurons attenuates neuropathic pain in mice: Role of autophagy" (C. Altmann, S. Hardt, C. Fischer, J. Heidler, H.Y. Lim, A. Haussler, B. Albuquerque, B. Zimmer, C. Moser, C. Behrends, F. Koentgen, I. Wittig, M.H. Schmidt, A.M. Clement, T. Deller, I. Tegeder, 2016) [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.

A tool to include gamma analysis software into a quality assurance program.

PubMed

Agnew, Christina E; McGarry, Conor K

2016-03-01

To provide a tool to enable gamma analysis software algorithms to be included in a quality assurance (QA) program. Four image sets were created comprising two geometric images to independently test the distance to agreement (DTA) and dose difference (DD) elements of the gamma algorithm, a clinical step and shoot IMRT field and a clinical VMAT arc. The images were analysed using global and local gamma analysis with 2 in-house and 8 commercially available software encompassing 15 software versions. The effect of image resolution on gamma pass rates was also investigated. All but one software accurately calculated the gamma passing rate for the geometric images. Variation in global gamma passing rates of 1% at 3%/3mm and over 2% at 1%/1mm was measured between software and software versions with analysis of appropriately sampled images. This study provides a suite of test images and the gamma pass rates achieved for a selection of commercially available software. This image suite will enable validation of gamma analysis software within a QA program and provide a frame of reference by which to compare results reported in the literature from various manufacturers and software versions. Copyright © 2015. Published by Elsevier Ireland Ltd.

What an open source clinical trial community can learn from hackers

PubMed Central

Dunn, Adam G.; Day, Richard O.; Mandl, Kenneth D.; Coiera, Enrico

2014-01-01

Summary Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. Since a similar gap has already been addressed in the software industry by the open source software movement, we examine how the social and technical principles of the movement can be used to guide the growth of an open source clinical trial community. PMID:22553248

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.

Management of an affiliated Physics Residency Program using a commercial software tool.

PubMed

Zacarias, Albert S; Mills, Michael D

2010-06-01

A review of commercially available allied health educational management software tools was performed to evaluate their capacity to manage program data associated with a CAMPEP-accredited Therapy Physics Residency Program. Features of these software tools include: a) didactic course reporting and organization, b) competency reporting by topic, category and didactic course, c) student time management and accounting, and d) student patient case reporting by topic, category and course. The software package includes features for recording school administrative information; setting up lists of courses, faculty, clinical sites, categories, competencies, and time logs; and the inclusion of standardized external documents. There are provisions for developing evaluation and survey instruments. The mentors and program may be evaluated by residents, and residents may be evaluated by faculty members using this feature. Competency documentation includes the time spent on the problem or with the patient, time spent with the mentor, date of the competency, and approval by the mentor and program director. Course documentation includes course and lecture title, lecturer, topic information, date of lecture and approval by the Program Director. These software tools have the facility to include multiple clinical sites, with local subadministrators having the ability to approve competencies and attendance at clinical conferences. In total, these software tools have the capability of managing all components of a CAMPEP-accredited residency program. The application database lends the software to the support of multiple affiliated clinical sites within a single residency program. Such tools are a critical and necessary component if the medical physics profession is to meet the projected needs for qualified medical physicists in future years.

Isolating the Effects of a Mobile Phone on the Usability and Safety of eHealth Software Applications.

PubMed

Borycki, Elizabeth M; Griffith, Janessa; Monkman, Helen; Reid-Haughian, Cheryl

2017-01-01

Mobile phones are used in conjunction with mobile eHealth software applications. These mobile software applications can be used to access, review and document clinical information. The objective of this research was to explore the relationship between mobile phones, usability and safety. Clinical simulations and semi-structured interviews were used to investigate this relationship. The findings revealed that mobile phones may lead to specific types of usability issues that may introduce some types of errors.

The Evolving Threat of al Qaeda in the Islamic Maghreb (Strategic Forum, Number 268, July 2011)

DTIC Science & Technology

2011-07-01

Recruitment.” 40 NEFA Foundation, “AQIM: ‘The Annihilation of the Mus- lims in Nigeria,’” February 1, 2010, available at <www.nefafoundation. org...miscellaneous/ NEFA %20AQIM%200210.pdf>. 41 More recently, the group’s propaganda statements have used the name Jama’atu Ahlu Sunna Lidda’awati wal Jihad or

JPRS Report, Science & Technology, China: Energy

DTIC Science & Technology

1989-02-15

tion, the Xinjiang Petroleum Management Bureau of the former Ministry of Petroleum Industry did a very lim- ited amount of gravity and magnetic ...expand interna- tional trade at our boundaries , strengthen nationality unity, and consolidate our defenses along the southwest border. Development of...1) There are excellent terrain and geological conditions, it is a narrow gorge-type reservoir, the lithology is mostly igneous and metamorphic

U.S. EPA, Pesticide Product Label, , 05/21/1982

EPA Pesticide Factsheets

2011-04-14

... l I ~ 1 I \\ , r.;v 111'01 fJIM'"''' 0 ~~.~ ClN<1'N' rtffdJ /It ~ ... 'f r.(yO {;"?f!IeNI"~iH ... ·It « fl¥l.tlP''t~. liM I "p"IGf fSnAO~~Cor~~"i'"''' J,."""f ... ,'I iI--.:ft.,·j. ...

Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes.

PubMed

Tsai, Albert; Singer, Robert H; Crocker, Justin

2018-04-19

Lim et al. (2018) use live imaging in Drosophila embryos to show that enhancers can drive transcription from promoters on another chromosome when they are in close proximity. In addition, they show that multiple promoters can access the same enhancer without competition, potentially sharing a pool of factors in a transcriptional "hub." Copyright © 2018 Elsevier Inc. All rights reserved.

Faking Bad: Do High-Ability Elementary Students Intentionally Underachieve When Their Work Is Peer-Reviewed?

ERIC Educational Resources Information Center

Black, Kasey M. K.

2012-01-01

While faking bad, or the intentional distortion of assessment results, has been studied extensively with self-report measures (Lim & Butcher, 1996; Roskes, 2009), the possible presence of this behavior on direct measures has only just begun to be examined. Previous studies of faking bad on academic measures have been limited to students at the…

Development of a Web-Enabled Informatics Platform for Manipulation of Gene Expression Data

DTIC Science & Technology

2004-12-01

genomic platforms such as metabolomics and proteomics , and to federated databases for knowledge management. A successful SBIR Phase I completed...measurements that require sophisticated bioinformatic platforms for data archival, management, integration, and analysis if researchers are to derive...web-enabled bioinformatic platform consisting of a Laboratory Information Management System (LIMS), an Analysis Information Management System (AIMS

Wintertime nitric acid chemistry - Implications from three-dimensional model calculations

NASA Technical Reports Server (NTRS)

Rood, Richard B.; Kaye, Jack A.; Douglass, Anne R.; Allen, Dale J.; Steenford, Stephen

1990-01-01

A three-dimensional simulation of the evolution of HNO3 has been run for the winter of 1979. Winds and temperatures are taken from a stratospheric data assimilation analysis, and the chemistry is based on Limb Infrared Monitor of the Stratosphere (LIMS) observations. The model is compared to LIMS observations to investigate the problem of 'missing' nitric acid chemistry in the winter hemisphere. Both the model and observations support the contention that a nitric acid source is needed outside of the polar vortex and north of the subtropics. Observations suggest that HNO3 is not dynamically controlled in middle latitudes. The model shows that given the time scales of conventional chemistry, dynamical control is expected. Therefore, an error exists in the conventional chemistry or additional processes are needed to bring the model and data into agreement. Since the polar vortex is dynamically isolated from the middle latitudes, and since the highest HNO3 values are observed in October and November, a source associated solely with polar stratospheric clouds cannot explain the deficiencies in the chemistry. The role of heterogeneous processes on background aerosols is reviewed in light of these results.

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

Gas engineering studies for high pressure self-sustained diffuse discharge closing switches

NASA Astrophysics Data System (ADS)

Hunter, S. R.; Christophorou, L. G.; Carter, J. G.

The operating voltage and discharge stability of diffuse discharges for fast-closing switch applications are critically dependent on the variation of the ionization (alpha/N) and attachment (eta/N) coefficients with E/N (gas density normalized electric field strength). Gases and gas mixtures which possess low (E/N)/sub lim/ values (i.e., the E/N value when anti alpha/N = alpha/N - eta/N = 0) and effective ionization coefficients, anti alpha/N, which vary slowly with E/N near (E/N)(sub lim) lead to lower voltage (i.e., more efficient) operation with increased discharge stability. Several gas mixtures with these characteristics are discussed. It is argued that further improvements in switch efficiency and discharge stability can be obtained by adding a low ionization onset gas additive to these binary mixtures, such that at low E/N, alpha/N is greater than eta/N, while at higher E/N, eta/N is greater than alpha/N over a restricted E/N range. Several low ionization onset gas additives are suggested and the electron attachment and ionization coefficients in selected gas mixtures which possess these desirable characteristics are given.

A33 antibody-functionalized exosomes for targeted delivery of doxorubicin against colorectal Cancer.

PubMed

Li, Yan; Gao, Yuan; Gong, Chunai; Wang, Zhuo; Xia, Qingming; Gu, Fenfen; Hu, Chuling; Zhang, Lijuan; Guo, Huiling; Gao, Shen

2018-06-20

Exosomes have emerged as a promising drug carrier with low immunogenicity, high biocompatibility and delivery efficiency. Here in, we isolated exosomes from A33-positive LIM1215 cells (A33-Exo) and loaded them with doxorubicin (Dox). Furthermore, we coated surface-carboxyl superparamagnetic iron oxide nanoparticles (US) with A33 antibodies (A33Ab-US), expecting that these A33 antibodies on the surface of the nanoparticles could bind to A33-positive exosomes and form a complex (A33Ab-US-Exo/Dox) to target A33-positive colon cancer cells. The results showed that A33Ab-US-Exo/Dox had good binding affinity and antiproliferative effect in LIM1215 cells, as shown by increased uptake of the complex. In vivo study showed that A33Ab-US-Exo/Dox had an excellent tumor targeting ability, and was able to inhibit tumor growth and prolong the survival of the mice with reduced cardiotoxicity. In summary, exosomes functionalized by targeting ligands through coating with high-density antibodies may prove to be a novel delivery system for targeted drugs against human cancers. Copyright © 2018 Elsevier Inc. All rights reserved.

DLH1 is a functional Candida albicans homologue of the meiosis-specific gene DMC1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diener, A.C.; Fink, G.R.

1996-06-01

DMC1/LIM15 homologue 1 (DLH1), a gene related to meiosis-specific genes, has been isolated from Candida albicans, a fungus thought not to undergo meiosis. The deduced protein sequence of DLH1 contains 74% amino acid identity with Dmc1p from Saccharomyces cerevisiae and 63% with Lim15p from the plant Lilium longiflorum, meiosis-specific homologous of Escherichia coli RecA. Candida DLH1 complements a dmc1/dmc1 null mutant in S. cerevisiae. High copy expression of DLH1 restores both sporulation and meiotic recombination to a Saccharomyces dmc1/{Delta}/dmc1{Delta} strain. Unlike the DMC1 gene, which is transcribed only in meiotic cells, the heterologous Candida DLH1 gene is transcribed in bothmore » vegetative and meiotic cells of S. cerevisiae. Transcription of DLH1 is not detected or induced in C. albicans under conditions that induce DMC1 and meiosis in S. cerevisiae. The presence of an intact homologue of a meiosis-specific gene in C. albicans raises the possibility that this organism has a cryptic meiotic pathway. 25 refs., 6 figs., 3 tabs.« less

Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faehnle, Christopher R.; Walleshauser, Jack; Joshua-Tor, Leemor

2017-07-03

The uridyl transferases TUT4 and TUT7 (collectively called TUT4(7)) switch between two modes of activity, either promoting expression of let-7 microRNA (monoU) or marking it for degradation (oligoU). Lin28 modulates the switch via recruitment of TUT4(7) to the precursor pre-let-7 in stem cells and human cancers. We found that TUT4(7) utilize two multidomain functional modules during the switch from monoU to oligoU. The catalytic module (CM) is essential for both activities, while the Lin28-interacting module (LIM) is indispensable for oligoU. A TUT7 CM structure trapped in the monoU activity staterevealed a duplex-RNA-binding pocket that orients group II pre-let-7 hairpins tomore » favor monoU addition. Conversely, the switch to oligoU requires the ZK domain of Lin28 to drive the formation of a stable ternary complex between pre-let-7 and the inactive LIM. Finally, ZK2 of TUT4(7) aids oligoU addition by engaging the growing oligoU tail through uracil-specific interactions.« less

Nuclear translocation of the cytoskeleton-associated protein, smALP, upon induction of skeletal muscle differentiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cambier, Linda; Pomies, Pascal, E-mail: pascal.pomies@crbm.cnrs.fr

2011-06-17

Highlights: {yields} The cytoskeleton-associated protein, smALP, is expressed in differentiated skeletal muscle. {yields} smALP is translocated from the cytoplasm to the nucleus of C2C12 myoblasts upon induction of myogenesis. {yields} The differentiation-dependent nuclear translocation of smALP occurs in parallel with the nuclear accumulation of myogenin. {yields} The LIM domain of smALP is essential for the nuclear accumulation of the protein. {yields} smALP might act in the nucleus to control some critical aspect of the muscle differentiation process. -- Abstract: The skALP isoform has been shown to play a critical role in actin organization and anchorage within the Z-discs of skeletalmore » muscles, but no data is available on the function of the smALP isoform in skeletal muscle cells. Here, we show that upon induction of differentiation a nuclear translocation of smALP from the cytoplasm to the nucleus of C2C12 myoblasts, concomitant to an up-regulation of the protein expression, occurs in parallel with the nuclear accumulation of myogenin. Moreover, we demonstrate that the LIM domain of smALP is essential for the nuclear translocation of the protein.« less

A Model For the Limiting Time in Vortex Ring Formation

NASA Technical Reports Server (NTRS)

Shariff, Karim; Gharib, Morteza; Rambod, Edmond; Merriam, Marshal (Technical Monitor)

1997-01-01

In another presentation, Gharib et at provide experimental results to show that when a vortex ring is created from a pipe by a piston, there is a limiting time or piston stroke length beyond which multiple rings appear. This time appeared to be insensitive to piston velocity history and Reynolds number. Nature might exploit such a. limit in different contexts to coherently deliver mass or momentum flux with the least number of strokes. Here, a simple hypothesis is considered: the limiting time occurs when the apparatus is no longer able to deliver energy at a rate compatible with the requirement, due to Kelvin, that a steady vortex ring have maximum energy given circulation and impulse. More specifically, the limit is expected to occur when the quantity alpha = E/square root of Gamma(sup 3)I delivered by the piston drops below the value, alpha(sub lim) for a limiting steady vortex ring solution. The resulting predictions agree very well with the experiments (after using alpha(sub lim) measured using the experimental flow fields). The insensitivity to piston history also emerges from the model. Finally, piston histories are designed that may extend the limiting time somewhat.

ISPyB: an information management system for synchrotron macromolecular crystallography.

PubMed

Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

2011-11-15

Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

DEEP U BAND AND R IMAGING OF GOODS-SOUTH: OBSERVATIONS, DATA REDUCTION AND FIRST RESULTS ,

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nonino, M.; Cristiani, S.; Vanzella, E.

2009-08-01

We present deep imaging in the U band covering an area of 630 arcmin{sup 2} centered on the southern field of the Great Observatories Origins Deep Survey (GOODS). The data were obtained with the VIMOS instrument at the European Southern Observatory (ESO) Very Large Telescope. The final images reach a magnitude limit U {sub lim} {approx} 29.8 (AB, 1{sigma}, in a 1'' radius aperture), and have good image quality, with full width at half-maximum {approx}0.''8. They are significantly deeper than previous U-band images available for the GOODS fields, and better match the sensitivity of other multiwavelength GOODS photometry. The deepermore » U-band data yield significantly improved photometric redshifts, especially in key redshift ranges such as 2 < z < 4, and deeper color-selected galaxy samples, e.g., Lyman break galaxies at z {approx} 3. We also present the co-addition of archival ESO VIMOS R-band data, with R {sub lim} {approx} 29 (AB, 1{sigma}, 1'' radius aperture), and image quality {approx}0.''75. We discuss the strategies for the observations and data reduction, and present the first results from the analysis of the co-added images.« less

An audit of half-count myocardial perfusion imaging using resolution recovery software.

PubMed

Lawson, Richard S; White, Duncan; Nijran, Kuldip; Cade, Sarah C; Hall, David O; Kenny, Bob; Knight, Andy; Livieratos, Lefteris; Murray, Anthony; Towey, David

2014-05-01

The Nuclear Medicine Software Quality Group of the Institute of Physics and Engineering in Medicine has conducted a multicentre, multivendor audit to evaluate the use of resolution recovery software from several manufacturers when applied to myocardial perfusion data with half the normal counts acquired under a variety of clinical protocols in a range of departments. The objective was to determine whether centres could obtain clinical results with half-count data processed with resolution recovery software that were equivalent to those obtained using their normal protocols. Sixteen centres selected 50 routine myocardial perfusion studies each, from which the Nuclear Medicine Software Quality Group generated simulated half-count studies using Poisson resampling. These half-count studies were reconstructed using resolution recovery and the clinical reports compared with the original reports from the full-count data. A total of 769 patient studies were processed and compared. Eight centres found only a small number of clinically relevant discrepancies between the two reports, whereas eight had an unacceptably high number of discrepancies. There were no significant differences in acquisition parameters between the two groups, although centres finding a high number of discrepancies were more likely to perform both rest and stress scans on normal studies. Half of the participating centres could potentially make use of resolution recovery to reduce the administered activity for myocardial perfusion scans without changing their routine acquisition protocols. The other half could consider adjusting the reconstruction parameters used with their resolution recovery software if they wish to use reduced activity successfully.

Measuring outcomes in children's rehabilitation: a decision protocol.

PubMed

Law, M; King, G; Russell, D; MacKinnon, E; Hurley, P; Murphy, C

1999-06-01

To develop and test the feasibility and clinical utility of a computerized self-directed software program designed to enable service providers in children's rehabilitation to make decisions about the most appropriate outcome measures to use in client and program evaluation. A before-and-after design was used to test the feasibility and initial impact of the decision-making outcome software in improving knowledge and use of clinical outcome measures. A children's rehabilitation center in a city of 50,000. All service providers in the children's rehabilitation center. Disciplines represented included early childhood education, occupational therapy, physical therapy, speech and language pathology, audiology, social work, and psychology. Using a conceptual framework based on the International Classification of Impairment, Disability, and Handicap (ICIDH), an outcome measurement decision-making protocol was developed. The decision-making protocol was computerized in an educational software program with an attached database of critically appraised measures. Participants learned about outcome measures through the program and selected outcome measures that met their specifications. The computer software was tested for feasibility in the children's rehabilitation center for 6 months. Knowledge and use of clinical outcome measures were determined before and after the feasibility testing using a survey of all service providers currently at the centre and audits of 30 randomly selected rehabilitation records (at pretest, posttest, and follow-up). Service providers indicated that the outcomes software was easy to follow and believed that the use of the ICIDH framework helped them in making decisions about selecting outcome measures. Results of the survey indicated that there were significant changes in the service providers' level of comfort with selecting measures and knowing what measures were available. Use of outcome measures as identified through the audit did not change. The "All About Outcomes" software is clinically useful. Further research should evaluate whether using the software affects the use of outcome measures in clinical practice.

Use and Perceived Benefits of Handheld Computer-based Clinical References

PubMed Central

Rothschild, Jeffrey M.; Fang, Edward; Liu, Vincent; Litvak, Irina; Yoon, Cathy; Bates, David W.

2006-01-01

Objective Clinicians are increasingly using handheld computers (HC) during patient care. We sought to assess the role of HC-based clinical reference software in medical practice by conducting a survey and assessing actual usage behavior. Design During a 2-week period in February 2005, 3600 users of a HC-based clinical reference application were asked by e-mail to complete a survey and permit analysis of their usage patterns. The software includes a pharmacopeia, an infectious disease reference, a medical diagnostic and therapeutic reference and transmits medical alerts and other notifications during HC synchronizations. Software usage data were captured during HC synchronization for the 4 weeks prior to survey completion. Measurements Survey responses and software usage data. Results The survey response rate was 42% (n = 1501). Physicians reported using the clinical reference software for a mean of 4 years and 39% reported using the software during more than half of patient encounters. Physicians who synchronized their HC during the data collection period (n = 1249; 83%) used the pharmacopeia for unique drug lookups a mean of 6.3 times per day (SD 12.4). The majority of users (61%) believed that in the prior 4 weeks, use of the clinical reference prevented adverse drug events or medication errors 3 or more times. Physicians also believed that alerts and other notifications improved patient care if they were public health warnings (e.g. about influenza), new immunization guidelines or drug alert warnings (e.g. rofecoxib withdrawal). Conclusion Current adopters of HC-based medical references use these tools frequently, and found them to improve patient care and be valuable in learning of recent alerts and warnings. PMID:16929041

SEURAT: Visual analytics for the integrated analysis of microarray data

PubMed Central

2010-01-01

Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data. PMID:20525257

CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

PubMed

Bumm, Klaus; Zheng, Mingzhong; Bailey, Clyde; Zhan, Fenghuang; Chiriva-Internati, M; Eddlemon, Paul; Terry, Julian; Barlogie, Bart; Shaughnessy, John D

2002-02-01

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.

[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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.« less

Application of CT-PSF-based computer-simulated lung nodules for evaluating the accuracy of computer-aided volumetry.

PubMed

Funaki, Ayumu; Ohkubo, Masaki; Wada, Shinichi; Murao, Kohei; Matsumoto, Toru; Niizuma, Shinji

2012-07-01

With the wide dissemination of computed tomography (CT) screening for lung cancer, measuring the nodule volume accurately with computer-aided volumetry software is increasingly important. Many studies for determining the accuracy of volumetry software have been performed using a phantom with artificial nodules. These phantom studies are limited, however, in their ability to reproduce the nodules both accurately and in the variety of sizes and densities required. Therefore, we propose a new approach of using computer-simulated nodules based on the point spread function measured in a CT system. The validity of the proposed method was confirmed by the excellent agreement obtained between computer-simulated nodules and phantom nodules regarding the volume measurements. A practical clinical evaluation of the accuracy of volumetry software was achieved by adding simulated nodules onto clinical lung images, including noise and artifacts. The tested volumetry software was revealed to be accurate within an error of 20 % for nodules >5 mm and with the difference between nodule density and background (lung) (CT value) being 400-600 HU. Such a detailed analysis can provide clinically useful information on the use of volumetry software in CT screening for lung cancer. We concluded that the proposed method is effective for evaluating the performance of computer-aided volumetry software.

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://www.dragonsys.com/ http://www.software.ibm/com/is/voicetype/ http://www.lhs.com/

SU-E-P-05: Electronic Brachytherapy: A Physics Perspective On Field Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pai, S; Ayyalasomayajula, S; Lee, S

2015-06-15

Purpose: We want to summarize our experience implementing a successful program of electronic brachytherapy at several dermatology clinics with the help of a cloud based software to help us define the key program parameters and capture physics QA aspects. Optimally developed software helps the physicist in peer review and qualify the physical parameters. Methods: Using the XOFT™ Axxent™ electronic brachytherapy system in conjunction with a cloud-based software, a process was setup to capture and record treatments. It was implemented initially at about 10 sites in California. For dosimetric purposes, the software facilitated storage of the physics parameters of surface applicatorsmore » used in treatment and other source calibration parameters. In addition, the patient prescription, pathology and other setup considerations were input by radiation oncologist and the therapist. This facilitated physics planning of the treatment parameters and also independent check of the dwell time. From 2013–2014, nearly1500 such calculation were completed by a group of physicists. A total of 800 patients with multiple lesions have been treated successfully during this period. The treatment log files have been uploaded and documented in the software which facilitated physics peer review of treatments per the standards in place by AAPM and ACR. Results: The program model was implemented successfully at multiple sites. The cloud based software allowed for proper peer review and compliance of the program at 10 clinical sites. Dosimtery was done on 800 patients and executed in a timely fashion to suit the clinical needs. Accumulated physics data in the software from the clinics allows for robust analysis and future development. Conclusion: Electronic brachytherapy implementation experience from a quality assurance perspective was greatly enhanced by using a cloud based software. The comprehensive database will pave the way for future developments to yield superior physics outcomes.« less

Report to Congress on the Defense Industrial Base: Critical Industries Planning

DTIC Science & Technology

1990-10-01

interactions between fibers and matrices, and production, each exhibiting its own unique the adhesive or fastening systems used to join characteristics. The... interaction among companies specializing in the Douglas and Custom Machine Inc.. although various areas in order to optimize the total Japanese suppliers...Minarad Scientific Inc. Barrianeer Research Lim. Contraves Goerz Corp. Geophysical Environmental Research Corp IRIS Fiber Optics ITT Corp. Magnavox

Species Profiles: Life Histories and Environmental Requirements of Coastal Fishes and Invertebrates (Pacific Southwest). Chinook Salmon.

DTIC Science & Technology

1986-04-01

LAS UN SFED M AALLE NET A 6 F iS-82- 49 F/G /3 U INLA E NEhhIhLson1hsohhIN I flflflfl.... 1.0 ~2𔃻’l lim MICROCOPY RESOLUTION TESI CHART NATIONAL...22 II it released from Coleman National Fish Nordstrom, D. 1977. Hydrogeochemical Hatchery, on naturally produced and microbiological factors affect

Southeast Asia Report.

DTIC Science & Technology

1984-10-05

Outlines New National Economic Policy (SIN CHEW JIT POH MALAYSIA, 17 Jul 84) .,. 32 DAP Prepares To Stage Comeback (KIN KWOK DAILY NEWS, 17 Jul 84...51 Cars Import Banned 51 Joint Exercise With Indonesia 51 Neo on MCA Rift 51 DAP Election Preparations 52 PHILIPPINES Health, Social Workers...Lim Kit Siang, secretary general of the Democratic Action Party [ DAP ], today urged the Malaysian government to change its so-called "Chinese

Ahdaf al-ta'lim al-fanni, al-tujari, al-zira'i, wal-sina'i (Vocational Education Objectives: Commercial, Agricultural and Industrial).

ERIC Educational Resources Information Center

Ministry of Education, Cairo (United Arab Republic).

This document is an English-language abstract (approximately 1,500 words) of a publication outlining the objectives and problems of vocational education in the United Arab Republic. The data presented include both the general objectives of vocational education and the specific goals of each type. The goal of vocational education is to prepare…

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

A Business Case Analysis for the Vulture Program

DTIC Science & Technology

2010-12-01

HARNESSING SOLAR POWER FOR UNMANNED AERIAL VEHICLES Marty Curry noted in a NASA Dryden Fact Sheet, “The first flight of a solar- powered aircraft...wavelength of light absorbed. In order to produce enough power to be 20 Marty Curry , “Solar Power...40 Lim, “Global Observer,” 37. 41 Marty Curry , “Global Hawk – Performance & Specifications,” NASA Dryden Fact Sheet, 7

Qanun raqam 68 li-sanat 1968 fi sha'n al-ta'lim al-am (Law No. 68 of 1968 Concerning General Education).

ERIC Educational Resources Information Center

United Arab Republic.

This document is an English-language abstract (approximately 1,500 words) of a law passed by the UAR legislation covering elementary, preparatory, and secondary education. This law covers general regulations common to all three stages of education, the objectives of which are defined as the general intellectual, physical, moral, civic and national…

Impact of Regional Differences within State on the Factors Influencing Youth Entrepreneurship--A Case of Garhwal and Kumaun Regions of Uttarakhand

ERIC Educational Resources Information Center

Sharma, Lalit

2015-01-01

Lee, Chang & Lim (2005) state that the impact of entrepreneurship education in each country is different because of each country's unique culture with regard to entrepreneurship. Going by the above argument, this research paper intends to make a formal enquiry on whether the above effect holds true for different regions within a particular…

Incorporation of diet information derived from Bayesian stable isotope mixing models into mass-balanced marine ecosystem models: A case study from the Marennes-Oleron Estuary, France

EPA Science Inventory

We investigated the use of output from Bayesian stable isotope mixing models as constraints for a linear inverse food web model of a temperate intertidal seagrass system in the Marennes-Oléron Bay, France. Linear inverse modeling (LIM) is a technique that estimates a complete net...

Validity of the KABC-II Culture-Language Interpretive Matrix: A Comparison of Native English Speakers and Spanish-Speaking English Language Learners

ERIC Educational Resources Information Center

Van Deth, Leah M.

2013-01-01

The purpose of the present study was to investigate the validity of the Culture-Language Interpretive Matrix (C-LIM; Flanagan, Ortiz, & Alfonso, 2013) when applied to scores from the Kaufman Assessment Battery for Children, 2nd Edition (KABC-II; Kaufman & Kaufman, 2004). Data were analyzed from the KABC-II standardization sample as well as…

Variability in total ozone associated with baroclinic waves

NASA Technical Reports Server (NTRS)

Mote, Philip W.; Holton, James R.; Wallace, John M.

1991-01-01

One-point regression maps of total ozone formed by regressing the time series of bandpass-filtered geopotential height data have been analyzed against Total Ozone Mapping Spectrometer data. Results obtained reveal a strong signature of baroclinic waves in the ozone variability. The regressed patterns are found to be similar in extent and behavior to the relative vorticity patterns reported by Lim and Wallace (1991).

Hippi Care Hospital: Towards Proactive Business Processes in Emergency Room Services. Teaching Case

ERIC Educational Resources Information Center

Tan, Kar Way; Shankararaman, Venky

2014-01-01

It was 2:35 am on a Saturday morning. Wiki Lim, process specialist from the Process Innovation Centre (PIC) of Hippi Care Hospital (HCH), desperately doodling on her notepad for ideas to improve service delivery at HCH's Emergency Department (ED). HCH has committed to the public that its ED would meet the service quality criterion of serving 90%…

Identifying sustainable foods: the relationship between environmental impact, nutritional quality, and prices of foods representative of the French diet.

PubMed

Masset, Gabriel; Soler, Louis-Georges; Vieux, Florent; Darmon, Nicole

2014-06-01

Sustainable diets, as defined by the Food and Agriculture Organization, need to combine environment, nutrition, and affordability dimensions. However, it is unknown whether these dimensions are compatible, and no guidance is available in the official recommendations. To identify foods with compatible sustainability dimensions. For 363 of the most commonly consumed foods in the Second French Individual and National Study on Food Consumption, environmental impact indicators (ie, greenhouse gas [GHG] emissions, acidification, and eutrophication), and prices were collected. The nutritional quality of the foods was assessed by calculating the score for the nutritional adequacy of individual foods (SAIN) to score for disqualifying nutrients (LIM) ratio. A sustainability score based on the median GHG emissions, price, and SAIN:LIM was calculated for each food; the foods with the best values for all three variables received the highest score. The environmental indicators were strongly and positively correlated. Meat, fish, and eggs and dairy products had the strongest influence on the environment; starchy foods, legumes, and fruits and vegetables had the least influence. GHG emissions were inversely correlated with SAIN:LIM (r=-0.37) and positively correlated with price per kilogram (r=0.59); the correlation with price per kilocalorie was null. This showed that foods with a heavy environmental impact tend to have lower nutritional quality and a higher price per kilogram but not a lower price per kilocalorie. Using price per kilogram, 94 foods had a maximum sustainability score, including most plant-based foods and excluding all foods with animal ingredients except milk, yogurt, and soups. Using price per kilocalorie restricted the list to 42 foods, including 52% of all starchy foods and legumes but only 11% of fruits and vegetables (mainly 100% fruit juices). Overall, the sustainability dimensions seemed to be compatible when considering price per kilogram of food. However, this conclusion is too simplistic when considering price per kilocalorie, which highlights the need to integrate the data at the diet level. Copyright © 2014 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Bioaccessibility of nitro- and oxy-PAHs in fuel soot assessed by an in vitro digestive model with absorptive sink.

PubMed

Zhang, Yanyan; Pignatello, Joseph J; Tao, Shu

2016-11-01

Ingestion of soot present in soil or other environmental particles is expected to be an important route of exposure to nitro and oxygenated derivatives of polycyclic aromatic hydrocarbons (PAHs). We measured the apparent bioaccessibility (B app ) of native concentrations of 1-nitropyrene (1N-PYR), 9-fluorenone (9FLO), anthracene-9,10-dione (ATQ), benzo[a]anthracene-7,12-dione (BaAQ), and benzanthrone (BZO) in a composite fuel soot sample using a previously-developed in vitro human gastrointestinal model that includes silicone sheet as a third-phase absorptive sink. Along with B app , we determined the 24-h sheet-digestive fluid partition coefficient (K s,24h ), the soot residue-fluid distribution ratio of the labile sorbed fraction after digestion (K r,lab ), and the maximum possible (limiting) bioaccessibility, B lim . The B app of PAH derivatives was positively affected by the presence of the sheet due to mass-action removal of the sorbed compounds. In all cases B app increased with imposition of fed conditions. The enhancement of B app under fed conditions is due to increasingly favorable mass transfer of target compounds from soot to fluid (increasing bile acid concentration, or adding food lipids) or transfer from fluid to sheet (by raising small intestinal pH). Food lipids may also enhance B app by mobilizing contaminants from nonlabile to labile states of the soot. Compared to the parent PAH, the derivatives had larger K r,lab , despite having lower partition coefficients to various hydrophobic reference phases including silicone sheet. The B lim of the derivatives under the default conditions of the model ranged from 65.5% to 34.4%, in the order, 1N-PYR > ATQ > 9FLO > BZO > BaAQ, with no significant correlation with hydrophobic parameters, nor consistent relationship with B lim of the parent PAH. Consistent with earlier experiments on a wider range of PAHs, the results suggest that a major determinant of bioaccessibility is the distribution of chemical between nonlabile and labile states in the original solid. Copyright © 2016 Elsevier Ltd. All rights reserved.

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 that major faunal and oceanic changes occurred in the westem Caribbean over the last 4 million years, probably related to changes in ocean circulation due to the emergence of the Isthmus as well as other climatic events.

Effective ionization coefficient of C5 perfluorinated ketone and its mixtures with air

NASA Astrophysics Data System (ADS)

Aints, Märt; Jõgi, Indrek; Laan, Matti; Paris, Peeter; Raud, Jüri

2018-04-01

C5 perfluorinated ketone (C5 PFK with UIPAC chemical name 1,1,1,3,4,4,4-heptafluoro-3-(trifluoromethyl)-2-butanone and sold by 3M as Novec™ 5110) has a high dielectric strength and a low global warming potential, which makes it interesting as an insulating gas in medium and high-voltage applications. The study was carried out to determine the effective Townsend ionization coefficient α eff as a function of electric field strength and gas density for C5 PFK and for its mixtures with air. The non-self-sustained Townsend discharge between parallel plate electrodes was initiated by illuminating the cathode by UV radiation. The discharge current, I, was measured as a function of inter-electrode distance, d, at different gas densities, N, and electric field strengths, E. The effective ionization coefficient α eff was determined from the semi-logarithmic plots of I/I 0 against d. For each tested gas mixture, the density normalized effective ionization coefficient α eff/N was found to be a unique function of reduced electric field strength E/N. The measurements were carried out in the absolute pressure range of 0.05-1.3 bar and E/N range of 150-1200 Td. The increasing fraction of C5 PFK in air resulted in the decrease of effective ionization coefficient. The limiting electric field strength (E/N)lim where the effective ionization coefficient α eff became zero was 770 Td (190 kV cm-1 at 1 bar) for pure C5 PFK and decreased to 225 Td (78 kV cm-1 at 1.4 bar) for 7.6% C5 PFK/air mixture. The latter value of (E/N)lim is still more than two times higher than the (E/N)lim value of synthetic air and about two-thirds of the value corresponding to pure SF6. The investigated gas mixtures have the potential to become an alternative to SF6 in numerous high- and medium-voltage applications.

Sinusoidal high-intensity exercise does not elicit ventilatory limitation in chronic obstructive pulmonary disease.

PubMed

Porszasz, Janos; Rambod, Mehdi; van der Vaart, Hester; Rossiter, Harry B; Ma, Shuyi; Kiledjian, Rafi; Casaburi, Richard

2013-06-01

During exercise at critical power (CP) in chronic obstructive pulmonary disease (COPD) patients, ventilation approaches its maximum. As a result of the slow ventilatory dynamics in COPD, ventilatory limitation during supramaximal exercise might be escaped using rapid sinusoidal forcing. Nine COPD patients [age, 60.2 ± 6.9 years; forced expiratory volume in the first second (FEV(1)), 42 ± 17% of predicted; and FEV(1)/FVC, 39 ± 12%] underwent an incremental cycle ergometer test and then four constant work rate cycle ergometer tests; tolerable duration (t(lim)) was recorded. Critical power was determined from constant work rate testing by linear regression of work rate versus 1/t(lim). Patients then completed fast (FS; 60 s period) and slow (SS; 360 s period) sinusoidally fluctuating exercise tests with mean work rate at CP and peak at 120% of peak incremental test work rate, and one additional test at CP; each for a 20 min target. The value of t(lim) did not differ between CP (19.8 ± 0.6 min) and FS (19.0 ± 2.5 min), but was shorter in SS (13.2 ± 4.2 min; P < 0.05). The sinusoidal ventilatory amplitude was minimal (37.4 ± 34.9 ml min(-1) W(-1)) during FS but much larger during SS (189.6 ± 120.4 ml min(-1) W(-1)). The total ventilatory response in SS reached 110 ± 8.0% of the incremental test peak, suggesting ventilatory limitation. Slow components in ventilation during constant work rate and FS exercises were detected in most subjects and contributed appreciably to the total response asymptote. The SS exercise was associated with higher mid-exercise lactate concentrations (5.2 ± 1.7, 7.6 ± 1.7 and 4.5 ± 1.3 mmol l(-1) in FS, SS and CP). Large-amplitude, rapid sinusoidal fluctuation in work rate yields little fluctuation in ventilation despite reaching 120% of the incremental test peak work rate. This high-intensity exercise strategy might be suitable for programmes of rehabilitative exercise training in COPD.

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.

Remediation of Deficits in Recognition of Facial Emotions in Children with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Weinger, Paige M.; Depue, Richard A.

2011-01-01

This study evaluated the efficacy of the Mind Reading interactive computer software to remediate emotion recognition deficits in children with autism spectrum disorders (ASD). Six unmedicated children with ASD and 11 unmedicated non-clinical control subjects participated in the study. The clinical sample used the software for five sessions. The…

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…

Clinical data miner: an electronic case report form system with integrated data preprocessing and machine-learning libraries supporting clinical diagnostic model research.

PubMed

Installé, Arnaud Jf; Van den Bosch, Thierry; De Moor, Bart; Timmerman, Dirk

2014-10-20

Using machine-learning techniques, clinical diagnostic model research extracts diagnostic models from patient data. Traditionally, patient data are often collected using electronic Case Report Form (eCRF) systems, while mathematical software is used for analyzing these data using machine-learning techniques. Due to the lack of integration between eCRF systems and mathematical software, extracting diagnostic models is a complex, error-prone process. Moreover, due to the complexity of this process, it is usually only performed once, after a predetermined number of data points have been collected, without insight into the predictive performance of the resulting models. The objective of the study of Clinical Data Miner (CDM) software framework is to offer an eCRF system with integrated data preprocessing and machine-learning libraries, improving efficiency of the clinical diagnostic model research workflow, and to enable optimization of patient inclusion numbers through study performance monitoring. The CDM software framework was developed using a test-driven development (TDD) approach, to ensure high software quality. Architecturally, CDM's design is split over a number of modules, to ensure future extendability. The TDD approach has enabled us to deliver high software quality. CDM's eCRF Web interface is in active use by the studies of the International Endometrial Tumor Analysis consortium, with over 4000 enrolled patients, and more studies planned. Additionally, a derived user interface has been used in six separate interrater agreement studies. CDM's integrated data preprocessing and machine-learning libraries simplify some otherwise manual and error-prone steps in the clinical diagnostic model research workflow. Furthermore, CDM's libraries provide study coordinators with a method to monitor a study's predictive performance as patient inclusions increase. To our knowledge, CDM is the only eCRF system integrating data preprocessing and machine-learning libraries. This integration improves the efficiency of the clinical diagnostic model research workflow. Moreover, by simplifying the generation of learning curves, CDM enables study coordinators to assess more accurately when data collection can be terminated, resulting in better models or lower patient recruitment costs.

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

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

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.

AnyWave: a cross-platform and modular software for visualizing and processing electrophysiological signals.

PubMed

Colombet, B; Woodman, M; Badier, J M; Bénar, C G

2015-03-15

The importance of digital signal processing in clinical neurophysiology is growing steadily, involving clinical researchers and methodologists. There is a need for crossing the gap between these communities by providing efficient delivery of newly designed algorithms to end users. We have developed such a tool which both visualizes and processes data and, additionally, acts as a software development platform. AnyWave was designed to run on all common operating systems. It provides access to a variety of data formats and it employs high fidelity visualization techniques. It also allows using external tools as plug-ins, which can be developed in languages including C++, MATLAB and Python. In the current version, plug-ins allow computation of connectivity graphs (non-linear correlation h2) and time-frequency representation (Morlet wavelets). The software is freely available under the LGPL3 license. AnyWave is designed as an open, highly extensible solution, with an architecture that permits rapid delivery of new techniques to end users. We have developed AnyWave software as an efficient neurophysiological data visualizer able to integrate state of the art techniques. AnyWave offers an interface well suited to the needs of clinical research and an architecture designed for integrating new tools. We expect this software to strengthen the collaboration between clinical neurophysiologists and researchers in biomedical engineering and signal processing. Copyright © 2015 Elsevier B.V. All rights reserved.

Practical Applications of Digital Pathology.

PubMed

Saeed-Vafa, Daryoush; Magliocco, Anthony M

2015-04-01

Virtual microscopy and advances in machine learning have paved the way for the ever-expanding field of digital pathology. Multiple image-based computing environments capable of performing automated quantitative and morphological analyses are the foundation on which digital pathology is built. The applications for digital pathology in the clinical setting are numerous and are explored along with the digital software environments themselves, as well as the different analytical modalities specific to digital pathology. Prospective studies, case-control analyses, meta-analyses, and detailed descriptions of software environments were explored that pertained to digital pathology and its use in the clinical setting. Many different software environments have advanced platforms capable of improving digital pathology and potentially influencing clinical decisions. The potential of digital pathology is vast, particularly with the introduction of numerous software environments available for use. With all the digital pathology tools available as well as those in development, the field will continue to advance, particularly in the era of personalized medicine, providing health care professionals with more precise prognostic information as well as helping them guide treatment decisions.

Browsing Software of the Visible Korean Data Used for Teaching Sectional Anatomy

ERIC Educational Resources Information Center

Shin, Dong Sun; Chung, Min Suk; Park, Hyo Seok; Park, Jin Seo; Hwang, Sung Bae

2011-01-01

The interpretation of computed tomographs (CTs) and magnetic resonance images (MRIs) to diagnose clinical conditions requires basic knowledge of sectional anatomy. Sectional anatomy has traditionally been taught using sectioned cadavers, atlases, and/or computer software. The computer software commonly used for this subject is practical and…

Canary: An NLP Platform for Clinicians and Researchers.

PubMed

Malmasi, Shervin; Sandor, Nicolae L; Hosomura, Naoshi; Goldberg, Matt; Skentzos, Stephen; Turchin, Alexander

2017-05-03

Information Extraction methods can help discover critical knowledge buried in the vast repositories of unstructured clinical data. However, these methods are underutilized in clinical research, potentially due to the absence of free software geared towards clinicians with little technical expertise. The skills required for developing/using such software constitute a major barrier for medical researchers wishing to employ these methods. To address this, we have developed Canary, a free and open-source solution designed for users without natural language processing (NLP) or software engineering experience. It was designed to be fast and work out of the box via a user-friendly graphical interface.

Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

NASA Astrophysics Data System (ADS)

Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

2016-12-01

3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

Two is Better than One, but Mine is Better than Ours: Preschoolers' Executive Function during Co-Play

ERIC Educational Resources Information Center

Qu, Li

2011-01-01

The current study investigated how playing with another individual may influence 3- and 4-year-olds' executive function in the Less-Is-More (LIM) task, where children point to the tray with the smaller amount of treats so as to obtain the larger amount of treats in the other tray. In Experiment 1, 35 Singaporean children were tested with a self…

Informed Questions on Malaysia

DTIC Science & Technology

2003-03-01

deputy Anwar Ibrahim before the last election, but ended up jailing him instead on highly suspect corruption and homosexual charges. His designated...his desire to see through a smooth transition, or his fear that Anwar Ibrahim may rise again to wreak revenge on his family and his cronies? US...2] AP, “Iraq Disappointed in Weak Arab Support”, Feb 24, 2003. [3] Quoted in Media statement, Lim Kit Siang, DAP National Chairman, 18/9/2002

Tatwir al-ta'lim al-sina'i fi al-Jumhurriyah al-'arabiyah al-Muttahidah (Development of Industrial Education in the United Arab Republic).

ERIC Educational Resources Information Center

Ministry of Education, Cairo (United Arab Republic).

This document is an English-language abstract (approximately 1,500 words) of a publication giving the steps to be taken to develop industrial education to conform to the socialist economic planning in the UAR. It is divided into eight sections dealing with various aspects of development: (1) curricula of technical schools; (2) general description…

Review of U.S. Army Aviation Accident Reports: Prevalence of Environmental Stressors and Medical Conditions

DTIC Science & Technology

2017-10-18

including spatial disorientation, hypoxia, altitude, thermal stress, noise, vibration, psychological stress, cognitive workload, and fatigue. In most...in the fields of aviation and human factors for many years. In fact, a recent article provides a brief description of military aviation psychology ... cognitive performance, loss of attention, decreased reaction time, and memory impairments (e.g., Lim & Dinges, 2008, attention/reaction time; Van

Results from two years of ozone data taken with a new, ground-based microwave instrument: An overview

NASA Technical Reports Server (NTRS)

Parrish, A.; Connor, B. J.; Tsou, J. J.; Mcdermid, I. S.; Chu, W. P.; Siskind, D. E.

1994-01-01

An overview of two years of data obtained with a ground-based microwave instrument is given. Intercomparisons with data obtained by the co-located JPL lidar and by SAGE 2 during near overpasses of the site are discussed, as are comparisons with mesospheric data taken earlier by SME and LIMS. Observations of diurnal variations of mesospheric ozone are shown.

Improved Therapeutic Regimens for Treatment of Post-Traumatic Ocular Infections

DTIC Science & Technology

2011-05-01

cystoid macular oedema in uveitis . Clin. Exp. Ophthalmol. 29, 2–6 (2001). 36 Campochiaro PA, Lim JI. Aminoglycoside toxicity in the treatment of...TELEPHONE NUMBER (include area code) Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 Improved Therapeutic Regimens for Treatment of...injury and adequate treatment . This proposal was designed to analyze the effectiveness of antibiotics, anti-inflammatory drugs, and non-conventional

Specific Inhibition of HER-2/neu Transcription Initiation

DTIC Science & Technology

2006-07-01

normoxia due to posttranslational processing involving proline hy- droxylation and the von Hippel Lindau (VHL) protein, a multifunctional adapter...inducible factor 1 alpha; VHL, Von Hippel Lindau; HRE, hypoxia response element; VEGF, vascular endothelial growth factor; PI3K, phosphatidyl inositol...Biol. 13, 167-171. 3. Zhong, H., De Marzo, A. M., Laughner, E., Lim, M., Hilton , D. A., Zagzag, D., Buechler, P ., Isaacs, W. B., Semenza, G. L., and

The Role of Drosophila Merlin in the Control of Mitosis Exit and Development

DTIC Science & Technology

2007-07-01

presenta- tion would be severe and consistent with the con- ventional form of NF2. Schwannomatosis , a recently defined form of neu- rofibromatosis, is...characterized by multiple sch- wannomas without any NF2-associated vestibular schwannomas. Patients with schwannomatosis fre- quently present with...approximately one-third of patients with schwannomatosis had tumors in an anatomically lim- ited distribution, such as a single limb, several con- tiguous

Informativeness of Wind Data in Linear Madden-Julian Oscillation Prediction

DTIC Science & Technology

2016-08-15

Linear inverse models (LIMs) are used to explore predictability and information content of the Madden–Julian Oscillation (MJO). Hindcast skill for...mostly at the largest scales, adds 1–2 days of skill. Keywords: linear inverse modeling; Madden–Julian Oscillation; sub-seasonal prediction 1...tion that may reflect on the MJO’s incompletely under- stood dynamics. Cavanaugh et al. (2014, hereafter C14) explored the skill of linear inverse

Predictability and Coupled Dynamics of MJO During DYNAMO

DTIC Science & Technology

2013-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Predictability and Coupled Dynamics of MJO During DYNAMO ...Model (LIM) for MJO predictions and apply it in retrospective cross-validated forecast mode to the DYNAMO time period. APPROACH We are working as...a team to study MJO dynamics and predictability using several models as team members of the ONR DRI associated with the DYNAMO experiment. This is a

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.

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

Abnormal expression of leiomyoma cytoskeletal proteins involved in cell migration.

PubMed

Ura, Blendi; Scrimin, Federica; Arrigoni, Giorgio; Athanasakis, Emmanouil; Aloisio, Michelangelo; Monasta, Lorenzo; Ricci, Giuseppe

2016-05-01

Uterine leiomyomas are monoclonal tumors. Several factors are involved in the neoplastic transformation of the myometrium. In our study we focused on dysregulated cytoskeletal proteins in the leiomyoma as compared to the myometrium. Paired tissue samples of ten leiomyomas and adjacent myometria were obtained and analyzed by two‑dimensional gel electrophoresis (2-DE). Mass spectrometry was used for protein identification, and western blotting for 2-DE data validation. The values of ten cytoskeletal proteins were found to be significantly different: eight proteins were upregulated in the leiomyoma and two proteins were downregulated. Three of the upregulated proteins (myosin regulatory light polypeptide 9, four and a half LIM domains protein 1 and LIM and SH3 domain protein 1) are involved in cell migration, while downregulated protein transgelin is involved in replicative senescence. Myosin regulatory light polypeptide 9 (MYL9) was further validated by western blotting because it is considered to be a cell migration marker in several cancers and could play a key role in leiomyoma development. Our data demonstrate significant alterations in the expression of cytoskeletal proteins involved in leiomyoma growth. A better understanding of the involvement of cytoskeletal proteins in leiomyoma pathogenesis may contribute to the identification of new therapeutic targets and the development of new pharmacological approaches.

Evidence for the involvement of cofilin in Aspergillus fumigatus internalization into type II alveolar epithelial cells.

PubMed

Bao, Zhiyao; Han, Xuelin; Chen, Fangyan; Jia, Xiaodong; Zhao, Jingya; Zhang, Changjian; Yong, Chen; Tian, Shuguang; Zhou, Xin; Han, Li

2015-08-13

The internalization of Aspergillus fumigatus into alveolar epithelial cells (AECs) is tightly controlled by host cellular actin dynamics, which require close modulation of the ADF (actin depolymerizing factor)/cofilin family. However, the role of cofilin in A. fumigatus internalization into AECs remains unclear. Here, we demonstrated that germinated A. fumigatus conidia were able to induce phosphorylation of cofilin in A549 cells during the early stage of internalization. The modulation of cofilin activity by overexpression, knockdown, or mutation of the cofilin gene in A549 cells decreased the efficacy of A. fumigatus internalization. Reducing the phosphorylation status of cofilin with BMS-5 (LIM kinase inhibitor) or overexpression of the slingshot phosphatases also impeded A. fumigatus internalization. Both the C. botulimun C3 transferase (a specific RhoA inhibitor) and Y27632 (a specific ROCK inhibitor) reduced the internalization of A. fumigatus and the level of phosphorylated cofilin. β-1,3-glucan (the major component of the conidial cell wall) and its host cell receptor dectin-1 did not seem to be associated with cofilin phosphorylation during A. fumigatus infection. These results indicated that cofilin might be involved in the modulation of A. fumigatus internalization into type II alveolar epithelial cells through the RhoA-ROCK-LIM kinase pathway.

ISL1 and BRN3B co-regulate the differentiation of murine retinal ganglion cells

PubMed Central

Pan, Ling; Deng, Min; Xie, Xiaoling; Gan, Lin

2009-01-01

SUMMARY LIM-homeodomain (HD) and POU-HD transcription factors play critical roles in neurogenesis. However, it remains largely unknown how they cooperate in this process and what downstream target genes they regulate. Here we show that ISL1, a LIM-HD protein, is co-expressed with BRN3B, a POU-HD factor, in nascent, post-mitotic retinal ganglion cells (RGCs). Similar to the Brn3b-null retinas, retina-specific deletion of Isl1 results in the apoptosis of a majority of RGCs and in RGC axon guidance defects. The Isl1 and Brn3b double null mice display more severe retinal abnormalities with a near complete loss of RGCs, indicating the synergistic functions of these two factors. Furthermore, we show that both Isl1 and Brn3b function downstream of Math5 to regulate the expression of a common set of RGC-specific genes. Whole retina chromatin immunoprecipitation and in vitro transactivation assays reveal that ISL1 and BRN3B concurrently bind to and synergistically regulate the expression of a common set of RGC-specific genes. Thus, our results uncover a novel regulatory mechanism of BRN3B and ISL1 in RGC differentiation. PMID:18434421

Afzelin exhibits anti-cancer activity against androgen-sensitive LNCaP and androgen-independent PC-3 prostate cancer cells through the inhibition of LIM domain kinase 1.

PubMed

Zhu, Kai-Chang; Sun, Jian-Mei; Shen, Jian-Guo; Jin, Ji-Zhong; Liu, Feng; Xu, Xiao-Lin; Chen, Lin; Liu, Lin-Tao; Lv, Jia-Ju

2015-10-01

Prostate cancer presents high occurrence worldwide. Medicinal plants are a major source of novel and potentially therapeutic molecules; therefore, the aim of the present study was to investigate the possible anti-prostate cancer activity of afzelin, a flavonol glycoside that was previously isolated from Nymphaea odorata . The effect of afzelin on the proliferation of androgen-sensitive LNCaP and androgen-independent PC-3 cells was evaluated by performing a water soluble tetrazolium salt-1 assay. In addition, the effect of afzelin on the cell cycle of the LNCaP and PC-3 prostate cancer cell lines was evaluated. Western blot analysis was performed to evaluate the effect of afzelin on the kinases responsible for the regulation of actin organization. Afzelin was identified to inhibit the proliferation of LNCaP and PC3 cells, and block the cell cycle in the G 0 phase. The anticancer activity of afzelin in these cells was determined to be due to inhibition of LIM domain kinase 1 expression. Thus, the in vitro efficacy of afzelin against prostate cancer is promising; however, additional studies on different animal models are required to substantiate its anticancer potential.

Afzelin exhibits anti-cancer activity against androgen-sensitive LNCaP and androgen-independent PC-3 prostate cancer cells through the inhibition of LIM domain kinase 1

PubMed Central

ZHU, KAI-CHANG; SUN, JIAN-MEI; SHEN, JIAN-GUO; JIN, JI-ZHONG; LIU, FENG; XU, XIAO-LIN; CHEN, LIN; LIU, LIN-TAO; LV, JIA-JU

2015-01-01

Prostate cancer presents high occurrence worldwide. Medicinal plants are a major source of novel and potentially therapeutic molecules; therefore, the aim of the present study was to investigate the possible anti-prostate cancer activity of afzelin, a flavonol glycoside that was previously isolated from Nymphaea odorata. The effect of afzelin on the proliferation of androgen-sensitive LNCaP and androgen-independent PC-3 cells was evaluated by performing a water soluble tetrazolium salt-1 assay. In addition, the effect of afzelin on the cell cycle of the LNCaP and PC-3 prostate cancer cell lines was evaluated. Western blot analysis was performed to evaluate the effect of afzelin on the kinases responsible for the regulation of actin organization. Afzelin was identified to inhibit the proliferation of LNCaP and PC3 cells, and block the cell cycle in the G0 phase. The anticancer activity of afzelin in these cells was determined to be due to inhibition of LIM domain kinase 1 expression. Thus, the in vitro efficacy of afzelin against prostate cancer is promising; however, additional studies on different animal models are required to substantiate its anticancer potential. PMID:26622852

Skeletal muscle biopsy analysis in reducing body myopathy and other FHL1-related disorders.

PubMed

Malfatti, Edoardo; Olivé, Montse; Taratuto, Ana Lía; Richard, Pascale; Brochier, Guy; Bitoun, Marc; Gueneau, Lucie; Laforêt, Pascal; Stojkovic, Tanya; Maisonobe, Thierry; Monges, Soledad; Lubieniecki, Fabiana; Vasquez, Gabriel; Streichenberger, Nathalie; Lacène, Emmanuelle; Saccoliti, Maria; Prudhon, Bernard; Alexianu, Marilena; Figarella-Branger, Dominique; Schessl, Joachim; Bonnemann, Carsten; Eymard, Bruno; Fardeau, Michel; Bonne, Gisèle; Romero, Norma Beatriz

2013-09-01

FHL1 mutations have been associated with various disorders that include reducing body myopathy (RBM), Emery-Dreifuss-like muscular dystrophy, isolated hypertrophic cardiomyopathy, and some overlapping conditions. We report a detailed histochemical, immunohistochemical, electron microscopic, and immunoelectron microscopic analyses of muscle biopsies from 18 patients carrying mutations in FHL1: 14 RBM patients (Group 1), 3 Emery-Dreifuss muscular dystrophy patients (Group 2), and 1 patient with hypertrophic cardiomyopathy and muscular hypertrophy (Group 2). Group 1 muscle biopsies consistently showed RBs associated with cytoplasmic bodies. The RBs showed prominent FHL1 immunoreactivity whereas desmin, αB-crystallin, and myotilin immunoreactivity surrounded RBs. By electron microscopy, RBs were composed of electron-dense tubulofilamentous material that seemed to spread progressively between the myofibrils and around myonuclei. By immunoelectron microscopy, FHL1 protein was found exclusively inside RBs. Group 2 biopsies showed mild dystrophic abnormalities without RBs; only minor nonspecific myofibrillar abnormalities were observed under electron microscopy. Molecular analysis revealed missense mutations in the second FHL1 LIM domain in Group 1 patients and ins/del or missense mutations within the fourth FHL1 LIM domain in Group 2 patients. Our findings expand the morphologic features of RBM, clearly demonstrate the localization of FHL1 in RBs, and further illustrate major morphologic differences among different FHL1-related myopathies.

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.

Evaluation of occupation hot exposure in industrial workplaces in a subtropical country.

PubMed

Yang, Yu-Chiao; Wei, Ming-Chi; Hong, Show-Jen

2017-05-08

The objective of this study has been to evaluate the occupational heat exposure of 12 workers at 5 plants in a subtropical country. The heat stresses and strain on workers in 5 plants were assessed by the International Organization for Standardization (ISO) 7243 index (wet bulb globe temperature - WBGT) and the ISO 7933 index (maximum allowable exposure time - D_lim). Results indicated that 42% of the subjects (5 workers) surpassed the WBGT limits. According to the D_lim, 42% of the subjects could not continue working in the hot environments. The relationships between the various heat stress indices and the WBGT index were also correlated. However, further studies from different heat environments and more subjects should be performed. The sensitive dependence of skin temperature on meteorological and physiological indices for each subject was clearly observed. Obviously, the heart rate response to metabolic rate was much greater than that caused by environmental heat alone. The exponential relationship between workers' duration-limited exposure time, predicted by various estimated criteria, and WBGT were also found. Int J Occup Med Environ Health 2017;30(3):379-395. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

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.

Tuft (caveolated) cells in two human colon carcinoma cell lines.

PubMed

Barkla, D H; Whitehead, R H; Foster, H; Tutton, P J

1988-09-01

The presence of an unusual cell type in two human colon carcinoma cell lines is reported. The cells show the same morphology as "tuft" (caveolated) cells present in normal gastrointestinal epithelium. Tuft cells were seen in cell line LIM 1863 growing in vitro and in human colon carcinoma cell line LIM 2210 growing as subcutaneous solid tumour xenografts in nude mice. Characteristic morphologic features of tuft cells included a wide base, narrow apex and a tuft of long microvilli projecting from the apical surface. The microvilli are attached by a core of long microfilaments passing deep into the apical cytoplasm. Between the microvilli are parallel arrays of vesicles (caveoli) containing flocculent material. Two different but not mutually exclusive explanations for the presence of tuft cells are proposed. The first explanation is that tuft cells came from the resected tumour and have survived by mitotic division during subsequent passages. The second explanation suggests that tuft cells are the progeny of undifferentiated tumour cells. Descriptions of tuft cells in colon carcinomas are uncommon and possible reasons for this are presented. The morphology of tuft cells is consistent with that of a highly differentiated cell specialised for absorption, and these new models provide an opportunity to further investigate the structure and function of tuft cells.

Spectrally resolved laser interference microscopy

NASA Astrophysics Data System (ADS)

Butola, Ankit; Ahmad, Azeem; Dubey, Vishesh; Senthilkumaran, P.; Singh Mehta, Dalip

2018-07-01

We developed a new quantitative phase microscopy technique, namely, spectrally resolved laser interference microscopy (SR-LIM), with which it is possible to quantify multi-spectral phase information related to biological specimens without color crosstalk using a color CCD camera. It is a single shot technique where sequential switched on/off of red, green, and blue (RGB) wavelength light sources are not required. The method is implemented using a three-wavelength interference microscope and a customized compact grating based imaging spectrometer fitted at the output port. The results of the USAF resolution chart while employing three different light sources, namely, a halogen lamp, light emitting diodes, and lasers, are discussed and compared. The broadband light sources like the halogen lamp and light emitting diodes lead to stretching in the spectrally decomposed images, whereas it is not observed in the case of narrow-band light sources, i.e. lasers. The proposed technique is further successfully employed for single-shot quantitative phase imaging of human red blood cells at three wavelengths simultaneously without color crosstalk. Using the present technique, one can also use a monochrome camera, even though the experiments are performed using multi-color light sources. Finally, SR-LIM is not only limited to RGB wavelengths, it can be further extended to red, near infra-red, and infra-red wavelengths, which are suitable for various biological applications.

The LIM protein LIMD1 influences osteoblast differentiation and function

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Zyxin regulates migration of renal epithelial cells through activation of hepatocyte nuclear factor-1β.

PubMed

Choi, Yun-Hee; McNally, Brian T; Igarashi, Peter

2013-07-01

Hepatocyte nuclear factor-1β (HNF-1β) is an epithelial tissue-specific transcription factor that regulates gene expression in the kidney, liver, pancreas, intestine, and other organs. Mutations of HNF-1β in humans produce renal cysts and congenital kidney anomalies. Here, we identify the LIM-domain protein zyxin as a novel binding partner of HNF-1β in renal epithelial cells. Zyxin shuttles to the nucleus where it colocalizes with HNF-1β. Immunoprecipitation of zyxin in leptomycin B-treated cells results in coprecipitation of HNF-1β. The protein interaction requires the second LIM domain of zyxin and two distinct domains of HNF-1β. Overexpression of zyxin stimulates the transcriptional activity of HNF-1β, whereas small interfering RNA silencing of zyxin inhibits HNF-1β-dependent transcription. Epidermal growth factor (EGF) induces translocation of zyxin into the nucleus and stimulates HNF-1β-dependent promoter activity. The EGF-mediated nuclear translocation of zyxin requires activation of Akt. Expression of dominant-negative mutant HNF-1β, knockdown of zyxin, or inhibition of Akt inhibits EGF-stimulated cell migration. These findings reveal a novel pathway by which extracellular signals are transmitted to the nucleus to regulate the activity of a transcription factor that is essential for renal epithelial differentiation.

Ameliorative effects of gallic acid, quercetin and limonene on urethane-induced genotoxicity and oxidative stress in Drosophila melanogaster.

PubMed

Nagpal, Isha; Abraham, Suresh K

2017-05-01

The main objective of our present work was to ascertain the efficacy of Drosophila melanogaster model for assessing antigenotoxic and antioxidant effects of dietary phytochemicals gallic acid (GA), quercetin (QC) and limonene (Lim) against urethane (URE), a genotoxic environmental carcinogen. Oregon-K (ORK) adult male flies were fed GA, QC and Lim in combination with URE (20 mM) in 10% sucrose for 72 h. Third instar larvae were fed instant medium containing the above phytochemicals and URE for 24 h. Sex-linked recessive lethal (SLRL) test and assays for estimating glutathione content (GSH), glutathione S-transferase (GST), catalase (CAT), superoxide dismutase (SOD) and lipid peroxidation (MDA content) were performed. Adult feeding experiments demonstrated that co-treatment of flies with URE and the test phytochemicals has significantly decreased the frequencies of SLRL mutations in all the germ cell stages when compared to that with URE alone. Larval feeding experiments also showed a similar pattern. The above results correlate well with antioxidative potentials of the test agents where we observed the elevated enzymatic levels with a significant reduction in MDA level in Drosophila larvae. The results further suggest that the dietary phytochemicals have an antioxidant and antimutagenic property which can be assessed using D. melanogaster.

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.

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