ANTLR Tree Grammar Generator and Extensions

NASA Technical Reports Server (NTRS)

Craymer, Loring

2005-01-01

A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

Designing a Constraint Based Parser for Sanskrit

NASA Astrophysics Data System (ADS)

Kulkarni, Amba; Pokar, Sheetal; Shukl, Devanand

Verbal understanding (śā bdabodha) of any utterance requires the knowledge of how words in that utterance are related to each other. Such knowledge is usually available in the form of cognition of grammatical relations. Generative grammars describe how a language codes these relations. Thus the knowledge of what information various grammatical relations convey is available from the generation point of view and not the analysis point of view. In order to develop a parser based on any grammar one should then know precisely the semantic content of the grammatical relations expressed in a language string, the clues for extracting these relations and finally whether these relations are expressed explicitly or implicitly. Based on the design principles that emerge from this knowledge, we model the parser as finding a directed Tree, given a graph with nodes representing the words and edges representing the possible relations between them. Further, we also use the Mīmā ṃsā constraint of ākā ṅkṣā (expectancy) to rule out non-solutions and sannidhi (proximity) to prioritize the solutions. We have implemented a parser based on these principles and its performance was found to be satisfactory giving us a confidence to extend its functionality to handle the complex sentences.

MASCOT HTML and XML parser: an implementation of a novel object model for protein identification data.

PubMed

Yang, Chunguang G; Granite, Stephen J; Van Eyk, Jennifer E; Winslow, Raimond L

2006-11-01

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

Syntactic dependency parsers for biomedical-NLP.

PubMed

Cohen, Raphael; Elhadad, Michael

2012-01-01

Syntactic parsers have made a leap in accuracy and speed in recent years. The high order structural information provided by dependency parsers is useful for a variety of NLP applications. We present a biomedical model for the EasyFirst parser, a fast and accurate parser for creating Stanford Dependencies. We evaluate the models trained in the biomedical domains of EasyFirst and Clear-Parser in a number of task oriented metrics. Both parsers provide stat of the art speed and accuracy in the Genia of over 89%. We show that Clear-Parser excels at tasks relating to negation identification while EasyFirst excels at tasks relating to Named Entities and is more robust to changes in domain.

The Mystro system: A comprehensive translator toolkit

NASA Technical Reports Server (NTRS)

Collins, W. R.; Noonan, R. E.

1985-01-01

Mystro is a system that facilities the construction of compilers, assemblers, code generators, query interpretors, and similar programs. It provides features to encourage the use of iterative enhancement. Mystro was developed in response to the needs of NASA Langley Research Center (LaRC) and enjoys a number of advantages over similar systems. There are other programs available that can be used in building translators. These typically build parser tables, usually supply the source of a parser and parts of a lexical analyzer, but provide little or no aid for code generation. In general, only the front end of the compiler is addressed. Mystro, on the other hand, emphasizes tools for both ends of a compiler.

GazeParser: an open-source and multiplatform library for low-cost eye tracking and analysis.

PubMed

Sogo, Hiroyuki

2013-09-01

Eye movement analysis is an effective method for research on visual perception and cognition. However, recordings of eye movements present practical difficulties related to the cost of the recording devices and the programming of device controls for use in experiments. GazeParser is an open-source library for low-cost eye tracking and data analysis; it consists of a video-based eyetracker and libraries for data recording and analysis. The libraries are written in Python and can be used in conjunction with PsychoPy and VisionEgg experimental control libraries. Three eye movement experiments are reported on performance tests of GazeParser. These showed that the means and standard deviations for errors in sampling intervals were less than 1 ms. Spatial accuracy ranged from 0.7° to 1.2°, depending on participant. In gap/overlap tasks and antisaccade tasks, the latency and amplitude of the saccades detected by GazeParser agreed with those detected by a commercial eyetracker. These results showed that the GazeParser demonstrates adequate performance for use in psychological experiments.

A translator writing system for microcomputer high-level languages and assemblers

NASA Technical Reports Server (NTRS)

Collins, W. R.; Knight, J. C.; Noonan, R. E.

1980-01-01

In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

76 FR 60937 - Draft License Renewal Interim Staff Guidance LR-ISG-2011-02; Aging Management Program for Steam...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-30

...-2011-02; Aging Management Program for Steam Generators AGENCY: Nuclear Regulatory Commission. ACTION... License Renewal Interim Staff Guidance (LR-ISG), LR-ISG-2011-02, ``Aging Management Program for Steam... using Revision 3 of NEI 97-06 to manage steam generator aging. The Draft LR-ISG revises the NRC staff's...

The Impact of Pre-Hospital Administration of Lactated Ringer's Solution versus Normal Saline in Patients with Traumatic Brain Injury

PubMed Central

Rowell, Susan E.; Barbosa, Ronald R.; Watters, Jennifer M.; Bulger, Eileen M.; Holcomb, John B.; Cohen, Mitchell J.; Rahbar, Mohammad H.; Fox, Erin E.; Schreiber, Martin A.

2016-01-01

Abstract Lactated Ringer's (LR) and normal saline (NS) are both used for resuscitation of injured patients. NS has been associated with increased resuscitation volume, blood loss, acidosis, and coagulopathy compared with LR. We sought to determine if pre-hospital LR is associated with improved outcome compared with NS in patients with and without traumatic brain injury (TBI). We included patients receiving pre-hospital LR or NS from the PRospective Observational Multicenter Major Trauma Transfusion (PROMMTT) study. Patients with TBI (Abbreviated Injury Scale [AIS] head ≥3) and without TBI (AIS head ≤2) were compared. Cox proportional hazards models including Injury Severity Score (ISS), AIS head, AIS extremity, age, fluids, intubation status, and hospital site were generated for prediction of mortality. Linear regression models were generated for prediction of red blood cell (RBC) and crystalloid requirement, and admission biochemical/physiological parameters. Seven hundred ninety-one patients received either LR (n = 117) or NS (n = 674). Median ISS, AIS head, AIS extremity, and pre-hospital fluid volume were higher in TBI and non-TBI patients receiving LR compared with NS (p < 0.01). In patients with TBI (n = 308), LR was associated with higher adjusted mortality compared with NS (hazard rate [HR] = 1.78, confidence interval [CI] 1.04–3.04, p = 0.035). In patients without TBI (n = 483), no difference in mortality was demonstrated (HR = 1.49, CI 0.757–2.95, p = 0.247). Fluid type had no effect on admission biochemical or physiological parameters, 6-hour RBC, or crystalloid requirement in either group. LR was associated with increased mortality compared with NS in patients with TBI. These results underscore the need for a prospective randomized trial comparing pre-hospital LR with NS in patients with TBI. PMID:26914721

The Hermod Behavioral Synthesis System

DTIC Science & Technology

1988-06-08

LDescription 1 lib tech-independent Transformation & Parser Optimization lib Hardware • g - utSynhesze Generator li Datapath lb Hardware liCotllb...Proc. 22nd Design Automation Conference, ACM/IEEE, June 1985, pp. 475-481. [7] G . De Micheli, "Synthesis of Control Systems", in Design Systems for...VLSI Circuits: Logic Synthesis and Silicon Compilation, G . De Micheli, A. Sangiovanni-Vincentelli, and P. Antognetti, (editor), Martinus Nijhoff

Robo-Sensei's NLP-Based Error Detection and Feedback Generation

ERIC Educational Resources Information Center

Nagata, Noriko

2009-01-01

This paper presents a new version of Robo-Sensei's NLP (Natural Language Processing) system which updates the version currently available as the software package "ROBO-SENSEI: Personal Japanese Tutor" (Nagata, 2004). Robo-Sensei's NLP system includes a lexicon, a morphological generator, a word segmentor, a morphological parser, a syntactic…

Fibroblast growth factor receptor-Frs2α signaling is critical for nephron progenitors.

PubMed

Di Giovanni, Valeria; Walker, Kenneth A; Bushnell, Daniel; Schaefer, Caitlin; Sims-Lucas, Sunder; Puri, Pawan; Bates, Carlton M

2015-04-01

Previous studies using transgenic Pax3cre mice have revealed roles for fibroblast growth factor receptors (Fgfrs) and Fgfr substrate 2α (Frs2α) signaling in early metanephric mesenchyme patterning and in ureteric morphogenesis. The role of Fgfr/Frs2α signaling in nephron progenitors is unknown. Thus, we generated mouse models using BAC transgenic Six2EGFPcre (Six2cre) mediated deletion of Fgfrs and/or Frs2α in nephron progenitors. Six2cre mediated deletion of Fgfr1 or Fgfr2 alone led to no obvious kidney defects. Six2creFgfr1(flox/flox)Fgfr2(flox/flox) (Fgfr1/2(NP-/-)) mice generate a discernable kidney; however, they develop nephron progenitor depletion starting at embryonic day 12.5 (E12.5) and later demonstrate severe cystic dysplasia. To determine the role of Frs2α signaling downstream of Fgfr2 in Fgfr1/2(NP-/-) mice, we generated Six2cre(,)Fgfr1(flox/flox)Fgfr2(LR/LR) (Fgfr1(NP-/-)Fgfr2(LR/LR)) mice that have point mutations in the Frs2α binding site of Fgfr2. Like Fgfr1/2(NP-/-) mice, Fgfr1(NP-/-)Fgfr2(LR/LR) develop nephron progenitor depletion, but it does not start until E14.5 and older mice have less severe cystic dysplasia than Fgfr1/2(NP-/-) To determine the role of Frs2α alone in nephron progenitors, we generated Six2creFrs2'A(flox/flox) (Frs2a(NP-/-)) mice. Frs2a(NP-/-)mice also develop nephron progenitor depletion and renal cysts, although these occurred later and were less severe than in the other Six2cre mutant mice. The nephron progenitor loss in all Six2cre mutant lines was associated with decreased Cited1 expression and increased apoptosis versus controls. FAC-sorted nephron progenitors in Six2cre Frs2'A(flox/flox) mice demonstrated evidence of increased Notch activity versus controls, which likely drives the progenitor defects. Thus, Fgfr1 and Fgfr2 have synergistic roles in maintaining nephron progenitors; furthermore, Fgfr signaling in nephron progenitors appears to be mediated predominantly by Frs2α. Copyright © 2015 Elsevier Inc. All rights reserved.

Microcystin-LR impairs zebrafish reproduction by affecting oogenesis and endocrine system.

PubMed

Zhao, Yanyan; Xie, Liqiang; Yan, Yunjun

2015-02-01

Previous studies have shown that microcystins (MCs) are able to exert negative effects on the reproductive system of fish. However, few data are actually available on the effects of MC-LR on the reproductive system of female fish. In the present study, female zebrafish were exposed to 2, 10, and 50 μg L(-1) of MC-LR for 21 d, and its effects on oogenesis, sex hormones, transcription of genes on the hypothalamic-pituitary-gonad (HPG) axis, and reproduction were investigated for the first time. It was observed that egg production significantly declined at ⩾ 10 μg L(-1) MC-LR. MC-LR exposure to zebrafish increased the concentrations of 17β-estradiol (E2) and vitellogenin (VTG) at 10 μg L(-1) level, whereas concentrations of E2, VTG and testosterone declined at 50 μg L(-1) MC-LR. The transcriptions of steroidogenic pathway gene (cyp19a, cyp19b, 17βhsd, cyp17 and hmgra) changed as well after the exposure and corresponded well with the alterations of hormone levels. A number of intra- and extra-ovarian factors, such as gnrh3, gnrhr1, fshβ, fshr, lhr, bmp15, mrpβ, ptgs2 and vtg1 which regulate oogenesis, were significantly changed with a different dose-related effect. Moreover, MC-LR exposure to female zebrafish resulted in decreased fertilization and hatching rates, and may suggest the possibility of trans-generational effects of MC-LR exposure. The results demonstrate that MC-LR could modulate endocrine function and oogenesis, eventually leading to disruption of reproductive performance in female zebrafish. These data suggest there is a risk for aquatic population living in MC polluted areas. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional relationships of landfill and landraise capacity with design and operation parameters.

PubMed

Aivaliotis, Vassilis; Dokas, Ioannis; Hatzigiannakou, Maria; Panagiotakopoulos, Demetrios

2004-08-01

Solid waste management presses for effective landfill design and operation. While planning and operating a landfill (LF) or a landraise (LR), choices need to be made regarding: (1) LF-LR morphology (base shape, side slopes, final cover thickness, LR/LF height/depth); (2) cell geometry (height, length, slopes); and (3) operation parameters (waste density, working face length, cover thicknesses). These parameters affect LF/LR capacity, operation lifespan and construction/ operation costs. In this paper, relationships are generated between capacity (C, space available for waste) and the above parameters. Incorporating real data into simulation kgamma A1.38, runs, two types of functions are developed: first, C = where A is the LF/LR base area size and kgamma a base shape-dependent coefficient; and second, C = alpha(p,gamma,A) + delta(p,gamma,A)Xp for every parameter p, where Xp is the value of p and alpha(p,gamma,A) and delta(p,gamma,A) are parameter- and base (shape/size)-specific coefficients. Moreover, the relationship between LF depth and LR height that balances excavation volume with cover material, is identified. Another result is that, for a symmetrical combination of LF/LR, with base surface area shape between square and 1:2 orthogonal, and final density between 500 and 800 kg m(-3), waste quantity placed ranges from 1.76A1.38 to 2.55A1.38 tons. The significance of such functions is obvious, as they allow the analyst to investigate alternative LF/LR schemes and make trade-off analyses.

New insights into cytotoxicity induced by microcystin-LR, estradiol, and ractopamine with mathematical models: Individual and combined effects.

PubMed

Ma, Min; Pi, Fuwei; Wang, Jiasheng; Ji, Jian; Sun, Xiulan

2017-02-01

Humans are most likely to be exposed to microcystins (MCs) combined with other water pollutants rather than to individual compounds through the consumption of contaminated drinking water or through recreational activities, such as swimming. However, the combined effects of MC-LR, estradiol (EST), and ractopamine (RAC) have not been extensively researched. The goal of this study was to investigate the combined effects of these compounds. For this purpose, cytotoxicity was evaluated in HepG2 cells treated with single or combined doses of MC-LR, EST, and RAC based on concentration addition (CA), independent action (IA), and Chou-Talalay's combination-index (CI) methods. Singly applied MC-LR and EST induced HepG2 cellular proliferation at low-concentration levels (1 × 10 -12 -1 × 10 -9  M), and decreased viability at higher doses of exposure (1 × 10 -9 -1 × 10 -6  M). Exposure to binary or ternary mixtures of MC-LR, EST, and RAC exhibited synergistic effects at high concentrations, irrespective of the models used. In contrast, antagonism was observed for the mixture of MC-LR and EST at relatively low concentrations. A synergistic effect on reactive oxygen species (ROS) generation was observed for the combined drugs at high concentrations. Additionally, the ratio of apoptotic cells was increased more by the combined drugs than the single drugs, consistent with the inhibition of cell viability. The ROS increase after treatment with the combined drugs may enhance cytotoxicity and subsequently lead to cell apoptosis. Given the interactions between MC-LR, EST, and RAC, government regulatory standards for MC-LR should consider the toxicological interactions between MC-LR and other environment pollutions. Copyright © 2016 Elsevier Ltd. All rights reserved.

AtrbohD and AtrbohF negatively regulate lateral root development by changing the localized accumulation of superoxide in primary roots of Arabidopsis.

PubMed

Li, Ning; Sun, Lirong; Zhang, Liyue; Song, Yalin; Hu, Panpan; Li, Cui; Hao, Fu Shun

2015-03-01

NADPH oxidase AtrbohD an d AtrbohF negatively modulate lateral root development by changing the peroxidase activity and increasing the local generation of superoxide in primary roots of Arabidopsis in an auxin-independent manner. NADPH oxidase subunits AtrbohD and AtrbohF play pivotal roles in regulating growth, development and stress responses in Arabidopsis. However, whether they modulate lateral root (LR) formation has not yet been addressed, and the detailed mechanisms underlying the process remain unanswered. Here, we show that two null double mutants atrbohD1/F1 and atrbohD2/F2, in which both AtrbohD and AtrbohF genes are disrupted, had remarkably higher LR density than wild-type (WT), or the single mutant atrbohD1 and atrbohF1. Compared to WT, the double mutants exhibited early emerged LRs and enhanced density of lateral root primordia (LRP). Unexpectedly, the production of superoxide (O2 (-)), but not hydrogen peroxide, in the mature area of the primary root containing LRs significantly increased in the double mutants relative to that in WT. Further experiments revealed that the local accumulation of O2 (-) led to the enhancement of LR density in the double mutants. Moreover, the deficiency of AtrbohD and AtrbohF caused a marked increase in peroxidase activity in the mature root zone, which contributed to the localized accumulation of O2 (-) and the elevated LR density in the double mutants. Furthermore, the double mutants were not sensitive to exogenous auxin naphthalene acetic acid or auxin transport inhibitor 1-N-naphthylphthalamic acid in terms of LR formation. The auxin response of LRP in vivo in atrbohD1/F1 was also similar to that in WT. Taken together, these results suggest that AtrbohD and AtrbohF negatively modulate LR development by controlling the local generation of superoxide in an auxin-independent manner. These findings provide new insights into the mechanisms of NADPH oxidase-mediated regulation of LR branching in Arabidopsis.

Association of swine leukocyte antigen class II haplotypes and immune-related traits in a swine line selected for resistance to mycoplasmal pneumonia.

PubMed

Ando, Asako; Shigenari, Atsuko; Kojima-Shibata, Chihiro; Nakajoh, Mitsuru; Suzuki, Keiichi; Kitagawa, Hitoshi; Shiina, Takashi; Inoko, Hidetoshi; Uenishi, Hirohide

2016-10-01

By selective breeding for five generations, a Landrace line has been recently established to improve resistance to mycoplasmal pneumonia of swine (MPS), daily gain (DG), back fat thickness (BF), and plasma cortisol concentrations (COR). To clarify the involvement of swine leukocyte antigen (SLA) polymorphisms in the selection process, we investigated possible associations of 11 SLA-class II haplotypes with selected traits or immune parameters. Pigs with the low-resolution SLA haplotype Lr-0.23 or Lr-0.13, which increased in frequency with the passage of generations, had less severe pathological lesions of MPS, increased leukocyte phagocytic activity, and higher white blood cell counts. In contrast, Lr-0.12 and Lr-0.2, which decreased in subsequent generations, were weakly associated with more severe pathological lesions of MPS. Therefore, in the studied Landrace line, the Lr-0.23 and Lr-0.13 haplotypes are potentially useful genetic markers for selecting and breeding animals with less severe pathological lesions of MPS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Looking forwards and backwards: The real-time processing of Strong and Weak Crossover

PubMed Central

Lidz, Jeffrey; Phillips, Colin

2017-01-01

We investigated the processing of pronouns in Strong and Weak Crossover constructions as a means of probing the extent to which the incremental parser can use syntactic information to guide antecedent retrieval. In Experiment 1 we show that the parser accesses a displaced wh-phrase as an antecedent for a pronoun when no grammatical constraints prohibit binding, but the parser ignores the same wh-phrase when it stands in a Strong Crossover relation to the pronoun. These results are consistent with two possibilities. First, the parser could apply Principle C at antecedent retrieval to exclude the wh-phrase on the basis of the c-command relation between its gap and the pronoun. Alternatively, retrieval might ignore any phrases that do not occupy an Argument position. Experiment 2 distinguished between these two possibilities by testing antecedent retrieval under Weak Crossover. In Weak Crossover binding of the pronoun is ruled out by the argument condition, but not Principle C. The results of Experiment 2 indicate that antecedent retrieval accesses matching wh-phrases in Weak Crossover configurations. On the basis of these findings we conclude that the parser can make rapid use of Principle C and c-command information to constrain retrieval. We discuss how our results support a view of antecedent retrieval that integrates inferences made over unseen syntactic structure into constraints on backward-looking processes like memory retrieval. PMID:28936483

ACPYPE - AnteChamber PYthon Parser interfacE.

PubMed

Sousa da Silva, Alan W; Vranken, Wim F

2012-07-23

ACPYPE (or AnteChamber PYthon Parser interfacE) is a wrapper script around the ANTECHAMBER software that simplifies the generation of small molecule topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS. It is written in the Python programming language and was developed as a tool for interfacing with other Python based applications such as the CCPN software suite (for NMR data analysis) and ARIA (for structure calculations from NMR data). ACPYPE is open source code, under GNU GPL v3, and is available as a stand-alone application at http://www.ccpn.ac.uk/acpype and as a web portal application at http://webapps.ccpn.ac.uk/acpype. We verified the topologies generated by ACPYPE in three ways: by comparing with default AMBER topologies for standard amino acids; by generating and verifying topologies for a large set of ligands from the PDB; and by recalculating the structures for 5 protein-ligand complexes from the PDB. ACPYPE is a tool that simplifies the automatic generation of topology and parameters in different formats for different molecular mechanics programmes, including calculation of partial charges, while being object oriented for integration with other applications.

Solar photo-Fenton treatment of microcystin-LR in aqueous environment: Transformation products and toxicity in different water matrices.

PubMed

Karci, Akin; Wurtzler, Elizabeth M; de la Cruz, Armah A; Wendell, David; Dionysiou, Dionysios D

2018-05-05

Transformation products and toxicity patterns of microcystin-LR (MC-LR), a common cyanotoxin in freshwaters, during degradation by solar photo-Fenton process were studied in the absence and presence of two major water components, namely fulvic acid and alkalinity. The transformation products m/z 795, 835, 515/1030 and 532 can be formed through attack of OH on the conjugated carbon double bonds of Adda. Transformation products with m/z 1010, 966 and 513 can be generated through the attack of OH on the methoxy group of Adda. The transformation products m/z 783, 508 and 1012 can be originated from the attack of OH on the cyclic structure of MC-LR. Transformation products (m/z 522, 1028, 1012, 1046 and 514) formed after hydroxylation of the aromatic ring with OH were also identified in this study. The toxicity study revealed that fulvic acid and alkalinity strongly influence the toxicity profiles of solar photo-Fenton treated MC-LR. Fulvic acid enhanced the detoxification whereas low level total alkalinity (1.8 mg L -1 CaCO 3 ) inhibited the detoxification of MC-LR by solar photo-Fenton process as assessed by protein phosphatase-1 (PP-1) inhibition assay. This work provides insights on the utility of solar photo-Fenton destruction of MC-LR in water based on transformation products and toxicity data. Copyright © 2017 Elsevier B.V. All rights reserved.

A Protocol for Annotating Parser Differences. Research Report. ETS RR-16-02

ERIC Educational Resources Information Center

Bruno, James V.; Cahill, Aoife; Gyawali, Binod

2016-01-01

We present an annotation scheme for classifying differences in the outputs of syntactic constituency parsers when a gold standard is unavailable or undesired, as in the case of texts written by nonnative speakers of English. We discuss its automated implementation and the results of a case study that uses the scheme to choose a parser best suited…

Processing of ICARTT Data Files Using Fuzzy Matching and Parser Combinators

NASA Technical Reports Server (NTRS)

Rutherford, Matthew T.; Typanski, Nathan D.; Wang, Dali; Chen, Gao

2014-01-01

In this paper, the task of parsing and matching inconsistent, poorly formed text data through the use of parser combinators and fuzzy matching is discussed. An object-oriented implementation of the parser combinator technique is used to allow for a relatively simple interface for adapting base parsers. For matching tasks, a fuzzy matching algorithm with Levenshtein distance calculations is implemented to match string pair, which are otherwise difficult to match due to the aforementioned irregularities and errors in one or both pair members. Used in concert, the two techniques allow parsing and matching operations to be performed which had previously only been done manually.

Toward a theory of distributed word expert natural language parsing

NASA Technical Reports Server (NTRS)

Rieger, C.; Small, S.

1981-01-01

An approach to natural language meaning-based parsing in which the unit of linguistic knowledge is the word rather than the rewrite rule is described. In the word expert parser, knowledge about language is distributed across a population of procedural experts, each representing a word of the language, and each an expert at diagnosing that word's intended usage in context. The parser is structured around a coroutine control environment in which the generator-like word experts ask questions and exchange information in coming to collective agreement on sentence meaning. The word expert theory is advanced as a better cognitive model of human language expertise than the traditional rule-based approach. The technical discussion is organized around examples taken from the prototype LISP system which implements parts of the theory.

LACK OF TERATOGENICITY OF MICROCYSTIN-LR IN THE MOUSE AND TOAD

EPA Science Inventory

Abstract. Microcystin-LR (MC-LR) is a cyanobacterial toxin generated by the organism, Microcystis aeruginosa. Although the hepatotoxicity of this chemical has been characterized, the potential developmental toxicity in vertebrates has not been well studied. The purpose of this...

Grammar as a Programming Language. Artificial Intelligence Memo 391.

ERIC Educational Resources Information Center

Rowe, Neil

Student projects that involve writing generative grammars in the computer language, "LOGO," are described in this paper, which presents a grammar-running control structure that allows students to modify and improve the grammar interpreter itself while learning how a simple kind of computer parser works. Included are procedures for…

Domain Adaption of Parsing for Operative Notes

PubMed Central

Wang, Yan; Pakhomov, Serguei; Ryan, James O.; Melton, Genevieve B.

2016-01-01

Background Full syntactic parsing of clinical text as a part of clinical natural language processing (NLP) is critical for a wide range of applications, such as identification of adverse drug reactions, patient cohort identification, and gene interaction extraction. Several robust syntactic parsers are publicly available to produce linguistic representations for sentences. However, these existing parsers are mostly trained on general English text and often require adaptation for optimal performance on clinical text. Our objective was to adapt an existing general English parser for the clinical text of operative reports via lexicon augmentation, statistics adjusting, and grammar rules modification based on a set of biomedical text. Method The Stanford unlexicalized probabilistic context-free grammar (PCFG) parser lexicon was expanded with SPECIALIST lexicon along with statistics collected from a limited set of operative notes tagged with a two of POS taggers (GENIA tagger and MedPost). The most frequently occurring verb entries of the SPECIALIST lexicon were adjusted based on manual review of verb usage in operative notes. Stanford parser grammar production rules were also modified based on linguistic features of operative reports. An analogous approach was then applied to the GENIA corpus to test the generalizability of this approach to biomedical text. Results The new unlexicalized PCFG parser extended with the extra lexicon from SPECIALIST along with accurate statistics collected from an operative note corpus tagged with GENIA POS tagger improved the parser performance by 2.26% from 87.64% to 89.90%. There was a progressive improvement with the addition of multiple approaches. Most of the improvement occurred with lexicon augmentation combined with statistics from the operative notes corpus. Application of this approach on the GENIA corpus showed that parsing performance was boosted by 3.81% with a simple new grammar and the addition of the GENIA corpus lexicon. Conclusion Using statistics collected from clinical text tagged with POS taggers along with proper modification of grammars and lexicons of an unlexicalized PCFG parser can improve parsing performance. PMID:25661593

Syntactic analysis in sentence comprehension: effects of dependency types and grammatical constraints.

PubMed

De Vincenzi, M

1996-01-01

This paper presents three experiments on the parsing of Italian wh-questions that manipulate the wh-type (who vs. which-N) and the wh extraction site (main clause, dependent clause with or without complementizer). The aim of these manipulations is to see whether the parser is sensitive to the type of dependencies being processed and whether the processing effects can be explained by a unique processing principle, the minimal chain principle (MCP; De Vincenzi, 1991). The results show that the parser, following the MCP, prefers structures with fewer and less complex chains. In particular: (1) There is a processing advantage for the wh-subject extractions, the structures with less complex chains; (2) there is a processing dissociation between the who and which questions; (3) the parser respects the principle that governs the well-formedness of the empty categories (ECP).

PDB file parser and structure class implemented in Python.

PubMed

Hamelryck, Thomas; Manderick, Bernard

2003-11-22

The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Stomach curvature is generated by left-right asymmetric gut morphogenesis

PubMed Central

Davis, Adam; Amin, Nirav M.; Johnson, Caroline; Bagley, Kristen; Ghashghaei, H. Troy

2017-01-01

Left-right (LR) asymmetry is a fundamental feature of internal anatomy, yet the emergence of morphological asymmetry remains one of the least understood phases of organogenesis. Asymmetric rotation of the intestine is directed by forces outside the gut, but the morphogenetic events that generate anatomical asymmetry in other regions of the digestive tract remain unknown. Here, we show in mouse and Xenopus that the mechanisms that drive the curvature of the stomach are intrinsic to the gut tube itself. The left wall of the primitive stomach expands more than the right wall, as the left epithelium becomes more polarized and undergoes radial rearrangement. These asymmetries exist across several species, and are dependent on LR patterning genes, including Foxj1, Nodal and Pitx2. Our findings have implications for how LR patterning manifests distinct types of morphological asymmetries in different contexts. PMID:28242610

Stomach curvature is generated by left-right asymmetric gut morphogenesis.

PubMed

Davis, Adam; Amin, Nirav M; Johnson, Caroline; Bagley, Kristen; Ghashghaei, H Troy; Nascone-Yoder, Nanette

2017-04-15

Left-right (LR) asymmetry is a fundamental feature of internal anatomy, yet the emergence of morphological asymmetry remains one of the least understood phases of organogenesis. Asymmetric rotation of the intestine is directed by forces outside the gut, but the morphogenetic events that generate anatomical asymmetry in other regions of the digestive tract remain unknown. Here, we show in mouse and Xenopus that the mechanisms that drive the curvature of the stomach are intrinsic to the gut tube itself. The left wall of the primitive stomach expands more than the right wall, as the left epithelium becomes more polarized and undergoes radial rearrangement. These asymmetries exist across several species, and are dependent on LR patterning genes, including Foxj1 , Nodal and Pitx2 Our findings have implications for how LR patterning manifests distinct types of morphological asymmetries in different contexts. © 2017. Published by The Company of Biologists Ltd.

Effects of Zanthoxylum piperitum ethanol extract on osteoarthritis inflammation and pain.

PubMed

Hwang, Kyung-A; Kwon, Jeong Eun; Noh, YooHun; Park, BongKyun; Jeong, Yong Joon; Lee, Sun-Mee; Kim, Se-Young; Kim, InHye; Kang, Se Chan

2018-06-05

Degenerative arthritis, also known as osteoarthritis (OA), is the most common type of arthritis, which is caused by degenerative damage of the cartilage, which primarily protects the joints, leading to inflammation and pain. The objective of this study was to investigate the in vivo and in vitro effects of treatment with ZPE-LR (90% EtOH extract of Zanthoxylum piperitum) on pain severity and inflammation. When using an in vivo OA model MIA (monosodiumidoacetate-induced arthritis) rats, ZPE-LR (100 mg/kg) oral-administratio significantly inhibited MIA-induced change in loaded weight ratio on the left foot, and articular cartilage thickness. To confirm the positive effects on pain relief, acetic acid, heat and formalin-induced pain were remarkably decreased by 50 and 100 mg/kg ZPE-LR oral-administration. Pain related KCNJ6 mRNA expression as well as K + current was increased after ZPE-LR treatment in BV-2 cells. To confirm the positive effects on inflammation, TPA (12-O-tetradecanoylphorbol-13-acetate) induced inflammation measured by mouse ear thickness and biopsy punch weight and TPA-induced iNOS, COX-2 mRNA and protein expression were remarkably suppressed by 50 and 100 mg/kg ZPE-LR oral-administration. In addition, TPA-induced iNOS, COX-2 mRNA level and protein expression were reduced. Acetic acid, heat and formalin-induced pain were remarkably decreased by 50 and 100 mg/kg ZPE-LR oral-administration. We examined in vitro ZPE-LR effects in LPS-induced RAW 264.7 cells. LPS-induced p65 translocation to the nucleus was prohibited by ZPE-LR 100 μg/ml oral administration. Moreover, ROS generation by LPS was significantly inhibited by ZPE-LR 50 and 100 μg/ml treatment. To investigate new ZPE-LR activating mechanisms, the gene fishing method (not a typical term, should probably use PCR based genetic screening) was used. LPS-induced HPRT1 (hypoxanthine phosphoribosyltransferase 1) was decreased by ZPE-LR. However, RPL8 (Ribosomal protein L8) which showed no change in mRNA expression due to LPS, did show increased mRNA levels after ZPE-LR treatment. Our data elucidate mechanisms underlying ZPE-LR and suggest ZPE-LR may be a potential therapeutic agent to modulate osteoarthritis inflammation and pain. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

The V-ATPase accessory protein Atp6ap1b mediates dorsal forerunner cell proliferation and left-right asymmetry in zebrafish.

PubMed

Gokey, Jason J; Dasgupta, Agnik; Amack, Jeffrey D

2015-11-01

Asymmetric fluid flows generated by motile cilia in a transient 'organ of asymmetry' are involved in establishing the left-right (LR) body axis during embryonic development. The vacuolar-type H(+)-ATPase (V-ATPase) proton pump has been identified as an early factor in the LR pathway that functions prior to cilia, but the role(s) for V-ATPase activity are not fully understood. In the zebrafish embryo, the V-ATPase accessory protein Atp6ap1b is maternally supplied and expressed in dorsal forerunner cells (DFCs) that give rise to the ciliated organ of asymmetry called Kupffer's vesicle (KV). V-ATPase accessory proteins modulate V-ATPase activity, but little is known about their functions in development. We investigated Atp6ap1b and V-ATPase in KV development using morpholinos, mutants and pharmacological inhibitors. Depletion of both maternal and zygotic atp6ap1b expression reduced KV organ size, altered cilia length and disrupted LR patterning of the embryo. Defects in other ciliated structures-neuromasts and olfactory placodes-suggested a broad role for Atp6ap1b during development of ciliated organs. V-ATPase inhibitor treatments reduced KV size and identified a window of development in which V-ATPase activity is required for proper LR asymmetry. Interfering with Atp6ap1b or V-ATPase function reduced the rate of DFC proliferation, which resulted in fewer ciliated cells incorporating into the KV organ. Analyses of pH and subcellular V-ATPase localizations suggested Atp6ap1b functions to localize the V-ATPase to the plasma membrane where it regulates proton flux and cytoplasmic pH. These results uncover a new role for the V-ATPase accessory protein Atp6ap1b in early development to maintain the proliferation rate of precursor cells needed to construct a ciliated KV organ capable of generating LR asymmetry. Copyright © 2015 Elsevier Inc. All rights reserved.

The V-ATPase accessory protein Atp6ap1b mediates dorsal forerunner cell proliferation and left-right asymmetry in zebrafish

PubMed Central

Gokey, Jason J.; Dasgupta, Agnik; Amack, Jeffrey D.

2015-01-01

Asymmetric fluid flows generated by motile cilia in a transient ‘organ of asymmetry’ are involved in establishing the left-right (LR) body axis during embryonic development. The vacuolar-type H+-ATPase (V-ATPase) proton pump has been identified as an early factor in the LR pathway that functions prior to cilia, but the role(s) for V-ATPase activity are not fully understood. In the zebrafish embryo, the V-ATPase accessory protein Atp6ap1b is maternally supplied and expressed in dorsal forerunner cells (DFCs) that give rise to the ciliated organ of asymmetry called Kupffer’s vesicle (KV). V-ATPase accessory proteins modulate V-ATPase activity, but little is known about their functions in development. We investigated Atp6ap1b and V-ATPase in KV development using morpholinos, mutants and pharmacological inhibitors. Depletion of both maternal and zygotic atp6ap1b expression reduced KV organ size, altered cilia length and disrupted LR patterning of the embryo. Defects in other ciliated structures—neuromasts and olfactory placodes—suggested a broad role for Atp6ap1b during development of ciliated organs. V-ATPase inhibitor treatments reduced KV size and identified a window of development in which V-ATPase activity is required for proper LR asymmetry. Interfering with Atp6ap1b or V-ATPase function reduced the rate of DFC proliferation, which resulted in fewer ciliated cells incorporating into the KV organ. Analyses of pH and subcellular V-ATPase localizations suggested Atp6ap1b functions to localize the V-ATPase to the plasma membrane where it regulates proton flux and cytoplasmic pH. These results uncover a new role for the V-ATPase accessory protein Atp6ap1b in early development to maintain the proliferation rate of precursor cells needed to construct a ciliated KV organ capable of generating LR asymmetry. PMID:26254189

Cytogenetic and molecular identification of three Triticum aestivum-Leymus racemosus translocation addition lines.

PubMed

Wang, Le; Yuan, Jianhua; Bie, Tongde; Zhou, Bo; Chen, Peidu

2009-06-01

Chromosome 2C from Aegilops cylindrica has the ability to induce chromosome breakage in common wheat (Tritivum aestivum). In the BC(1)F(3) generation of the T. aestivum cv. Chinese Spring and a hybrid between T. aestivum-Leymus racemosus Lr.7 addition line and T. aestivum-Ae. cylindrica 2C addition line, three disomic translocation addition lines (2n = 44) were selected by mitotic chromosome C-banding and genomic in situ hybridization. We further characterized these T. aestivum-L. racemosus translocation addition lines, NAU636, NAU637 and NAU638, by chromosome C-banding, in situ hybridization using the A- and D-genome-specific bacterial artificial chromosome (BAC) clones 676D4 and 9M13; plasmids pAs1 and pSc119.2, and 45S rDNA; as well as genomic DNA of L. racemosus as probes, in combination with double ditelosomic test cross and SSR marker analysis. The translocation chromosomes were designated as T3AS-Lr7S, T6BS-Lr7S, and T5DS-Lr7L. The translocation line T3AS-Lr7S was highly resistant to Fusarium head blight and will be useful germplasm for resistance breeding.

77 FR 36015 - Atomic Safety and Licensing Board; Entergy Nuclear Operations, Inc. (Indian Point Nuclear...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... NUCLEAR REGULATORY COMMISSION [Docket Nos. 50-247-LR and 50-286-LR; ASLBP No. 07-858-03-LR-BD01] Atomic Safety and Licensing Board; Entergy Nuclear Operations, Inc. (Indian Point Nuclear Generating Units 2 and 3); Notice of Hearing (Application for License Renewal) June 8, 2012. Before Administrative Judges: Lawrence G. McDade, Chairman, Dr....

Dynamics of Total Microcystin LR Concentration in Three Subtropical Hydroelectric Generation Reservoirs in Uruguay, South America.

PubMed

González-Piana, Mauricio; Fabián, Daniel; Piccardo, Andrea; Chalar, Guillermo

2017-10-01

This study analyzed the temporal dynamics of total microcystin LR concentrations between the years of 2012 and 2015 in the Bonete, Baygorria and Palmar hydroelectric generation reservoirs in the central region of the Negro River, Uruguay. The three reservoirs showed differents total microcystin LR concentration, with no significant differences among them. Over 20 sampling dates, the three reservoirs exhibited total microcystin LR concentrations on eight occasions that corresponded to a slight to moderate human health risk according to WHO guideline values for recreational waters. By determining the concentration of microcystin LR in cyanobacterial biomass, we identified cyanobacterial populations that occurred over time with varying degrees of toxin production (maximal 85.4 µg/mm 3 ). The microcystin LR concentration in Bonete was positively correlated with temperature (r = 0.587) and cyanobacterial biomass (r = 0.736), in Baygorria with cyanobacterial biomass (r = 0.521), and in Palmar with temperature (r = 0.500) and negatively correlated with ammonia (r = -0.492). Action is needed to reduce the presence of toxic cyanobacteria in these systems. A decrease in the use of agrochemicals and management changes in the reservoir basins could be successful long-term measures.

Left-right asymmetry in the level of active Nodal protein produced in the node is translated into left-right asymmetry in the lateral plate of mouse embryos.

PubMed

Kawasumi, Aiko; Nakamura, Tetsuya; Iwai, Naomi; Yashiro, Kenta; Saijoh, Yukio; Belo, Jose Antonio; Shiratori, Hidetaka; Hamada, Hiroshi

2011-05-15

Left-right (L-R) asymmetry in the mouse embryo is generated in the node and is dependent on cilia-driven fluid flow, but how the initial asymmetry is transmitted from the node to the lateral plate has remained unknown. We have now identified a transcriptional enhancer (ANE) in the human LEFTY1 gene that exhibits marked L>R asymmetric activity in perinodal cells of the mouse embryo. Dissection of ANE revealed that it is activated in the perinodal cells on the left side by Nodal signaling, suggesting that Nodal activity in the node is asymmetric at a time when Nodal expression is symmetric. Phosphorylated Smad2/3 (pSmad2) indeed manifested an L-R asymmetric distribution at the node, being detected in perinodal cells preferentially on the left side. This asymmetry in pSmad2 distribution was found to be generated not by unidirectional transport of Nodal but rather as a result of LR distribution of active Nodal in the node is translated into the asymmetry in LPM. Copyright © 2011 Elsevier Inc. All rights reserved.

Dignity Therapy and Life Review for Palliative Care Patients: A Randomized Controlled Trial.

PubMed

Vuksanovic, Dean; Green, Heather J; Dyck, Murray; Morrissey, Shirley A

2017-02-01

Dignity therapy (DT) is a psychotherapeutic intervention with increasing evidence of acceptability and utility in palliative care settings. The aim of this study was to evaluate the legacy creation component of DT by comparing this intervention with life review (LR) and waitlist control (WC) groups. Seventy adults with advanced terminal disease were randomly allocated to DT, LR, or WC followed by DT, of which 56 completed the study protocol. LR followed an identical protocol to DT except that no legacy document was created in LR. Primary outcome measures were the Brief Generativity and Ego-Integrity Questionnaire, Patient Dignity Inventory, Functional Assessment of Cancer Therapy-General, version 4, and treatment evaluation questionnaires. Unlike LR and WC groups, DT recipients demonstrated significantly increased generativity and ego-integrity scores at study completion. There were no significant changes for dignity-related distress or physical, social, emotional, and functional well-being among the three groups. There were also no significant changes in primary outcomes after the provision of DT after the waiting period in the WC group. High acceptability and satisfaction with interventions were noted for recipients of both DT and LR and family/carers of DT participants. This study provides initial evidence that the specific process of legacy creation is able to positively affect sense of generativity, meaning, and acceptance near end of life. High acceptability and satisfaction rates for both DT and LR and positive impacts on families/carers of DT participants provide additional support for clinical utility of these interventions. Further evaluation of specific mechanisms of change post-intervention is required given DT's uncertain efficacy on other primary outcomes. Copyright © 2016 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

Observed to expected or logistic regression to identify hospitals with high or low 30-day mortality?

PubMed Central

Helgeland, Jon; Clench-Aas, Jocelyne; Laake, Petter; Veierød, Marit B.

2018-01-01

Introduction A common quality indicator for monitoring and comparing hospitals is based on death within 30 days of admission. An important use is to determine whether a hospital has higher or lower mortality than other hospitals. Thus, the ability to identify such outliers correctly is essential. Two approaches for detection are: 1) calculating the ratio of observed to expected number of deaths (OE) per hospital and 2) including all hospitals in a logistic regression (LR) comparing each hospital to a form of average over all hospitals. The aim of this study was to compare OE and LR with respect to correctly identifying 30-day mortality outliers. Modifications of the methods, i.e., variance corrected approach of OE (OE-Faris), bias corrected LR (LR-Firth), and trimmed mean variants of LR and LR-Firth were also studied. Materials and methods To study the properties of OE and LR and their variants, we performed a simulation study by generating patient data from hospitals with known outlier status (low mortality, high mortality, non-outlier). Data from simulated scenarios with varying number of hospitals, hospital volume, and mortality outlier status, were analysed by the different methods and compared by level of significance (ability to falsely claim an outlier) and power (ability to reveal an outlier). Moreover, administrative data for patients with acute myocardial infarction (AMI), stroke, and hip fracture from Norwegian hospitals for 2012–2014 were analysed. Results None of the methods achieved the nominal (test) level of significance for both low and high mortality outliers. For low mortality outliers, the levels of significance were increased four- to fivefold for OE and OE-Faris. For high mortality outliers, OE and OE-Faris, LR 25% trimmed and LR-Firth 10% and 25% trimmed maintained approximately the nominal level. The methods agreed with respect to outlier status for 94.1% of the AMI hospitals, 98.0% of the stroke, and 97.8% of the hip fracture hospitals. Conclusion We recommend, on the balance, LR-Firth 10% or 25% trimmed for detection of both low and high mortality outliers. PMID:29652941

Is human sentence parsing serial or parallel? Evidence from event-related brain potentials.

PubMed

Hopf, Jens-Max; Bader, Markus; Meng, Michael; Bayer, Josef

2003-01-01

In this ERP study we investigate the processes that occur in syntactically ambiguous German sentences at the point of disambiguation. Whereas most psycholinguistic theories agree on the view that processing difficulties arise when parsing preferences are disconfirmed (so-called garden-path effects), important differences exist with respect to theoretical assumptions about the parser's recovery from a misparse. A key distinction can be made between parsers that compute all alternative syntactic structures in parallel (parallel parsers) and parsers that compute only a single preferred analysis (serial parsers). To distinguish empirically between parallel and serial parsing models, we compare ERP responses to garden-path sentences with ERP responses to truly ungrammatical sentences. Garden-path sentences contain a temporary and ultimately curable ungrammaticality, whereas truly ungrammatical sentences remain so permanently--a difference which gives rise to different predictions in the two classes of parsing architectures. At the disambiguating word, ERPs in both sentence types show negative shifts of similar onset latency, amplitude, and scalp distribution in an initial time window between 300 and 500 ms. In a following time window (500-700 ms), the negative shift to garden-path sentences disappears at right central parietal sites, while it continues in permanently ungrammatical sentences. These data are taken as evidence for a strictly serial parser. The absence of a difference in the early time window indicates that temporary and permanent ungrammaticalities trigger the same kind of parsing responses. Later differences can be related to successful reanalysis in garden-path but not in ungrammatical sentences. Copyright 2003 Elsevier Science B.V.

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

PubMed

Huang, Yang; Lowe, Henry J; Klein, Dan; Cucina, Russell J

2005-01-01

The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

Substrate Stiffness Regulates the Development of Left-Right Asymmetry in Cell Orientation.

PubMed

Bao, Yuanye; Huang, Yaozhun; Lam, Miu Ling; Xu, Ting; Zhu, Ninghao; Guo, Zhaobin; Cui, Xin; Lam, Raymond H W; Chen, Ting-Hsuan

2016-07-20

Left-right (LR) asymmetry of tissue/organ structure is a morphological feature essential for many tissue functions. The ability to incorporate the LR formation in constructing tissue/organ replacement is important for recapturing the inherent tissue structure and functions. However, how LR asymmetry is formed remains largely underdetermined, which creates significant hurdles to reproduce and regulate the formation of LR asymmetry in an engineering context. Here, we report substrate rigidity functioning as an effective switch that turns on the development of LR asymmetry. Using micropatterned cell-adherent stripes on rigid substrates, we found that cells collectively oriented at a LR-biased angle relative to the stripe boundary. This LR asymmetry was initiated by a LR-biased migration of cells at stripe boundary, which later generated a velocity gradient propagating from stripe boundary to the center. After a series of cell translocations and rotations, ultimately, an LR-biased cell orientation within the micropatterned stripe was formed. Importantly, this initiation and propagation of LR asymmetry was observed only on rigid but not on soft substrates, suggesting that the LR asymmetry was regulated by rigid substrate probably through the organization of actin cytoskeleton. Together, we demonstrated substrate rigidity as a determinant factor that mediates the self-organizing LR asymmetry being unfolded from single cells to multicellular organization. More broadly, we anticipate that our findings would pave the way for rebuilding artificial tissue constructs with inherent LR asymmetry in the future.

Liver Transcriptome and miRNA Analysis of Silver Carp (Hypophthalmichthys molitrix) Intraperitoneally Injected With Microcystin-LR

PubMed Central

Qu, Xiancheng; Hu, Menghong; Shang, Yueyong; Pan, Lisha; Jia, Peixuan; Fu, Chunxue; Liu, Qigen; Wang, Youji

2018-01-01

Next-generation sequencing was used to analyze the effects of toxic microcystin-LR (MC-LR) on silver carp (Hypophthalmichthys molitrix). Silver carps were intraperitoneally injected with MC-LR, and RNA-seq and miRNA-seq in the liver were analyzed at 0.25, 0.5, and 1 h. The expression of glutathione S-transferase (GST), which acts as a marker gene for MC-LR, was tested to determine the earliest time point at which GST transcription was initiated in the liver tissues of the MC-LR-treated silver carps. Hepatic RNA-seq/miRNA-seq analysis and data integration analysis were conducted with reference to the identified time point. Quantitative PCR (qPCR) was performed to detect the expression of the following genes at the three time points: heme oxygenase 1 (HO-1), interleukin-10 receptor 1 (IL-10R1), apolipoprotein A-I (apoA-I), and heme binding protein 2 (HBP2). Results showed that the liver GST expression was remarkably decreased at 0.25 h (P < 0.05). RNA-seq at this time point revealed that the liver tissue contained 97,505 unigenes, including 184 significantly different unigenes and 75 unknown genes. Gene Ontology (GO) term enrichment analysis suggested that 35 of the 145 enriched GO terms were significantly enriched and mainly related to the immune system regulation network. KEGG pathway enrichment analysis showed that 18 of the 189 pathways were significantly enriched, and the most significant was a ribosome pathway containing 77 differentially expressed genes. miRNA-seq analysis indicated that the longest miRNA had 22 nucleotides (nt), followed by 21 and 23 nt. A total of 286 known miRNAs, 332 known miRNA precursor sequences, and 438 new miRNAs were predicted. A total of 1,048,575 mRNA–miRNA interaction sites were obtained, and 21,252 and 21,241 target genes were respectively predicted in known and new miRNAs. qPCR revealed that HO-1, IL-10R1, apoA-I, and HBP2 were significantly differentially expressed and might play important roles in the toxicity and liver detoxification of MC-LR in fish. These results were consistent with those of high-throughput sequencing, thereby verifying the accuracy of our sequencing data. RNA-seq and miRNA-seq analyses of silver carp liver injected with MC-LR provided valuable and new insights into the toxic effects of MC-LR and the antitoxic mechanisms of MC-LR in fish. The RNA/miRNA data are available from the NCBI database Registration No. : SRP075165. PMID:29692738

Testing a level of response to alcohol-based model of heavy drinking and alcohol problems in 1,905 17-year-olds.

PubMed

Schuckit, Marc A; Smith, Tom L; Heron, Jon; Hickman, Matthew; Macleod, John; Lewis, Glyn; Davis, John M; Hibbeln, Joseph R; Brown, Sandra; Zuccolo, Luisa; Miller, Laura L; Davey-Smith, George

2011-10-01

The low level of response (LR) to alcohol is one of several genetically influenced characteristics that increase the risk for heavy drinking and alcohol problems. Efforts to understand how LR operates through additional life influences have been carried out primarily in modest-sized U.S.-based samples with limited statistical power, raising questions about generalizability and about the importance of components with smaller effects. This study evaluates a full LR-based model of risk in a large sample of adolescents from the United Kingdom. Cross-sectional structural equation models were used for the approximate first half of the age 17 subjects assessed by the Avon Longitudinal Study of Parents and Children, generating data on 1,905 adolescents (mean age 17.8 years, 44.2% boys). LR was measured with the Self-Rating of the Effects of Alcohol Questionnaire, outcomes were based on drinking quantities and problems, and standardized questionnaires were used to evaluate peer substance use, alcohol expectancies, and using alcohol to cope with stress. In this young and large U.K. sample, a low LR related to more adverse alcohol outcomes both directly and through partial mediation by all 3 additional key variables (peer substance use, expectancies, and coping). The models were similar in boys and girls. These results confirm key elements of the hypothesized LR-based model in a large U.K. sample, supporting some generalizability beyond U.S. groups. They also indicate that with enough statistical power, multiple elements contribute to how LR relates to alcohol outcomes and reinforce the applicability of the model to both genders. Copyright © 2011 by the Research Society on Alcoholism.

Integrated Intelligence: Robot Instruction via Interactive Grounded Learning

DTIC Science & Technology

2016-02-14

ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Robotics; Natural Language Processing ; Grounded Language ...Logical Forms for Referring Expression Generation, Emperical Methods in Natural Language Processing (EMNLP). 18-OCT-13, . : , Tom Kwiatkowska, Eunsol...Choi, Yoav Artzi, Luke Zettlemoyer. Scaling Semantic Parsers with On-the-fly Ontology Matching, Emperical Methods in Natural Langauge Processing

Numerical Function Generators Using LUT Cascades

DTIC Science & Technology

2007-06-01

either algebraically (for example, sinðxÞ) or as a table of input/ output values. The user defines the numerical function by using the syntax of Scilab ...defined function in Scilab or specify it directly. Note that, by changing the parser of our system, any format can be used for the design entry. First...Methods for Multiple-Valued Input Address Generators,” Proc. 36th IEEE Int’l Symp. Multiple-Valued Logic (ISMVL ’06), May 2006. [29] Scilab 3.0, INRIA-ENPC

Kinetic and mechanistic study of microcystin-LR degradation by nitrous acid under ultraviolet irradiation.

PubMed

Ma, Qingwei; Ren, Jing; Huang, Honghui; Wang, Shoubing; Wang, Xiangrong; Fan, Zhengqiu

2012-05-15

Degradation of microcystin-LR (MC-LR) in the presence of nitrous acid (HNO(2)) under irradiation of 365nm ultraviolet (UV) was studied for the first time. The influence of initial conditions including pH value, NaNO(2) concentration, MC-LR concentration and UV intensity were studied. MC-LR was degraded in the presence of HNO(2); enhanced degradation of MC-LR was observed with 365nm UV irradiation, caused by the generation of hydroxyl radicals through the photolysis of HNO(2). The degradation processes of MC-LR could well fit the pseudo-first-order kinetics. Mass spectrometry was applied for identification of the byproducts and the analysis of degradation mechanisms. Major degradation pathways were proposed according to the results of LC-MS analysis. The degradation of MC-LR was initiated via three major pathways: attack of hydroxyl radicals on the conjugated carbon double bonds of Adda, attack of hydroxyl radicals on the benzene ring of Adda, and attack of nitrosonium ion on the benzene ring of Adda. Copyright © 2012 Elsevier B.V. All rights reserved.

Investigating AI with BASIC and Logo: Helping the Computer to Understand INPUTS.

ERIC Educational Resources Information Center

Mandell, Alan; Lucking, Robert

1988-01-01

Investigates using the microcomputer to develop a sentence parser to simulate intelligent conversation used in artificial intelligence applications. Compares the ability of LOGO and BASIC for this use. Lists and critiques several LOGO and BASIC parser programs. (MVL)

Use of General-purpose Negation Detection to Augment Concept Indexing of Medical Documents

PubMed Central

Mutalik, Pradeep G.; Deshpande, Aniruddha; Nadkarni, Prakash M.

2001-01-01

Objectives: To test the hypothesis that most instances of negated concepts in dictated medical documents can be detected by a strategy that relies on tools developed for the parsing of formal (computer) languages—specifically, a lexical scanner (“lexer”) that uses regular expressions to generate a finite state machine, and a parser that relies on a restricted subset of context-free grammars, known as LALR(1) grammars. Methods: A diverse training set of 40 medical documents from a variety of specialties was manually inspected and used to develop a program (Negfinder) that contained rules to recognize a large set of negated patterns occurring in the text. Negfinder's lexer and parser were developed using tools normally used to generate programming language compilers. The input to Negfinder consisted of medical narrative that was preprocessed to recognize UMLS concepts: the text of a recognized concept had been replaced with a coded representation that included its UMLS concept ID. The program generated an index with one entry per instance of a concept in the document, where the presence or absence of negation of that concept was recorded. This information was used to mark up the text of each document by color-coding it to make it easier to inspect. The parser was then evaluated in two ways: 1) a test set of 60 documents (30 discharge summaries, 30 surgical notes) marked-up by Negfinder was inspected visually to quantify false-positive and false-negative results; and 2) a different test set of 10 documents was independently examined for negatives by a human observer and by Negfinder, and the results were compared. Results: In the first evaluation using marked-up documents, 8,358 instances of UMLS concepts were detected in the 60 documents, of which 544 were negations detected by the program and verified by human observation (true-positive results, or TPs). Thirteen instances were wrongly flagged as negated (false-positive results, or FPs), and the program missed 27 instances of negation (false-negative results, or FNs), yielding a sensitivity of 95.3 percent and a specificity of 97.7 percent. In the second evaluation using independent negation detection, 1,869 concepts were detected in 10 documents, with 135 TPs, 12 FPs, and 6 FNs, yielding a sensitivity of 95.7 percent and a specificity of 91.8 percent. One of the words “no,” “denies/denied,” “not,” or “without” was present in 92.5 percent of all negations. Conclusions: Negation of most concepts in medical narrative can be reliably detected by a simple strategy. The reliability of detection depends on several factors, the most important being the accuracy of concept matching. PMID:11687566

Salient features of the ciliated organ of asymmetry

PubMed Central

Amack, Jeffrey D.

2014-01-01

Many internal organs develop distinct left and right sides that are essential for their functions. In several vertebrate embryos, motile cilia generate an asymmetric fluid flow that plays an important role in establishing left-right (LR) signaling cascades. These ‘LR cilia’ are found in the ventral node and posterior notochordal plate in mammals, the gastrocoel roof plate in amphibians and Kupffer’s vesicle in teleost fish. I consider these transient ciliated structures as the ‘organ of asymmetry’ that directs LR patterning of the developing embryo. Variations in size and morphology of the organ of asymmetry in different vertebrate species have raised questions regarding the fundamental features that are required for LR determination. Here, I review current models for how LR asymmetry is established in vertebrates, discuss the cellular architecture of the ciliated organ of asymmetry and then propose key features of this organ that are critical for orienting the LR body axis. PMID:24481178

Performance evaluation of continuity of care records (CCRs): parsing models in a mobile health management system.

PubMed

Chen, Hung-Ming; Liou, Yong-Zan

2014-10-01

In a mobile health management system, mobile devices act as the application hosting devices for personal health records (PHRs) and the healthcare servers construct to exchange and analyze PHRs. One of the most popular PHR standards is continuity of care record (CCR). The CCR is expressed in XML formats. However, parsing is an expensive operation that can degrade XML processing performance. Hence, the objective of this study was to identify different operational and performance characteristics for those CCR parsing models including the XML DOM parser, the SAX parser, the PULL parser, and the JSON parser with regard to JSON data converted from XML-based CCR. Thus, developers can make sensible choices for their target PHR applications to parse CCRs when using mobile devices or servers with different system resources. Furthermore, the simulation experiments of four case studies are conducted to compare the parsing performance on Android mobile devices and the server with large quantities of CCR data.

Normal platelet function in platelet concentrates requires non-platelet cells: a comparative in vitro evaluation of leucocyte-rich (type 1a) and leucocyte-poor (type 3b) platelet concentrates

PubMed Central

Parrish, William R; Roides, Breana; Hwang, Julia; Mafilios, Michael; Story, Brooks; Bhattacharyya, Samir

2016-01-01

Background Therapeutic success of platelet-rich plasma (PRP) may vary based on the composition and preparation method. The objective of this study was to evaluate the cellular components of platelet concentrates produced by a leucocyte-rich (LR-PRP) and a leucocyte-poor PRP systems (LP-PRP). Methods Parameters evaluated included platelet recovery, platelet concentration, red blood cell (RBC) and white blood cell (WBC) composition, platelet growth factor release and stimulation of human tendon cell proliferation in vitro. Results Platelet recoveries were 52% for LP-PRP and 89% for LR-PRP. LR-PRP demonstrated greater reproducibility with a 4.2% coefficient of variation (CV) compared with 19.4% for LP-PRP (p<0.001). LR-PRP demonstrated a greater increase in platelet concentration (7.9-fold) than LP-PRP (2.2-fold; p<0.001). LP-PRP showed 5.0-fold reductions in WBCs, while LR-PRP showed a 4.0-fold increase (p<0.001). LP-PRP reduced RBCs to a haematocrit of 0.25, while LR-PRP reduced haematocrit to 11.8. LP-PRP did not coagulate robustly on reactivation with CaCl2, and released significantly lower levels of epidermal growth factor (EGF) and transforming growth factor β1 (TGF-β1) than whole blood (p<0.03). LP-PRP also did not stimulate tendon cell proliferation greater than whole blood. In contrast, LR-PRP showed increases in each growth factor on activation with CaCl2 (p<0.01) and stimulated greater proliferation (p<0.05) compared with whole blood. Forced activation of LP-PRP with exogenous thrombin rescued the coagulation deficiency and induced greater growth factor release than comparable whole blood (p<0.03). Conclusions These data suggest that non-platelet cellular components in platelet concentrates are important for proper platelet function, including thrombin generation, growth factor release and clot retraction. PMID:27900155

Normal platelet function in platelet concentrates requires non-platelet cells: a comparative in vitro evaluation of leucocyte-rich (type 1a) and leucocyte-poor (type 3b) platelet concentrates.

PubMed

Parrish, William R; Roides, Breana; Hwang, Julia; Mafilios, Michael; Story, Brooks; Bhattacharyya, Samir

2016-01-01

Therapeutic success of platelet-rich plasma (PRP) may vary based on the composition and preparation method. The objective of this study was to evaluate the cellular components of platelet concentrates produced by a leucocyte-rich (LR-PRP) and a leucocyte-poor PRP systems (LP-PRP). Parameters evaluated included platelet recovery, platelet concentration, red blood cell (RBC) and white blood cell (WBC) composition, platelet growth factor release and stimulation of human tendon cell proliferation in vitro. Platelet recoveries were 52% for LP-PRP and 89% for LR-PRP. LR-PRP demonstrated greater reproducibility with a 4.2% coefficient of variation (CV) compared with 19.4% for LP-PRP (p<0.001). LR-PRP demonstrated a greater increase in platelet concentration (7.9-fold) than LP-PRP (2.2-fold; p<0.001). LP-PRP showed 5.0-fold reductions in WBCs, while LR-PRP showed a 4.0-fold increase (p<0.001). LP-PRP reduced RBCs to a haematocrit of 0.25, while LR-PRP reduced haematocrit to 11.8. LP-PRP did not coagulate robustly on reactivation with CaCl 2 , and released significantly lower levels of epidermal growth factor (EGF) and transforming growth factor β1 (TGF-β1) than whole blood (p<0.03). LP-PRP also did not stimulate tendon cell proliferation greater than whole blood. In contrast, LR-PRP showed increases in each growth factor on activation with CaCl 2 (p<0.01) and stimulated greater proliferation (p<0.05) compared with whole blood. Forced activation of LP-PRP with exogenous thrombin rescued the coagulation deficiency and induced greater growth factor release than comparable whole blood (p<0.03). These data suggest that non-platelet cellular components in platelet concentrates are important for proper platelet function, including thrombin generation, growth factor release and clot retraction.

Naringin attenuates the cytotoxicity of hepatotoxin microcystin-LR by the curious mechanisms to OATP1B1- and OATP1B3-expressing cells.

PubMed

Takumi, Shota; Ikema, Satoshi; Hanyu, Tamami; Shima, Yusuke; Kurimoto, Takashi; Shiozaki, Kazuhiro; Sugiyama, Yasumasa; Park, Ho-Dong; Ando, Seiichi; Furukawa, Tatsuhiko; Komatsu, Masaharu

2015-03-01

Microcystin-LR, which is an inhibitor of serine/threonine protein phosphatase (PP)1 and PP2A, induces liver injury by its selective uptake system into the hepatocyte. It is also thought that microcystin-LR induces reactive oxygen species (ROS). We tried to establish the chemical prevention of microcystin-LR poisoning. We investigated the effect of grapefruit flavanone glycoside naringin on cytotoxicity of microcystin-LR using human hepatocyte uptake transporter OATP1B3-expressing HEK293-OATP1B3 cells. We found cytotoxicity of microcystin-LR was attenuated by naringin in a dose dependent manner. The inhibition magnitude of total cellular serine/threonine protein phosphatase activity induced by microcystin-LR was suppressed by naringin. In addition, uptake of microcystin-LR into HEK293-OATP1B3 cells was inhibited by naringin. Furthermore, microcystin-LR induced phosphorylation of p53 was inhibited by naringin. Regardless of the difference in the exposure pattern of pre-processing and post-processing of naringin, the toxicity of microcystin-LR was comparable. These results suggested that naringin is promising remedy as well as preventive medicine for liver damage with microcystin-LR. In addition, involvement of ROS production after exposure to the sublethal concentrations of microcystin-LR in the onset of cytotoxicity was negligible. Therefore, inhibition of microcystin-LR uptake and the pathway other than ROS production would be involved in the effect of naringin on the attenuation of microcystin-LR toxicity. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of alien and intraspecies cytoplasms on manifestation of nuclear genes for wheat resistance to brown rust: II. Specificity of cytoplasm influence on different Lr genes

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

Voluevich, E.A.; Buloichik, A.A.; Palilova, A.N.

Specificity of expression of the major nuclear genes Lr to two brown rust clones in hybrids with the same maternal cytoplasm was analyzed. It was evaluated by a resistant: susceptible ratio in the F{sub 2}. Reciprocal hybrids were obtained from the cross between the progeny of homozygous susceptible plants of the cultivar Penjamo 62 and its alloplasmatic lines carrying cytoplasms of Triticum dicoccoides var. fulvovillosum, Aegilops squarrosa var. typical, Agropyron trichophorum, and isogenic lines of the cultivar Thatcher (Th) with the Lr1, Lr9, Lr15, and Lr19 genes. It was shown that the effect of the Lr1 gene in the cytoplasmmore » of cultivar Thatcher and in eu-, and alloplasmatic forms of Penjamo 62 was less expressed than that of other Lr genes. Cytoplasm of the alloplasmatic line (dicoccoides)-Penjamo 62 was the only exception: in the F{sub 2}, hybrids with Th (Lr1) had a higher yield of resistant forms than those with Th (Lr15). In the hybrid combinations studied, expression and/or transmission of the Lr19 gene was more significant than that of other genes. This gene had no advantages over Lr15 and Lr19 only in cytoplasm of the alloplasmatic line (squarrosa)-Penjamo 62. In certain hybrid cytoplasms, the display of the Lr1, Lr15, and Lr19 genes, in contrast to Lr9, varied with the virulence of the pathogen clones. 15 refs., 5 tabs.« less

Progress in The Semantic Analysis of Scientific Code

NASA Technical Reports Server (NTRS)

Stewart, Mark

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

PubMed

Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

2011-08-05

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

PubMed

Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

2012-04-01

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations. Copyright © 2011 Elsevier Inc. All rights reserved.

Memory Retrieval in Parsing and Interpretation

ERIC Educational Resources Information Center

Schlueter, Ananda Lila Zoe

2017-01-01

This dissertation explores the relationship between the parser and the grammar in error-driven retrieval by examining the mechanism underlying the illusory licensing of subject-verb agreement violations ("agreement attraction"). Previous work motivates a two-stage model of agreement attraction in which the parser predicts the verb's…

A prospective validation of the IOTA logistic regression models (LR1 and LR2) in comparison to subjective pattern recognition for the diagnosis of ovarian cancer.

PubMed

Nunes, Natalie; Ambler, Gareth; Hoo, Wee-Liak; Naftalin, Joel; Foo, Xulin; Widschwendter, Martin; Jurkovic, Davor

2013-11-01

This study aimed to assess the accuracy of the International Ovarian Tumour Analysis (IOTA) logistic regression models (LR1 and LR2) and that of subjective pattern recognition (PR) for the diagnosis of ovarian cancer. This was a prospective single-center study in a general gynecology unit of a tertiary hospital during 33 months. There were 292 consecutive women who underwent surgery after an ultrasound diagnosis of an adnexal tumor. All examinations were by a single level 2 ultrasound operator, according to the IOTA guidelines. The malignancy likelihood was calculated using the IOTA LR1 and LR2. The women were then examined separately by an expert operator using subjective PR. These were compared to operative findings and histology. The sensitivity, specificity, area under the curve (AUC), and accuracy of the 3 methods were calculated and compared. The AUCs for LR1 and LR2 were 0.94 [95% confidence interval (CI), 0.92-0.97] and 0.93 (95% CI, 0.90-0.96), respectively. Subjective PR gave a positive likelihood ratio (LR+ve) of 13.9 (95% CI, 7.84-24.6) and a LR-ve of 0.049 (95% CI, 0.022-0.107). The corresponding LR+ve and LR-ve for LR1 were 3.33 (95% CI, 2.85-3.55) and 0.03 (95% CI, 0.01-0.10), and for LR2 were 3.58 (95% CI, 2.77-4.63) and 0.052 (95% CI, 0.022-0.123). The accuracy of PR was 0.942 (95% CI, 0.908-0.966), which was significantly higher when compared with 0.829 (95% CI, 0.781-0.870) for LR1 and 0.836 (95% CI, 0.788-0.872) for LR2 (P < 0.001). The AUC of the IOTA LR1 and LR2 were similar in nonexpert's hands when compared to the original and validation IOTA studies. The PR method was the more accurate test to diagnose ovarian cancer than either of the IOTA models.

Facilitating Analysis of Multiple Partial Data Streams

NASA Technical Reports Server (NTRS)

Maimone, Mark W.; Liebersbach, Robert R.

2008-01-01

Robotic Operations Automation: Mechanisms, Imaging, Navigation report Generation (ROAMING) is a set of computer programs that facilitates and accelerates both tactical and strategic analysis of time-sampled data especially the disparate and often incomplete streams of Mars Explorer Rover (MER) telemetry data described in the immediately preceding article. As used here, tactical refers to the activities over a relatively short time (one Martian day in the original MER application) and strategic refers to a longer time (the entire multi-year MER missions in the original application). Prior to installation, ROAMING must be configured with the types of data of interest, and parsers must be modified to understand the format of the input data (many example parsers are provided, including for general CSV files). Thereafter, new data from multiple disparate sources are automatically resampled into a single common annotated spreadsheet stored in a readable space-separated format, and these data can be processed or plotted at any time scale. Such processing or plotting makes it possible to study not only the details of a particular activity spanning only a few seconds, but also longer-term trends. ROAMING makes it possible to generate mission-wide plots of multiple engineering quantities [e.g., vehicle tilt as in Figure 1(a), motor current, numbers of images] that, heretofore could be found only in thousands of separate files. ROAMING also supports automatic annotation of both images and graphs. In the MER application, labels given to terrain features by rover scientists and engineers are automatically plotted in all received images based on their associated camera models (see Figure 2), times measured in seconds are mapped to Mars local time, and command names or arbitrary time-labeled events can be used to label engineering plots, as in Figure 1(b).

Linking Parser Development to Acquisition of Syntactic Knowledge

ERIC Educational Resources Information Center

Omaki, Akira; Lidz, Jeffrey

2015-01-01

Traditionally, acquisition of syntactic knowledge and the development of sentence comprehension behaviors have been treated as separate disciplines. This article reviews a growing body of work on the development of incremental sentence comprehension mechanisms and discusses how a better understanding of the developing parser can shed light on two…

Reducible dictionaries for single image super-resolution based on patch matching and mean shifting

NASA Astrophysics Data System (ADS)

Rasti, Pejman; Nasrollahi, Kamal; Orlova, Olga; Tamberg, Gert; Moeslund, Thomas B.; Anbarjafari, Gholamreza

2017-03-01

A single-image super-resolution (SR) method is proposed. The proposed method uses a generated dictionary from pairs of high resolution (HR) images and their corresponding low resolution (LR) representations. First, HR images and the corresponding LR ones are divided into patches of HR and LR, respectively, and then they are collected into separate dictionaries. Afterward, when performing SR, the distance between every patch of the input LR image and those of available LR patches in the LR dictionary is calculated. The minimum distance between the input LR patch and those in the LR dictionary is taken, and its counterpart from the HR dictionary is passed through an illumination enhancement process. By this technique, the noticeable change of illumination between neighbor patches in the super-resolved image is significantly reduced. The enhanced HR patch represents the HR patch of the super-resolved image. Finally, to remove the blocking effect caused by merging the patches, an average of the obtained HR image and the interpolated image obtained using bicubic interpolation is calculated. The quantitative and qualitative analyses show the superiority of the proposed technique over the conventional and state-of-art methods.

Effect of Microcystin-LR on human trophoblast differentiation in vitro

EPA Science Inventory

Background: Microcystin LR is a potent protein phosphatase 2a (PP2a) inhibitor and generates reactive oxygen species (ROS) believed to be an essential component of a toxic effect. Toxicological studies have demonstrated microcystin (MCYST) disruption of cytoskeletal function and...

Omega-3 Fatty Acid Docosahexaenoic Acid Increases SorLA/LR11, a Sorting Protein with Reduced Expression in Sporadic Alzheimer’s Disease (AD): Relevance to AD Prevention

PubMed Central

Ma, Qiu-Lan; Teter, Bruce; Ubeda, Oliver J.; Morihara, Takashi; Dhoot, Dilsher; Nyby, Michael D.; Tuck, Michael L.; Frautschy, Sally A.; Cole, Greg M.

2008-01-01

Environmental and genetic factors, notably ApoE4, contribute to the etiology of late-onset Alzheimer’s disease (LOAD). Reduced mRNA and protein for an apolipoprotein E (ApoE) receptor family member, SorLA (LR11) has been found in LOAD but not early-onset AD, suggesting that LR11 loss is not secondary to pathology. LR11 is a neuronal sorting protein that reduces amyloid precursor protein (APP) trafficking to secretases that generate β-amyloid (Aβ). Genetic polymorphisms that reduce LR11 expression are associated with increased AD risk. However these polymorphisms account for only a fraction of cases with LR11 deficits, suggesting involvement of environmental factors. Because lipoprotein receptors are typically lipid-regulated, we postulated that LR11 is regulated by docosahexaenoic acid (DHA), an essential ω-3 fatty acid related to reduced AD risk and reduced Aβ accumulation. In this study, we report that DHA significantly increases LR11 in multiple systems, including primary rat neurons, aged non-Tg mice and an aged DHA-depleted APPsw AD mouse model. DHA also increased LR11 in a human neuronal line. In vivo elevation of LR11 was also observed with dietary fish oil in young rats with insulin resistance, a model for type II diabetes, another AD risk factor. These data argue that DHA induction of LR11 does not require DHA-depleting diets and is not age dependent. Because reduced LR11 is known to increase Aβ production and may be a significant genetic cause of LOAD, our results indicate that DHA increases in SorLA/LR11 levels may play an important role in preventing LOAD. PMID:18160637

Identification of Patients at Very Low Risk of Local Recurrence After Breast-Conserving Surgery

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

Smith, Sally L., E-mail: ssmith11@bccancer.bc.ca; Truong, Pauline T.; Lu, Linghong

2014-07-01

Purpose: To identify clinical and pathological factors that identify groups of women with stage I breast cancer with a 5-year risk of local recurrence (LR) ≤1.5% after breast-conserving therapy (BCS) plus whole-breast radiation therapy (RT). Methods and Materials: Study subjects were 5974 patients ≥50 years of age whose cancer was diagnosed between 1989 and 2006, and were referred with pT1 pN0 invasive breast cancer treated with BCS and RT. Cases of 5- and 10-year LR were examined using Kaplan-Meier methods. Recursive partitioning analysis was performed in patients treated with and without endocrine therapy to identify combinations of factors associated withmore » a 5-year LR risk ≤1.5%. Results: The median follow-up was 8.61 years. Median age was 63 years of age (range, 50 to 91). Overall 5-year LR was 1.5% (95% confidence interval [CI], 1.2%-1.9%) and 10-year LR was 3.4% (95% CI, 2.8%-4.0%). Of 2830 patients treated with endocrine therapy, patient subsets identified with 5-year LR ≤1.5% included patients with grade 1 histology (n=1038; LR, 0.2%; 95% CI, 0%-0.5%) or grade 2 histology plus ≥60 years of age (n=843; LR, 0.5%; 95% CI, 0%-1.0%). Ten-year LR for these groups were 0.8% (95% CI, 0.1%-1.6%) and 0.9% (95% CI, 0.2%-1.6%), respectively. Of 3144 patients treated without endocrine therapy, patients with grade 1 histology plus clear margins had 5-year LR ≤1.5% (n=821; LR, 0.6%; 95% CI, 0.1%-1.2%). Ten-year LR for this group was 2.2% (95% CI, 1.0%-3.4%). Conclusions: Histologic grade, age, margin status, and use of endocrine therapy identified 45% of a population-based cohort of female patients over age 50 with stage I breast cancer with a 5-year LR risk ≤1.5% after BCS plus RT. Prospective study is needed to evaluate the safety of omitting RT in patients with such a low risk of LR.« less

[The role of animacy in European Portuguese relative clause attachment: evidence from production and comprehension tasks].

PubMed

Soares, Ana Paula; Fraga, Isabel; Comesaña, Montserrat; Piñeiro, Ana

2010-11-01

This work presents an analysis of the role of animacy in attachment preferences of relative clauses to complex noun phrases in European Portuguese (EP). The study of how the human parser solves this kind of syntactic ambiguities has been focus of extensive research. However, what is known about EP is both limited and puzzling. Additionally, as recent studies have stressed the importance of extra-syntactic variables in this process, two experiments were carried out to assess EP attachment preferences considering four animacy conditions: Study 1 used a sentence-completion-task, and Study 2 a self-paced reading task. Both studies indicate a significant preference for high attachment in EP. Furthermore, they showed that this preference was modulated by the animacy of the host NP: if the first host was inanimate and the second one was animate, the parser's preference changed to low attachment preference. These findings shed light on previous results regarding EP and strengthen the idea that, even in early stages of processing, the parser seems to be sensitive to extra-syntactic information.

The Molecular Basis of Wound Healing Processes Induced by Lithospermi Radix: A Proteomics and Biochemical Analysis

PubMed Central

Hsiao, Chia-Yen; Tsai, Tung-Hu; Chak, Kin-Fu

2012-01-01

Lithospermi Radix (LR) is an effective traditional Chinese herb in various types of wound healing; however, its mechanism of action remains unknown. A biochemical and proteomic platform was generated to explore the biological phenomena associated with LR and its active component shikonin. We found that both LR ethanol extracts and shikonin are able to promote cell proliferation by up to 25%. The results of proteomic analysis revealed that twenty-two differentially expressed proteins could be identified when fibroblast cells were treated with LR or shikonin. The functions of those proteins are associated with antioxidant activity, antiapoptosis activity, the regulation of cell mobility, the secretion of collagen, the removal of abnormal proteins, and the promotion of cell proliferation, indicating that the efficacy of LR in wound healing may be derived from a synergistic effect on a number of factors induced by the herbal medicine. Furthermore, an animal model confirmed that LR is able to accelerate wound healing on the flank back of the SD rats. Together these findings help to pinpoint the molecular basis of wound healing process induced by LR. PMID:23024692

Removal of microcystin-LR from spiked water using either activated carbon or anthracite as filter material.

PubMed

Drogui, Patrick; Daghrir, Rimeh; Simard, Marie-Christine; Sauvageau, Christine; Blais, Jean François

2012-01-01

The occurrence of cyanobacterial toxins (blue-green algae) in drinking water sources is a big concern for human health. Removal of microcystin-LR (MC-LR) from drinking water was evaluated at the laboratory pilot scale using either granular activated carbon (GAC) or powdered activated carbon (PAC) and compared with the treatment using anthracite as filter material. Virgin GAC was more effective at removing MC-LR (initial concentration ranging from 9 to 47 microg L(-1)) to reach the World Health Organization recommended level (1.0 microg L(-1)). When the GAC filter was colonized by bacteria, the filter became less effective at removing MC-LR owing to competitive reactions occurring between protein adsorption (released by bacteria) and MC-LR adsorption. Using PAC, the concentration of MC-LR decreased from 22 to 3 microg L(-1) (removal of 86% of MC-LR) by the addition of 100 mg PAC L(-1).

A python tool for the implementation of domain-specific languages

NASA Astrophysics Data System (ADS)

Dejanović, Igor; Vaderna, Renata; Milosavljević, Gordana; Simić, Miloš; Vuković, Željko

2017-07-01

In this paper we describe textX, a meta-language and a tool for building Domain-Specific Languages. It is implemented in Python using Arpeggio PEG (Parsing Expression Grammar) parser library. From a single language description (grammar) textX will build a parser and a meta-model (a.k.a. abstract syntax) of the language. The parser is used to parse textual representations of models conforming to the meta-model. As a result of parsing, a Python object graph will be automatically created. The structure of the object graph will conform to the meta-model defined by the grammar. This approach frees a developer from the need to manually analyse a parse tree and transform it to other suitable representation. The textX library is independent of any integrated development environment and can be easily integrated in any Python project. The textX tool works as a grammar interpreter. The parser is configured at run-time using the grammar. The textX tool is a free and open-source project available at GitHub.

Oncologic outcome after local recurrence of chondrosarcoma: Analysis of prognostic factors.

PubMed

Kim, Han-Soo; Bindiganavile, Srimanth S; Han, Ilkyu

2015-06-01

Literature on outcome after local recurrence (LR) in chondrosarcoma is scarce and better appreciation of prognostic factors is needed. (1) To evaluate post-LR oncologic outcomes of disease-specific survival and subsequent LR and (2) to identify prognostic factors for post-LR oncologic outcomes. Review of 28 patients with locally recurrent chondrosarcoma from the original cohort of 150 patients, who were treated surgically with or without adjuvants between 1982 and 2011, was performed. Mean age was 46 years (range, 21-73) which included 20 males and 8 females with mean follow up of 8.4 ± 7.5 years (range, 1.2-31.0). Post-LR survival at 5 years was 58.6 ± 10.3%. Age greater than 50 years (P = 0.011) and LR occurring within 1 year of primary surgery (P = 0.011) independently predicted poor survival. Seven patients suffered subsequent LR, which was significantly affected by surgical margin for LR (P = 0.038). Long-term survival of locally recurrent chondrosarcoma is achievable in a substantial number of patients. Older age at onset of LR and shorter interval from primary surgery to LR identifies high risk patients for poor post-LR survival while, wide surgical margins at LR surgery reduces the risk of subsequent LR. © 2015 Wiley Periodicals, Inc.

A Formal Model of Ambiguity and its Applications in Machine Translation

DTIC Science & Technology

2010-01-01

structure indicates linguisti- cally implausible segmentation that might be generated using dictionary - driven approaches...derivation. As was done in the monolingual case, the functions LHS, RHSi, RHSo and υ can be extended to a derivation δ. D(q) where q ∈V denotes the... monolingual parses. My algorithm runs more efficiently than O(n6) with many grammars (including those that required using heuristic search with other parsers

Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon

PubMed Central

Huang, Yang; Lowe, Henry J.; Klein, Dan; Cucina, Russell J.

2005-01-01

Objective: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS® Specialist Lexicon to improve noun phrase identification within clinical radiology documents. Design: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)® Clinical Document Architecture (CDA)–compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. Results: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. Conclusion: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. PMID:15684131

Structure before Meaning: Sentence Processing, Plausibility, and Subcategorization

PubMed Central

Kizach, Johannes; Nyvad, Anne Mette; Christensen, Ken Ramshøj

2013-01-01

Natural language processing is a fast and automatized process. A crucial part of this process is parsing, the online incremental construction of a syntactic structure. The aim of this study was to test whether a wh-filler extracted from an embedded clause is initially attached as the object of the matrix verb with subsequent reanalysis, and if so, whether the plausibility of such an attachment has an effect on reaction time. Finally, we wanted to examine whether subcategorization plays a role. We used a method called G-Maze to measure response time in a self-paced reading design. The experiments confirmed that there is early attachment of fillers to the matrix verb. When this attachment is implausible, the off-line acceptability of the whole sentence is significantly reduced. The on-line results showed that G-Maze was highly suited for this type of experiment. In accordance with our predictions, the results suggest that the parser ignores (or has no access to information about) implausibility and attaches fillers as soon as possible to the matrix verb. However, the results also show that the parser uses the subcategorization frame of the matrix verb. In short, the parser ignores semantic information and allows implausible attachments but adheres to information about which type of object a verb can take, ensuring that the parser does not make impossible attachments. We argue that the evidence supports a syntactic parser informed by syntactic cues, rather than one guided by semantic cues or one that is blind, or completely autonomous. PMID:24116101

Structure before meaning: sentence processing, plausibility, and subcategorization.

PubMed

Kizach, Johannes; Nyvad, Anne Mette; Christensen, Ken Ramshøj

2013-01-01

Natural language processing is a fast and automatized process. A crucial part of this process is parsing, the online incremental construction of a syntactic structure. The aim of this study was to test whether a wh-filler extracted from an embedded clause is initially attached as the object of the matrix verb with subsequent reanalysis, and if so, whether the plausibility of such an attachment has an effect on reaction time. Finally, we wanted to examine whether subcategorization plays a role. We used a method called G-Maze to measure response time in a self-paced reading design. The experiments confirmed that there is early attachment of fillers to the matrix verb. When this attachment is implausible, the off-line acceptability of the whole sentence is significantly reduced. The on-line results showed that G-Maze was highly suited for this type of experiment. In accordance with our predictions, the results suggest that the parser ignores (or has no access to information about) implausibility and attaches fillers as soon as possible to the matrix verb. However, the results also show that the parser uses the subcategorization frame of the matrix verb. In short, the parser ignores semantic information and allows implausible attachments but adheres to information about which type of object a verb can take, ensuring that the parser does not make impossible attachments. We argue that the evidence supports a syntactic parser informed by syntactic cues, rather than one guided by semantic cues or one that is blind, or completely autonomous.

A study of the transferability of influenza case detection systems between two large healthcare systems

PubMed Central

Wagner, Michael M.; Cooper, Gregory F.; Ferraro, Jeffrey P.; Su, Howard; Gesteland, Per H.; Haug, Peter J.; Millett, Nicholas E.; Aronis, John M.; Nowalk, Andrew J.; Ruiz, Victor M.; López Pineda, Arturo; Shi, Lingyun; Van Bree, Rudy; Ginter, Thomas; Tsui, Fuchiang

2017-01-01

Objectives This study evaluates the accuracy and transferability of Bayesian case detection systems (BCD) that use clinical notes from emergency department (ED) to detect influenza cases. Methods A BCD uses natural language processing (NLP) to infer the presence or absence of clinical findings from ED notes, which are fed into a Bayesain network classifier (BN) to infer patients’ diagnoses. We developed BCDs at the University of Pittsburgh Medical Center (BCDUPMC) and Intermountain Healthcare in Utah (BCDIH). At each site, we manually built a rule-based NLP and trained a Bayesain network classifier from over 40,000 ED encounters between Jan. 2008 and May. 2010 using feature selection, machine learning, and expert debiasing approach. Transferability of a BCD in this study may be impacted by seven factors: development (source) institution, development parser, application (target) institution, application parser, NLP transfer, BN transfer, and classification task. We employed an ANOVA analysis to study their impacts on BCD performance. Results Both BCDs discriminated well between influenza and non-influenza on local test cases (AUCs > 0.92). When tested for transferability using the other institution’s cases, BCDUPMC discriminations declined minimally (AUC decreased from 0.95 to 0.94, p<0.01), and BCDIH discriminations declined more (from 0.93 to 0.87, p<0.0001). We attributed the BCDIH decline to the lower recall of the IH parser on UPMC notes. The ANOVA analysis showed five significant factors: development parser, application institution, application parser, BN transfer, and classification task. Conclusion We demonstrated high influenza case detection performance in two large healthcare systems in two geographically separated regions, providing evidentiary support for the use of automated case detection from routinely collected electronic clinical notes in national influenza surveillance. The transferability could be improved by training Bayesian network classifier locally and increasing the accuracy of the NLP parser. PMID:28380048

A study of the transferability of influenza case detection systems between two large healthcare systems.

PubMed

Ye, Ye; Wagner, Michael M; Cooper, Gregory F; Ferraro, Jeffrey P; Su, Howard; Gesteland, Per H; Haug, Peter J; Millett, Nicholas E; Aronis, John M; Nowalk, Andrew J; Ruiz, Victor M; López Pineda, Arturo; Shi, Lingyun; Van Bree, Rudy; Ginter, Thomas; Tsui, Fuchiang

2017-01-01

This study evaluates the accuracy and transferability of Bayesian case detection systems (BCD) that use clinical notes from emergency department (ED) to detect influenza cases. A BCD uses natural language processing (NLP) to infer the presence or absence of clinical findings from ED notes, which are fed into a Bayesain network classifier (BN) to infer patients' diagnoses. We developed BCDs at the University of Pittsburgh Medical Center (BCDUPMC) and Intermountain Healthcare in Utah (BCDIH). At each site, we manually built a rule-based NLP and trained a Bayesain network classifier from over 40,000 ED encounters between Jan. 2008 and May. 2010 using feature selection, machine learning, and expert debiasing approach. Transferability of a BCD in this study may be impacted by seven factors: development (source) institution, development parser, application (target) institution, application parser, NLP transfer, BN transfer, and classification task. We employed an ANOVA analysis to study their impacts on BCD performance. Both BCDs discriminated well between influenza and non-influenza on local test cases (AUCs > 0.92). When tested for transferability using the other institution's cases, BCDUPMC discriminations declined minimally (AUC decreased from 0.95 to 0.94, p<0.01), and BCDIH discriminations declined more (from 0.93 to 0.87, p<0.0001). We attributed the BCDIH decline to the lower recall of the IH parser on UPMC notes. The ANOVA analysis showed five significant factors: development parser, application institution, application parser, BN transfer, and classification task. We demonstrated high influenza case detection performance in two large healthcare systems in two geographically separated regions, providing evidentiary support for the use of automated case detection from routinely collected electronic clinical notes in national influenza surveillance. The transferability could be improved by training Bayesian network classifier locally and increasing the accuracy of the NLP parser.

QUEST/Ada: Query utility environment for software testing of Ada

NASA Technical Reports Server (NTRS)

Brown, David B.

1989-01-01

Results of research and development efforts are presented for Task 1, Phase 2 of a general project entitled, The Development of a Program Analysis Environment for Ada. A prototype of the QUEST/Ada system was developed to collect data to determine the effectiveness of the rule-based testing paradigm. The prototype consists of five parts: the test data generator, the parser/scanner, the test coverage analyzer, a symbolic evaluator, and a data management facility, known as the Librarian. These components are discussed at length. Also presented is an experimental design for the evaluations, an overview of the project, and a schedule for its completion.

Long-Term, Low-Dose Exposure to Microcystin-LR Does not Cause or Increase the Severity of Liver Disease in Rodents.

PubMed

Labine, Meaghan; Gong, Yuewen; Minuk, Gerald Y

Acute exposure to high concentrations of microcystin-LR (MC-LR) can cause significant hepatocyte injury. To document the effects of long-term, low-dose MC-LR exposure on hepatic inflammation and fibrosis in mice with healthy and diseased livers. Male CD1 mice (N = 20/group) were exposed to 1.0 μg/L of MC-LR in drinking water; 1.0 μg/L MC-LR plus 300 mg/L of the hepatotoxin thioacetamide (MC-LR/TAA); or 300 mg/L TAA alone for 28 weeks. Liver biochemistry and histology were documented at the end of the study period. In addition, hepatic stellate cells (HSCs), were exposed in vitro to MC-LR (0.1-10,000 μg/L) and monitored for changes in cell metabolism, proliferation and activation. Liver biochemistry and histology were essentially normal in MC-LR alone exposed mice. MC-LR/TAA and TAA alone exposed mice had significant hepatic inflammation and fibrosis but the extent of the changes were similar in the two groups. In vitro, MC-LR had no effect on HSC metabolism, proliferation or activation. Long-term, low-dose exposure to MC-LR is unlikely to lead to chronic liver disease in the setting of a normal liver or exacerbate existing liver disease in the setting of ongoing hepatitis.

A photoelectrochemical aptasensor constructed with core-shell CuS-TiO2 heterostructure for detection of microcystin-LR.

PubMed

Tang, Yunfei; Chai, Yun; Liu, Xiaoqiang; Li, Lele; Yang, Liwei; Liu, Peipei; Zhou, Yanmei; Ju, Huangxian; Cheng, Yunzhi

2018-06-05

In this work, a CuS-TiO 2 heterojunction composite was prepared by dispersedly depositing CuS nanoparticles on TiO 2 nanospheres surface with a hydrothermal method, and was then used to construct a photoelectrochemical (PEC) aptasensor for sensitive detection of microcystin-LR (MC-LR) in aquatic environment. The energy bands of CuS nanoparticles and spherical anatase TiO 2 were well matched, which enhanced the photo-to-current conversion efficiency. The composite exhibited the enhanced visible light absorption, the improved separation of photo-generated charges, and the reduced self-aggregation of CuS nanoparticles, leading to the enhanced photocurrent response. The PEC aptasensor was constructed by immobilizing CuS-TiO 2 composite on ITO electrode with chitosan film that further covalently bound aminated aptamer. After the target, microcystin-LR (MC-LR) as an analyte model, was captured by the aptamer on the aptasensor, it could be oxidized by the photo-generated hole to impede the electron-hole recombination and further amplify the photocurrent. The PEC aptasensor showed superior analytical performance for MC-LR with a linear range of 5.0 × 10 -5 nM to 250 nM and a detection limit of 2.0 × 10 -5 nM. The detection results with the aptasensor for practical water samples indicated its promising application in environmental monitoring. Copyright © 2018 Elsevier B.V. All rights reserved.

1,3-Propanediol dehydrogenases in Lactobacillus reuteri: impact on central metabolism and 3-hydroxypropionaldehyde production.

PubMed

Stevens, Marc J A; Vollenweider, Sabine; Meile, Leo; Lacroix, Christophe

2011-08-03

Lactobacillus reuteri metabolizes glycerol to 3-hydroxypropionaldehyde (3-HPA) and further to 1,3-propanediol (1,3-PDO), the latter step catalysed by a propanediol dehydrogenase (PDH). The last step in this pathway regenerates NAD+ and enables therefore the energetically more favourable production of acetate over ethanol during growth on glucose. A search throughout the genome of L. reuteri DSM 20016 revealed two putative PDHs encoded by ORFs lr_0030 and lr_1734. ORF lr_1734 is situated in the pdu operon encoding the glycerol conversion machinery and therefore likely involved in 1,3-PDO formation. ORF lr_0030 has not been associated with PDH-activity so far. To elucidate the role of these two PDHs, gene deletion mutant strains were constructed. Growth behaviour on glucose was comparable between the wild type and both mutant strains. However, on glucose + glycerol, the exponential growth rate of Δlr_0030 was lower compared to the wild type and the lr_1734 mutant. Furthermore, glycerol addition resulted in decreased ethanol production in the wild type and Δlr_1734, but not in Δlr_0030. PDH activity measurements using 3-HPA as a substrate revealed lower activity of Δlr_0030 extracts from exponential growing cells compared to wild type and Δlr_1734 extracts.During biotechnological 3-HPA production using non-growing cells, the ratio 3-HPA to 1,3-PDO was approximately 7 in the wild type and Δlr_0030, whereas this ratio was 12.5 in the mutant Δlr_1734. The enzyme encoded by lr_0030 plays a pivotal role in 3-HPA conversion in exponential growing L. reuteri cells. The enzyme encoded by lr_1734 is active during 3-HPA production by non-growing cells and this enzyme is a useful target to enhance 3-HPA production and minimize formation of the by-product 1,3-PDO.

75 FR 9956 - PSEG Nuclear LLC, Hope Creek Generating Station and Salem Nuclear Generating Station, Unit Nos. 1...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... letter number LR-N09- 0248 and the second enclosure is an environmental impact statement. Based on a... November 3, and November 20, 2009, submittals, with the exception of the environmental impact statement... M. S. Fertel, Nuclear Energy Institute, ADAMS Accession No. ML091410309). The licensee's request for...

An Experiment in Scientific Code Semantic Analysis

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1998-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, distributed expert parsers. These semantic parser are designed to recognize formulae in different disciplines including physical and mathematical formulae and geometrical position in a numerical scheme. The parsers will automatically recognize and document some static, semantic concepts and locate some program semantic errors. Results are shown for a subroutine test case and a collection of combustion code routines. This ability to locate some semantic errors and document semantic concepts in scientific and engineering code should reduce the time, risk, and effort of developing and using these codes.

Molecular and analysis of a phenylalanine ammonia-lyase gene (LrPAL2) from Lycoris radiata.

PubMed

Jiang, Yumei; Xia, Bing; Liang, Lijian; Li, Xiaodan; Xu, Sheng; Peng, Feng; Wang, Ren

2013-03-01

Phenylalanine ammonia-lyase (PAL), the first enzyme of phenylpropanoid biosynthesis, participates in the biosynthesis of flavonoids, lignins, stilbenes and many other compounds. In this study, we cloned a 2,326 bp full-length PAL2 gene from Lycoris radiata by using degenerate oligonucleotide primer PCR (DOP-PCR) and the rapid amplification of cDNA ends method. The cDNA contains a 2,124 bp coding region encoding 707 amino acids. The LrPAL2 shares about 77.0 % nucleic acid identity and 83 % amino acid identity with LrPAL1. Furthermore, genome sequence analysis demonstrated that LrPAL2 gene contains one intron and two exons. The 5' flanking sequence of LrPAL2 was also cloned by self-formed adaptor PCR (SEFA-PCR), and a group of putative cis-acting elements such as TATA box, CAAT box, G box, TC-rich repeats, CGTCA motif and TCA-element were identified. The LrPAL2 was detected in all tissues examined, with high abundance in bulbs at leaf sprouting stage and in petals at blooming stage. Besides, LrPAL2 drastically responded to MJ, SNP and UV, moderately responded to GA and SA, and a little increased under wounding. Comparison of LrPAL2 expression and LrPAL1 expression demonstrated that LrPAL2 can be more significantly induced than LrPAL1 under the above treatments, and LrPAL2 transcripts accumulated prominently at blooming stage, especially in petals, while LrPAL1 transcripts did not accumulated significantly at blooming stage. All these results suggested that LrPAL2 might play distinct roles in different branches of the phenylpropanoid pathway.

Crystalloid Fluid Choice and Clinical Outcomes in Pediatric Sepsis: A Matched Retrospective Cohort Study.

PubMed

Weiss, Scott L; Keele, Luke; Balamuth, Fran; Vendetti, Neika; Ross, Rachael; Fitzgerald, Julie C; Gerber, Jeffrey S

2017-03-01

To test the hypothesis that resuscitation with balanced fluids (lactated Ringer [LR]) is associated with improved outcomes compared with normal saline (NS) in pediatric sepsis. We performed matched analyses using data from 12 529 patients <18 years of age with severe sepsis/septic shock at 382 US hospitals between 2000 and 2013 to compare outcomes with vs without LR as part of initial resuscitation. Patients receiving LR were matched 1:1 to patients receiving only NS (NS group), including separate matches for any (LR-any group) or exclusive (LR-only group) LR use. Outcomes included 30-day hospital mortality, acute kidney injury, new dialysis, and length of stay. The LR-any group was older, received larger crystalloid volumes, and was less likely to have malignancies than the NS group. After matching, mortality was not different between LR-any (7.2%) and NS (7.9%) groups (risk ratio 0.99, 95% CI 0.98, 1.01; P = .20). There were no differences in secondary outcomes except longer hospital length of stay in LR-any group (absolute difference 2.4, 95% CI 1.4, 5.0 days; P < .001). Although LR was preferentially used as adjunctive fluid with large-volume resuscitation or first-line fluid in patients with lower illness severity, outcomes were not different after matching stratified by volume and proportionate LR utilization, including for patients in the LR-only group. Balanced fluid resuscitation with LR was not associated with improved outcomes compared with NS in pediatric sepsis. Although the current practice of NS resuscitation is justified, selective LR use necessitates a prospective trial to definitively determine comparative effectiveness among crystalloids. Copyright © 2016 Elsevier Inc. All rights reserved.

Crystalloid Fluid Choice and Clinical Outcomes in Pediatric Sepsis: A Matched Retrospective Cohort Study

PubMed Central

Weiss, Scott L.; Keele, Luke; Balamuth, Fran; Vendetti, Neika; Ross, Rachael; Fitzgerald, Julie C.; Gerber, Jeffrey S.

2017-01-01

Objective To test the hypothesis that resuscitation with balanced fluids (lactated Ringer [LR]) is associated with improved outcomes compared with normal saline (NS) in pediatric sepsis. Study design We performed matched analyses using data from 12 529 patients <18 years of age with severe sepsis/septic shock at 382 US hospitals between 2000 and 2013 to compare outcomes with vs without LR as part of initial resuscitation. Patients receiving LR were matched 1:1 to patients receiving only NS (NS group), including separate matches for any (LR-any group) or exclusive (LR-only group) LR use. Outcomes included 30-day hospital mortality, acute kidney injury, new dialysis, and length of stay. Results The LR-any group was older, received larger crystalloid volumes, and was less likely to have malignancies than the NS group. After matching, mortality was not different between LR-any (7.2%) and NS (7.9%) groups (risk ratio 0.99, 95% CI 0.98, 1.01; P = .20). There were no differences in secondary outcomes except longer hospital length of stay in LR-any group (absolute difference 2.4, 95% CI 1.4, 5.0 days; P < .001). Although LR was preferentially used as adjunctive fluid with large-volume resuscitation or first-line fluid in patients with lower illness severity, outcomes were not different after matching stratified by volume and proportionate LR utilization, including for patients in the LR-only group. Conclusions Balanced fluid resuscitation with LR was not associated with improved outcomes compared with NS in pediatric sepsis. Although the current practice of NS resuscitation is justified, selective LR use necessitates a prospective trial to definitively determine comparative effectiveness among crystalloids. PMID:28063688

SLC7 family transporters control the establishment of left-right asymmetry during organogenesis in medaka by activating mTOR signaling.

PubMed

Asaoka, Yoichi; Nagai, Yoko; Namae, Misako; Furutani-Seiki, Makoto; Nishina, Hiroshi

2016-05-20

The precise government of the left-right (LR) specification of an organ is an essential aspect of its morphogenesis. Multiple signaling cascades have been implicated in the establishment of vertebrate LR asymmetry. Recently, mTOR signaling was found to critically regulate the development of LR asymmetry in zebrafish. However, the upstream factor(s) that activate mTOR signaling in the context of LR specification are as yet unknown. In this study, we identify the SLC7 amino acid transporters Slc7a7 and Slc7a8 as novel regulators of LR asymmetry development in the small fish medaka. Knockdown of Slc7a7 and/or Slc7a8 in medaka embryos disrupted LR organ asymmetries. Depletion of Slc7a7 hindered left-sided expression of the southpaw (spaw) gene, which is responsible for LR axis determination. Work at the cellular level revealed that Slc7a7 coordinates ciliogenesis in the epithelium of Kupffer's vesicle and thereby the generation of the nodal fluid flow required for LR asymmetry. Interestingly, knockdown of Slc7a7 depressed mTOR signaling activity in medaka embryos. Treatment with rapamycin, an inhibitor of mTOR signaling, together with Slc7a7 knockdown synergistically perturbed spaw expression, indicating an interaction between Slc7a7 and mTOR signaling affecting gene expression required for LR specification. Taken together, our results demonstrate that Slc7a7 governs the regulation of LR asymmetry development via the activation of mTOR signaling. Copyright © 2016 Elsevier Inc. All rights reserved.

The parser doesn't ignore intransitivity, after all

PubMed Central

Staub, Adrian

2015-01-01

Several previous studies (Adams, Clifton, & Mitchell, 1998; Mitchell, 1987; van Gompel & Pickering, 2001) have explored the question of whether the parser initially analyzes a noun phrase that follows an intransitive verb as the verb's direct object. Three eyetracking experiments examined this issue in more detail. Experiment 1 strongly replicated the finding (van Gompel & Pickering, 2001) that readers experience difficulty on this noun phrase in normal reading, and found that this difficulty occurs even with a class of intransitive verbs for which a direct object is categorically prohibited. Experiment 2, however, demonstrated that this effect is not due to syntactic misanalysis, but is instead due to disruption that occurs when a comma is absent at a subordinate clause/main clause boundary. Exploring a different construction, Experiment 3 replicated the finding (Pickering & Traxler, 2003; Traxler & Pickering, 1996) that when a noun phrase “filler” is an implausible direct object for an optionally transitive relative clause verb, processing difficulty results; however, there was no evidence for such difficulty when the relative clause verb was strictly intransitive. Taken together, the three experiments undermine the support for the claim that the parser initially ignores a verb's subcategorization restrictions. PMID:17470005

Morphotype-Dependent Flow Characteristics in Bicuspid Aortic Valve Ascending Aortas: A Benchtop Particle Image Velocimetry Study

PubMed Central

McNally, Andrew; Madan, Ashish; Sucosky, Philippe

2017-01-01

The bicuspid aortic valve (BAV) is a major risk factor for secondary aortopathy such as aortic dilation. The heterogeneous BAV morphotypes [left-right-coronary cusp fusion (LR), right-non-coronary cusp fusion (RN), and left-non-coronary cusp fusion (LN)] are associated with different dilation patterns, suggesting a role for hemodynamics in BAV aortopathogenesis. However, assessment of this theory is still hampered by the limited knowledge of the hemodynamic abnormalities generated by the distinct BAV morphotypes. The objective of this study was to compare experimentally the hemodynamics of a normal (i.e., non-dilated) ascending aorta (AA) subjected to tricuspid aortic valve (TAV), LR-BAV, RN-BAV, and NL-BAV flow. Tissue BAVs reconstructed from porcine TAVs were subjected to physiologic pulsatile flow conditions in a left-heart simulator featuring a realistic aortic root and compliant aorta. Phase-locked particle image velocimetry experiments were carried out to characterize the flow in the aortic root and in the tubular AA in terms of jet skewness and displacement, as well as mean velocity, viscous shear stress and Reynolds shear stress fields. While all three BAVs generated skewed and asymmetrical orifice jets (up to 1.7- and 4.0-fold increase in flow angle and displacement, respectively, relative to the TAV at the sinotubular junction), the RN-BAV jet was out of the plane of observation. The LR- and NL-BAV exhibited a 71% increase in peak-systolic orifice jet velocity relative to the TAV, suggesting an inherent degree of stenosis in BAVs. While these two BAV morphotypes subjected the convexity of the aortic wall to viscous shear stress overloads (1.7-fold increase in maximum peak-systolic viscous shear stress relative to the TAV-AA), the affected sites were morphotype-dependent (LR-BAV: proximal AA, NL-BAV: distal AA). Lastly, the LR- and NL-BAV generated high degrees of turbulence in the AA (up to 2.3-fold increase in peak-systolic Reynolds shear stress relative to the TAV) that were sustained from peak systole throughout the deceleration phase. This in vitro study reveals substantial flow abnormalities (increased jet skewness, asymmetry, jet velocity, turbulence, and shear stress overloads) in non-dilated BAV aortas, which differ from those observed in dilated aortas but still coincide with aortic wall regions prone to dilation. PMID:28203207

Resveratrol Ameliorates Microcystin-LR-Induced Testis Germ Cell Apoptosis in Rats via SIRT1 Signaling Pathway Activation.

PubMed

Liu, Haohao; Zhang, Shenshen; Liu, Chuanrui; Wu, Jinxia; Wang, Yueqin; Yuan, Le; Du, Xingde; Wang, Rui; Marwa, Phelisters Wegesa; Zhuang, Donggang; Cheng, Xuemin; Zhang, Huizhen

2018-06-09

Microcystin-leucine arginine (MC-LR), a cyclic heptapeptide produced by cyanobacteria, is a strong reproductive toxin. Studies performed in rat Sertoli cells and Chinese hamster ovary cells have demonstrated typical apoptosis after MC-LR exposure. However, little is known on how to protect against the reproductive toxicity induced by MC-LR. The present study aimed to explore the possible molecular mechanism underlying the anti-apoptosis and protective effects of resveratrol (RES) on the co-culture of Sertoli⁻germ cells and rat testes. The results demonstrated that MC-LR treatment inhibited the proliferation of Sertoli⁻germ cells and induced apoptosis. Furthermore, sirtuin 1 (SIRT1) and Bcl-2 were inhibited, while p53 and Ku70 acetylation, Bax expression, and cleaved caspase-3 were upregulated by MC-LR. However, RES pretreatment ameliorated MC-LR-induced apoptosis and SIRT1 inhibition, and downregulated the MC-LR-induced increase in p53 and Ku70 acetylation, Bax expression, and caspase-3 activation. In addition, RES reversed the MC-LR-mediated reduction in Ku70 binding to Bax. The present study indicated that the administration of RES could ameliorate MC-LR-induced Sertoli⁻germ cell apoptosis and protect against reproductive toxicity in rats by stimulating the SIRT1/p53 pathway, suppressing p53 and Ku70 acetylation and enhancing the binding of Ku70 to Bax.

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

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

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

DOE PAGES

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

2015-12-09

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

[Influences of arbuscular mycorrhizal fungus and phosphorus level on the lateral root formation of tomato seedlings].

PubMed

Jiang, Xia; Chen, Wei-li; Xu, Chun-xiang; Zhu, Hong-hui; Yao, Qing

2015-04-01

To explore the influences of arbuscular mycorrhizal fungi (AMF) and P level on plant root system architecture, tomato seedlings were inoculated with AMF strain Rhizophagus irregularis BGC JX04B under two P levels, and the influences of AMF and P level on lateral root (LR) formation of tomato seedlings were studied. Results indicated that the promoting effect of AMF on plant biomass was not evident, but significantly decreased the root to shoot ratio of plants. AMF significantly increased the primary root length but decreased the 1st order LR length and interacted with the mycorrhizal colonization period. AMF significantly lowered the 2nd-3rd order LR number and the ratio of 2nd order LR number to 1st order LR number, but did not significantly affect the 1st-2nd order LR density. High P level (50 mg x kg(-1) P) significantly promoted the plant growth and decreased the root to shoot ratio of plants. It had no significant effect on the primary root length and the 1st order root length, but significantly enhanced the 1st-3rd order LR number and the ratio of 2nd order LR number to P order LR number, increased the 1st-2nd order LR density. It suggested that AMF and P level did not share a common mechanism to influence the LR formation of tomato plants. The influence of high P level may depend on its promoting effects on nutrient uptake and plant growth, while the influence of AMF is more complex. Furthermore, the interaction between AMF and mycorrhizal colonization period implies the possible involvement of carbohydrate distribution (sugar signaling) in the regulation of root system architecture by AMF.

An Experiment in Scientific Program Understanding

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.; Owen, Karl (Technical Monitor)

2000-01-01

This paper concerns a procedure that analyzes aspects of the meaning or semantics of scientific and engineering code. This procedure involves taking a user's existing code, adding semantic declarations for some primitive variables, and parsing this annotated code using multiple, independent expert parsers. These semantic parsers encode domain knowledge and recognize formulae in different disciplines including physics, numerical methods, mathematics, and geometry. The parsers will automatically recognize and document some static, semantic concepts and help locate some program semantic errors. Results are shown for three intensively studied codes and seven blind test cases; all test cases are state of the art scientific codes. These techniques may apply to a wider range of scientific codes. If so, the techniques could reduce the time, risk, and effort required to develop and modify scientific codes.

Likelihood ratio data to report the validation of a forensic fingerprint evaluation method.

PubMed

Ramos, Daniel; Haraksim, Rudolf; Meuwly, Didier

2017-02-01

Data to which the authors refer to throughout this article are likelihood ratios (LR) computed from the comparison of 5-12 minutiae fingermarks with fingerprints. These LRs data are used for the validation of a likelihood ratio (LR) method in forensic evidence evaluation. These data present a necessary asset for conducting validation experiments when validating LR methods used in forensic evidence evaluation and set up validation reports. These data can be also used as a baseline for comparing the fingermark evidence in the same minutiae configuration as presented in (D. Meuwly, D. Ramos, R. Haraksim,) [1], although the reader should keep in mind that different feature extraction algorithms and different AFIS systems used may produce different LRs values. Moreover, these data may serve as a reproducibility exercise, in order to train the generation of validation reports of forensic methods, according to [1]. Alongside the data, a justification and motivation for the use of methods is given. These methods calculate LRs from the fingerprint/mark data and are subject to a validation procedure. The choice of using real forensic fingerprint in the validation and simulated data in the development is described and justified. Validation criteria are set for the purpose of validation of the LR methods, which are used to calculate the LR values from the data and the validation report. For privacy and data protection reasons, the original fingerprint/mark images cannot be shared. But these images do not constitute the core data for the validation, contrarily to the LRs that are shared.

Iron overload prevents oxidative damage to rat brain after chlorpromazine administration.

PubMed

Piloni, Natacha E; Caro, Andres A; Puntarulo, Susana

2018-05-15

The hypothesis tested is that Fe administration leads to a response in rat brain modulating the effects of later oxidative challenges such as chlorpromazine (CPZ) administration. Either a single dose (acute Fe overload) or 6 doses every second day (sub-chronic Fe overload) of 500 or 50 mg Fe-dextran/kg, respectively, were injected intraperitoneally (ip) to rats. A single dose of 10 mg CPZ/kg was injected ip 8 h after Fe treatment. DNA integrity was evaluated by quantitative PCR, lipid radical (LR · ) generation rate by electron paramagnetic resonance (EPR), and catalase (CAT) activity by UV spectrophotometry in isolated brains. The maximum increase in total Fe brain was detected after 6 or 2 h in the acute and sub-chronic Fe overload model, respectively. Mitochondrial and nuclear DNA integrity decreased after acute Fe overload at the time of maximal Fe content; the decrease in DNA integrity was lower after sub-chronic than after acute Fe overload. CPZ administration increased LR · generation rate in control rat brain after 1 and 2 h; however, CPZ administration after acute or sub-chronic Fe overload did not affect LR · generation rate. CPZ treatment did not affect CAT activity after 1-4 h neither in control rats nor in acute Fe-overloaded rats. However, CPZ administration to rats treated sub-chronically with Fe showed increased brain CAT activity after 2 or 4 h, as compared to control values. Fe supplementation prevented brain damage in both acute and sub-chronic models of Fe overload by selectively activating antioxidant pathways.

System Data Model (SDM) Source Code

DTIC Science & Technology

2012-08-23

CROSS_COMPILE=/opt/gumstix/build_arm_nofpu/staging_dir/bin/arm-linux-uclibcgnueabi- 8 : CC=$(CROSS_COMPILE)gcc 9: CXX=$(CROSS_COMPILE)g++ 10 : AR...and flags to pass to it 6: LEX=flex 7: LEXFLAGS=-B 8 : 9: ## The parser generator to invoke and flags to pass to it 10 : YACC=bison 11: YACCFLAGS...5: # Point to default PetaLinux root directory 6: ifndef ROOTDIR 7: ROOTDIR=$(PETALINUX)/software/petalinux-dist 8 : endif 9: 10 : PATH:=$(PATH

The relationship of leaf rust resistance gene Lr13 and hybrid necrosis gene Ne2m on wheat chromosome 2BS.

PubMed

Zhang, Peng; Hiebert, Colin W; McIntosh, Robert A; McCallum, Brent D; Thomas, Julian B; Hoxha, Sami; Singh, Davinder; Bansal, Urmil

2016-03-01

Genetic and mutational analyses of wheat leaf rust resistance gene Lr13 and hybrid necrosis gene Ne2 m indicated that they are the same gene. Hybrid necrosis in wheat characterized by chlorosis and eventual necrosis of plant tissues in certain wheat hybrids is controlled by the interaction of complementary dominant genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. Multiple alleles at each locus can be identified by differences in necrotic phenotypes when varieties are crossed with a fixed accession of the other genotype. Some of at least five Ne2 alleles were described as s (strong), m (medium) and w (weak); alleles of Ne1 were similarly described. Ne2m causes moderate necrosis in hybrids with genotypes having Ne1s. Ne2 is located on chromosome arm 2BS in close proximity to Lr13. Most wheat lines with Ne2m carry Lr13, and all wheat lines with Lr13 appear to carry Ne2m. To further dissect the relationship between Lr13 and Ne2m, more than 350 crosses were made between cv. Spica (Triticum aestivum) or Kubanka (T. durum) carrying Ne1s and recombinant inbred lines or doubled haploid lines from three crosses segregating for Lr13. F1 plants from lines carrying Lr13 crossed with Spica (Ne1s) always showed progressive necrosis; those lacking Lr13 did not. Four wheat cultivars/lines carrying Lr13 were treated with the mutagen EMS. Thirty-five susceptible mutants were identified; eight were distinctly less glaucous and late maturing indicative of chromosome 2B or sub-chromosome loss. Hybrids of phenotypically normal Lr13 mutant plants crossed with Spica did not produce symptoms of hybrid necrosis. Thus, Lr13 and one particular Ne2m allele may be the same gene.

A novel murine allele of Intraflagellar Transport Protein 172 causes a syndrome including VACTERL-like features with hydrocephalus.

PubMed

Friedland-Little, Joshua M; Hoffmann, Andrew D; Ocbina, Polloneal Jymmiel R; Peterson, Mike A; Bosman, Joshua D; Chen, Yan; Cheng, Steven Y; Anderson, Kathryn V; Moskowitz, Ivan P

2011-10-01

The primary cilium is emerging as a crucial regulator of signaling pathways central to vertebrate development and human disease. We identified atrioventricular canal 1 (avc1), a mouse mutation that caused VACTERL association with hydrocephalus, or VACTERL-H. We showed that avc1 is a hypomorphic mutation of intraflagellar transport protein 172 (Ift172), required for ciliogenesis and Hedgehog (Hh) signaling. Phenotypically, avc1 caused VACTERL-H but not abnormalities in left-right (L-R) axis formation. Avc1 resulted in structural cilia defects, including truncated cilia in vivo and in vitro. We observed a dose-dependent requirement for Ift172 in ciliogenesis using an allelic series generated with Ift172(avc1) and Ift172(wim), an Ift172 null allele: cilia were present on 42% of avc1 mouse embryonic fibroblast (MEF) and 28% of avc1/wim MEFs, in contrast to >90% of wild-type MEFs. Furthermore, quantitative cilium length analysis identified two specific cilium populations in mutant MEFS: a normal population with normal IFT and a truncated population, 50% of normal length, with disrupted IFT. Cells from wild-type embryos had predominantly full-length cilia, avc1 embryos, with Hh signaling abnormalities but not L-R abnormalities, had cilia equally divided between full-length and truncated, and avc1/wim embryos, with both Hh signaling and L-R abnormalities, were primarily truncated. Truncated Ift172 mutant cilia showed defects of the distal ciliary axoneme, including disrupted IFT88 localization and Hh-dependent Gli2 localization. We propose a model in which mutation of Ift172 results in a specific class of abnormal cilia, causing disrupted Hh signaling while maintaining L-R axis determination, and resulting in the VACTERL-H phenotype.

A conserved RxLR effector interacts with host RABA-type GTPases to inhibit vesicle-mediated secretion of antimicrobial proteins.

PubMed

Tomczynska, Iga; Stumpe, Michael; Mauch, Felix

2018-04-19

Plant pathogens of the oomycete genus Phytophthora produce virulence factors, known as RxLR effector proteins that are transferred into host cells to suppress disease resistance. Here, we analyse the function of the highly conserved RxLR24 effector of Phytophthora brassicae. RxLR24 was expressed early in the interaction with Arabidopsis plants and ectopic expression in the host enhanced leaf colonization and zoosporangia formation. Co-immunoprecipitation (Co-IP) experiments followed by mass spectrometry identified different members of the RABA GTPase family as putative RxLR24 targets. Physical interaction of RxLR24 or its homologue from the potato pathogen Phytophthora infestans with different RABA GTPases of Arabidopsis or potato, respectively, was confirmed by reciprocal Co-IP. In line with the function of RABA GTPases in vesicular secretion, RxLR24 co-localized with RABA1a to vesicles and the plasma membrane. The effect of RxLR24 on the secretory process was analysed with fusion constructs of secreted antimicrobial proteins with a pH-sensitive GFP tag. PATHOGENESIS RELATED PROTEIN 1 (PR-1) and DEFENSIN (PDF1.2) were efficiently exported in control tissue, whereas in the presence of RxLR24 they both accumulated in the endoplasmic reticulum. Together our results imply a virulence function of RxLR24 effectors as inhibitors of RABA GTPase-mediated vesicular secretion of antimicrobial PR-1, PDF1.2 and possibly other defence-related compounds. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Autologous leukocyte-reduced platelet-rich plasma therapy for Achilles tendinopathy induced by collagenase in a rabbit model

PubMed Central

González, Juan C.; López, Catalina; Álvarez, María E.; Pérez, Jorge E.; Carmona, Jorge U.

2016-01-01

Leukocyte-reduced platelet-rich plasma (LR-PRP) is a therapy for tendinopathy of the Achilles tendon (TAT); however, there is scarce information regarding LR-PRP effects in rabbit models of TAT. We compared, at 4 and 12 weeks (w), the LR-PRP and placebo (PBS) effects on ultrasonography, histology and relative gene expression of collagen types I (COL1A1) and III (COL3A1) and vascular endothelial growth factor (VEGF) in 24 rabbits with TAT induced by collagenase. The rabbits (treated with both treatments) were euthanatised after either 4 or 12 w. A healthy group (HG (n = 6)) was included. At 4 and 12 w, the LR-PRP group had a no statistically different histology score to the HG. At w 4, the COL1A1 expression was significantly higher in the LR-PRP group when compared to HG, and the expression of COL3A1from both LR-PRP and PBS-treated tendons was significantly higher when compared to the HG. At w 12, the expression of COL3A1 remained significantly higher in the PBS group in comparison to the LR-PRP group and the HG. At w 4, the LR-PRP group presented a significantly higher expression of VEGF when compared to the PBS group and the HG. In conclusion, LR-PRP treatment showed regenerative properties in rabbits with TAT. PMID:26781753

Morphosyntactic annotation of CHILDES transcripts*

PubMed Central

SAGAE, KENJI; DAVIS, ERIC; LAVIE, ALON; MACWHINNEY, BRIAN; WINTNER, SHULY

2014-01-01

Corpora of child language are essential for research in child language acquisition and psycholinguistics. Linguistic annotation of the corpora provides researchers with better means for exploring the development of grammatical constructions and their usage. We describe a project whose goal is to annotate the English section of the CHILDES database with grammatical relations in the form of labeled dependency structures. We have produced a corpus of over 18,800 utterances (approximately 65,000 words) with manually curated gold-standard grammatical relation annotations. Using this corpus, we have developed a highly accurate data-driven parser for the English CHILDES data, which we used to automatically annotate the remainder of the English section of CHILDES. We have also extended the parser to Spanish, and are currently working on supporting more languages. The parser and the manually and automatically annotated data are freely available for research purposes. PMID:20334720

Homogeneous time-resolved fluoroimmunoassay of microcystin-LR using layered WS2 nanosheets as a transducer

NASA Astrophysics Data System (ADS)

Qin, Xiaodan; Wang, Yuanxiu; Song, Bo; Wang, Xin; Ma, Hua; Yuan, Jingli

2017-06-01

A homogeneous time-resolved fluoroimmunoassay method for rapid and sensitive detection of microcystin-LR (MC-LR) in water samples was developed based on the interaction between water-soluble WS2 nanosheets and the conjugate of MC-LR with a luminescent Eu3+ complex BHHBCB-Eu3+ (BHHBCB: 1,2-bis[4‧-(1″,1″,1″,2″,2″,3″,3″-heptafluoro-4″,6″-hexanedion-6″-yl)- benzyl]-4-chlorosulfobenzene). The large lateral dimensions and high surface areas of two-dimensional layered WS2 nanosheets enable easy adsorption of the MC-LR-BHHBCB-Eu3+ conjugate, that lead to efficient quenching of the luminescence of Eu3+ complex via energy transfer or electron transfer process. However, the addition of monoclonal anti-MC-LR antibody can induce the formation of MC-LR-BHHBCB-Eu3+/antibody immune complex, which prevents the interaction between WS2 nanosheets and MC-LR-BHHBCB-Eu3+ to result in the restoration of Eu3+ luminescence. This signal transduction mechanism made it possible for analysis of the target MC-LR in a homogeneous system. The present method has advantages of rapidity and simplicity since the B/F (bound reagent/free reagent) separation steps, the solid-phase carrier and antibody labeling or modification process are not necessary. The proposed immunosensing system displayed a wide linear range, good precision and accuracy, and comparable sensitivity with a detection limit of 0.3 μg l-1, which satisfied the World Health Organization (WHO) provisional guideline limit of 1.0 μg l-1 for MC-LR in drinking water.

Anti-LRP/LR Specific Antibody IgG1-iS18 Impedes Adhesion and Invasion of Liver Cancer Cells

PubMed Central

Chetty, Carryn; Khumalo, Thandokuhle; Da Costa Dias, Bianca; Reusch, Uwe; Knackmuss, Stefan; Little, Melvyn; Weiss, Stefan F. T.

2014-01-01

Two key events, namely adhesion and invasion, are pivotal to the occurrence of metastasis. Importantly, the 37 kDa/67 kDa laminin receptor (LRP/LR) has been implicated in enhancing these two events thus facilitating cancer progression. In the current study, the role of LRP/LR in the adhesion and invasion of liver cancer (HUH-7) and leukaemia (K562) cells was investigated. Flow cytometry revealed that the HUH-7 cells displayed significantly higher cell surface LRP/LR levels compared to the poorly-invasive breast cancer (MCF-7) control cells, whilst the K562 cells displayed significantly lower cell surface LRP/LR levels in comparison to the MCF-7 control cells. However, Western blotting and densitometric analysis revealed that all three tumorigenic cell lines did not differ significantly with regards to total LRP/LR levels. Furthermore, treatment of liver cancer cells with anti-LRP/LR specific antibody IgG1-iS18 (0.2 mg/ml) significantly reduced the adhesive potential of cells to laminin-1 and the invasive potential of cells through the ECM-like Matrigel, whilst leukaemia cells showed no significant differences in both instances. Additionally, Pearson's correlation coefficients suggested direct proportionality between cell surface LRP/LR levels and the adhesive and invasive potential of liver cancer and leukaemia cells. These findings suggest the potential use of anti-LRP/LR specific antibody IgG1-iS18 as an alternative therapeutic tool for metastatic liver cancer through impediment of the LRP/LR- laminin-1 interaction. PMID:24798101

Spatial Modeling and Uncertainty Assessment of Fine Scale Surface Processes Based on Coarse Terrain Elevation Data

NASA Astrophysics Data System (ADS)

Rasera, L. G.; Mariethoz, G.; Lane, S. N.

2017-12-01

Frequent acquisition of high-resolution digital elevation models (HR-DEMs) over large areas is expensive and difficult. Satellite-derived low-resolution digital elevation models (LR-DEMs) provide extensive coverage of Earth's surface but at coarser spatial and temporal resolutions. Although useful for large scale problems, LR-DEMs are not suitable for modeling hydrologic and geomorphic processes at scales smaller than their spatial resolution. In this work, we present a multiple-point geostatistical approach for downscaling a target LR-DEM based on available high-resolution training data and recurrent high-resolution remote sensing images. The method aims at generating several equiprobable HR-DEMs conditioned to a given target LR-DEM by borrowing small scale topographic patterns from an analogue containing data at both coarse and fine scales. An application of the methodology is demonstrated by using an ensemble of simulated HR-DEMs as input to a flow-routing algorithm. The proposed framework enables a probabilistic assessment of the spatial structures generated by natural phenomena operating at scales finer than the available terrain elevation measurements. A case study in the Swiss Alps is provided to illustrate the methodology.

Wh-filler-gap dependency formation guides reflexive antecedent search

PubMed Central

Frazier, Michael; Ackerman, Lauren; Baumann, Peter; Potter, David; Yoshida, Masaya

2015-01-01

Prior studies on online sentence processing have shown that the parser can resolve non-local dependencies rapidly and accurately. This study investigates the interaction between the processing of two such non-local dependencies: wh-filler-gap dependencies (WhFGD) and reflexive-antecedent dependencies. We show that reflexive-antecedent dependency resolution is sensitive to the presence of a WhFGD, and argue that the filler-gap dependency established by WhFGD resolution is selected online as the antecedent of a reflexive dependency. We investigate the processing of constructions like (1), where two NPs might be possible antecedents for the reflexive, namely which cowgirl and Mary. Even though Mary is linearly closer to the reflexive, the only grammatically licit antecedent for the reflexive is the more distant wh-NP, which cowgirl. (1). Which cowgirl did Mary expect to have injured herself due to negligence? Four eye-tracking text-reading experiments were conducted on examples like (1), differing in whether the embedded clause was non-finite (1 and 3) or finite (2 and 4), and in whether the tail of the wh-dependency intervened between the reflexive and its closest overt antecedent (1 and 2) or the wh-dependency was associated with a position earlier in the sentence (3 and 4). The results of Experiments 1 and 2 indicate the parser accesses the result of WhFGD formation during reflexive antecedent search. The resolution of a wh-dependency alters the representation that reflexive antecedent search operates over, allowing the grammatical but linearly distant antecedent to be accessed rapidly. In the absence of a long-distance WhFGD (Experiments 3 and 4), wh-NPs were not found to impact reading times of the reflexive, indicating that the parser's ability to select distant wh-NPs as reflexive antecedents crucially involves syntactic structure. PMID:26500579

The follicular hormonal profile in low-responder patients undergoing unstimulated cycles: Is it hypoandrogenic?

PubMed

de los Santos, M J; García-Laez, V; Beltrán, D; Labarta, E; Zuzuarregui, Jose Luis; Alamá, P; Gámiz, P; Crespo, J; Bosch, E; Pellicer, A

2013-01-01

What is the final hormonal milieu of pre-ovulatory follicles of low-responder (LR) patients undergoing unstimulated cycles? Neither androgen secretion nor LH was impaired in pre-ovulatory follicles of LR women. Therapies currently used to improve ovarian response in LR women have an impact on the final hormonal follicular milieu, and these changes are believed to be partially responsible for determining the success rate in these women. Surprisingly, as far as we know, there is no report of the final hormonal profile of LR women undergoing unstimulated cycles or evidence that follicular androgen secretion in LR women is impaired. A prospective case-control study including 94 women, 36 normal controls and 58 LR patients (19 Young ≤ 35 years LR and 39 Aged >35 years LR) from 2009 to 2011. Fifty-eight LR women were divided into two groups: Young LR (age ≤ 35; n = 19) and Aged LR (ALR; age >35; n = 39). The control group (group C) comprised 36 egg donors undergoing an unstimulated cycle in our IVF unit. Serum and follicular fluid hormonal concentrations for estradiol (E₂), progesterone, testosterone and androstendione were measured. The spindle parameters of metaphase II oocytes generated from these groups were also analysed. Pre-ovulatory follicles from LR patients had similar androgenic and LH concentrations to those observed in the control group. However, higher intrafollicular concentrations of FSH and progesterone were observed in ALR. Moreover, no differences were found for the spindle evaluation of oocytes between groups by the Oosight technology. The controls were younger and had a lower BMI than the LR women. The sample size available restricted statistical power. This study suggests that the problem with LR women is not the final pre-ovulatory follicular androgen concentration since this is similar to normal responders, but in the ability to respond to controlled ovarian stimulation protocols. Therefore, efforts should be focused on long-interval androgen priming to potentially increase the recruitment of small antral follicles rather than increasing the intraovarian androgen levels within the current cycle. The present project has been supported by the R+D programme from the Generalitat Valenciana (Regional Valencian Government) IMPIVA MIDTF/2010/95. The authors have no conflict of interest to declare.

DNA damage inhibits lateral root formation by up-regulating cytokinin biosynthesis genes in Arabidopsis thaliana.

PubMed

Davis, La Ode Muhammad Muchdar; Ogita, Nobuo; Inagaki, Soichi; Takahashi, Naoki; Umeda, Masaaki

2016-11-01

Lateral roots (LRs) are an important organ for water and nutrient uptake from soil. Thus, control of LR formation is crucial in the adaptation of plant growth to environmental conditions. However, the underlying mechanism controlling LR formation in response to external factors has remained largely unknown. Here, we found that LR formation was inhibited by DNA damage. Treatment with zeocin, which causes DNA double-strand breaks, up-regulated several DNA repair genes in the LR primordium (LRP) through the signaling pathway mediated by the transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1). Cell division was severely inhibited in the LRP of zeocin-treated sog1-1 mutant, which in turn inhibited LR formation. This result suggests that SOG1-mediated maintenance of genome integrity is crucial for proper cell division during LRP development. Furthermore, zeocin induced several cytokinin biosynthesis genes in a SOG1-dependent manner, thereby activating cytokinin signaling in the LRP. LR formation was less inhibited by zeocin in mutants defective in cytokinin biosynthesis or signaling, suggesting that elevated cytokinin signaling is crucial for the inhibition of LR formation in response to DNA damage. We conclude that SOG1 regulates DNA repair and cytokinin signaling separately and plays a key role in controlling LR formation under genotoxic stress. © 2016 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Differentiation between Wegener's granulomatosis and microscopic polyangiitis by an artificial neural network and by traditional methods.

PubMed

Linder, Roland; Orth, Isabelle; Hagen, E Christian; van der Woude, Fokko J; Schmitt, Wilhelm H

2011-06-01

To investigate the operating characteristics of the American College of Rheumatology (ACR) traditional format criteria for Wegener's granulomatosis (WG), the Sørensen criteria for WG and microscopic polyangiitis (MPA), and the Chapel Hill nomenclature for WG and MPA. Further, to develop and validate improved criteria for distinguishing WG from MPA by an artificial neural network (ANN) and by traditional approaches [classification tree (CT), logistic regression (LR)]. All criteria were applied to 240 patients with WG and 78 patients with MPA recruited by a multicenter study. To generate new classification criteria (ANN, CT, LR), 23 clinical measurements were assessed. Validation was performed by applying the same approaches to an independent monocenter cohort of 46 patients with WG and 21 patients with MPA. A total of 70.8% of the patients with WG and 7.7% of the patients with MPA from the multicenter cohort fulfilled the ACR criteria for WG (accuracy 76.1%). The accuracy of the Chapel Hill criteria for WG and MPA was only 35.0% and 55.3% (Sørensen criteria: 67.2% and 92.4%). In contrast, the ANN and CT achieved an accuracy of 94.3%, based on 4 measurements (involvement of nose, sinus, ear, and pulmonary nodules), all associated with WG. LR led to an accuracy of 92.8%. Inclusion of antineutrophil cytoplasmic antibodies did not improve the allocation. Validation of methods resulted in accuracy of 91.0% (ANN and CT) and 88.1% (LR). The ACR, Sørensen, and Chapel Hill criteria did not reliably separate WG from MPA. In contrast, an appropriately trained ANN and a CT differentiated between these disorders and performed better than LR.

DBPQL: A view-oriented query language for the Intel Data Base Processor

NASA Technical Reports Server (NTRS)

Fishwick, P. A.

1983-01-01

An interactive query language (BDPQL) for the Intel Data Base Processor (DBP) is defined. DBPQL includes a parser generator package which permits the analyst to easily create and manipulate the query statement syntax and semantics. The prototype language, DBPQL, includes trace and performance commands to aid the analyst when implementing new commands and analyzing the execution characteristics of the DBP. The DBPQL grammar file and associated key procedures are included as an appendix to this report.

LR-90 prevents methylglyoxal-induced oxidative stress and apoptosis in human endothelial cells

PubMed Central

Figarola, James L.; Singhal, Jyotsana; Rahbar, Samuel; Awasthi, Sanjay

2014-01-01

Methylglyoxal (MGO) is a highly reactive dicarbonyl compound known to induce cellular injury and cytoxicity, including apoptosis in vascular cells. Vascular endothelial cell apoptosis has been implicated in the pathophysiology and progression of atherosclerosis. We investigated whether the advanced glycation end-product inhibitor LR-90 could prevent MGO-induced apoptosis in human umbilical vascular endothelial cells (HUVECs). HUVECs were pre-treated with LR-90 and then stimulated with MGO. Cell morphology, cytotoxicity and apoptosis were evaluated by light microscopy, MTT assay, and Annexin V-FITC and propidium iodide double staining, respectively. Levels of Bax, Bcl-2, cytochrome c, mitogen-activated protein kinases (MAPKs) and caspase activities were assessed by Western blotting. Reactive oxygen species (ROS) generation and mitochondrial membrane potential (MMP) were measured with fluorescent probes. LR-90 dose-dependently prevented MGO-associated HUVEC cytotoxicity and apoptotic biochemical changes such as loss of MMP, increased Bax/Bcl-2 protein ratio, mitochondrial cytochrome c release and activation of caspase-3 and 9. Additionally, LR-90 blocked intracellular ROS formation and MAPK (p44/p42, p38, JNK) activation, though the latter seem to be not directly involved in MGO-induced HUVEC apoptosis. LR-90 prevents MGO-induced HUVEC apoptosis by inhibiting ROS and associated mitochondrial-dependent apoptotic signaling cascades, suggesting that LR-90 possess cytoprotective ability which could be beneficial in prevention of diabetic related-atherosclerosis. PMID:24615331

An Improved Tarpit for Network Deception

DTIC Science & Technology

2016-03-25

World” program was, to one who is ready to join the cyber security workforce. Thirdly, I thank my mom and dad for their constant love , support, and...arrow in a part-whole relationship . In the diagram GreaseMonkey contains the three packet handler classes. The numbers next to the PriorityQueue and...arrow from Greasy to the config_parser module represents a usage relationship , where Greasy uses functions from config_parser to parse the configuration

Extracting BI-RADS Features from Portuguese Clinical Texts.

PubMed

Nassif, Houssam; Cunha, Filipe; Moreira, Inês C; Cruz-Correia, Ricardo; Sousa, Eliana; Page, David; Burnside, Elizabeth; Dutra, Inês

2012-01-01

In this work we build the first BI-RADS parser for Portuguese free texts, modeled after existing approaches to extract BI-RADS features from English medical records. Our concept finder uses a semantic grammar based on the BIRADS lexicon and on iterative transferred expert knowledge. We compare the performance of our algorithm to manual annotation by a specialist in mammography. Our results show that our parser's performance is comparable to the manual method.

A Semantic Analysis Method for Scientific and Engineering Code

NASA Technical Reports Server (NTRS)

Stewart, Mark E. M.

1998-01-01

This paper develops a procedure to statically analyze aspects of the meaning or semantics of scientific and engineering code. The analysis involves adding semantic declarations to a user's code and parsing this semantic knowledge with the original code using multiple expert parsers. These semantic parsers are designed to recognize formulae in different disciplines including physical and mathematical formulae and geometrical position in a numerical scheme. In practice, a user would submit code with semantic declarations of primitive variables to the analysis procedure, and its semantic parsers would automatically recognize and document some static, semantic concepts and locate some program semantic errors. A prototype implementation of this analysis procedure is demonstrated. Further, the relationship between the fundamental algebraic manipulations of equations and the parsing of expressions is explained. This ability to locate some semantic errors and document semantic concepts in scientific and engineering code should reduce the time, risk, and effort of developing and using these codes.

Myosin1D is an evolutionarily conserved regulator of animal left-right asymmetry.

PubMed

Juan, Thomas; Géminard, Charles; Coutelis, Jean-Baptiste; Cerezo, Delphine; Polès, Sophie; Noselli, Stéphane; Fürthauer, Maximilian

2018-05-16

The establishment of left-right (LR) asymmetry is fundamental to animal development, but the identification of a unifying mechanism establishing laterality across different phyla has remained elusive. A cilia-driven, directional fluid flow is important for symmetry breaking in numerous vertebrates, including zebrafish. Alternatively, LR asymmetry can be established independently of cilia, notably through the intrinsic chirality of the acto-myosin cytoskeleton. Here, we show that Myosin1D (Myo1D), a previously identified regulator of Drosophila LR asymmetry, is essential for the formation and function of the zebrafish LR organizer (LRO), Kupffer's vesicle (KV). Myo1D controls the orientation of LRO cilia and interacts functionally with the planar cell polarity (PCP) pathway component VanGogh-like2 (Vangl2), to shape a productive LRO flow. Our findings identify Myo1D as an evolutionarily conserved regulator of animal LR asymmetry, and show that functional interactions between Myo1D and PCP are central to the establishment of animal LR asymmetry.

Applications of Parsing Theory to Computer-Assisted Instruction.

ERIC Educational Resources Information Center

Markosian, Lawrence Z.; Ager, Tryg A.

1983-01-01

Applications of an LR-1 parsing algorithm to intelligent programs for computer assisted instruction in symbolic logic and foreign languages are discussed. The system has been adequately used for diverse instructional applications, including analysis of student input, generation of pattern drills, and modeling the student's understanding of the…

Measurement of locally resonant band gaps in a surface phononic crystal with inverted conical pillars

NASA Astrophysics Data System (ADS)

Hsu, Jin-Chen; Lin, Fan-Shun

2018-07-01

In this paper, we numerically and experimentally study locally resonant (LR) band gaps for surface acoustic waves (SAWs) in a honeycomb array of inverted conical pillars grown on the surface of a 128°YX lithium-niobate substrate. We show that the inverted conical pillars can be used to generate lower LR band gaps below the sound cone. This lowering effect is caused by the increase in the effective pillar mass without increasing the effective stiffness. We employ the finite-element method to calculate the LR band gaps and wideband slanted-finger interdigital transducers to measure the transmission of SAWs. Numerical results show that SAWs are prohibited from propagating through the structure in the lowered LR band gaps. Obvious LR band-gap lowering is observed in the experimental result of a surface phononic crystal with a honeycomb array of inverted conical pillars. The results enable enhanced control over the phononic metamaterial and surface structures, which may have applications in low-frequency waveguiding, acoustic isolation, acoustic absorbers, and acoustic filters.

Adsorption of microcystin-LR on mesoporous carbons and its potential use in drinking water source.

PubMed

Park, Jeong-Ann; Jung, Sung-Mok; Yi, In-Geol; Choi, Jae-Woo; Kim, Song-Bae; Lee, Sang-Hyup

2017-06-01

Microcystin-LR (MC-LR) is a common toxin derived from cyanobacterial blooms an effective, rapid and non-toxic method needs to be developed for its removal from drinking water treatment plants (DWTP). For an adsorption-based method, mesoporous carbon can be a promising supplemental adsorbent. The effect of mesoporous carbon (MC1, MC2, and MC3) properties and water quality parameters on the adsorption of MC-LR were investigated and the results were analyzed by kinetic, isotherm, thermodynamic, Derjaguin-Landau-Verwey-Overbeek (DLVO), and intraparticle diffusion models. MC1 was the most appropriate type for the removal of MC-LR with a maximum adsorption capacity of 35,670.49 μg/g. Adsorption of MC-LR is a spontaneous reaction dominated by van der Waals interactions. Pore sizes of 8.5-14 nm enhance the pore diffusion of MC-LR from the surface to the mesopores of MC1. The adsorption capacity was not sensitive to changes in the pH (3.2-8.0) and the existence of organic matter (2-5 mg/L). Furthermore, the final concentration of MC-LR was below the WHO guideline level after a 10-min reaction with 20 mg/L of MC1 in the Nak-Dong River, a drinking water source. The MC-LR adsorption mainly competed with humic substances (500-1000 g/mole); however, they did not have a great effect on adsorption. Copyright © 2017. Published by Elsevier Ltd.

In vitro translocation experiments with RxLR-reporter fusion proteins of Avr1b from Phytophthora sojae and AVR3a from Phytophthora infestans fail to demonstrate specific autonomous uptake in plant and animal cells.

PubMed

Wawra, Stephan; Djamei, Armin; Albert, Isabell; Nürnberger, Thorsten; Kahmann, Regine; van West, Pieter

2013-05-01

Plant-pathogenic oomycetes have a large set of secreted effectors that can be translocated into their host cells during infection. One group of these effectors are the RxLR effectors for which it has been shown, in a few cases, that the RxLR motif is important for their translocation. It has been suggested that the RxLR-leader sequences alone are enough to translocate the respective effectors into eukaryotic cells through binding to surface-exposed phosphoinositol-3-phosphate. These conclusions were primary based on translocation experiments conducted with recombinant fusion proteins whereby the RxLR leader of RxLR effectors (i.e., Avr1b from Phytophthora sojae) were fused to the green fluorescent protein reporter-protein. However, we failed to observe specific cellular uptake for a comparable fusion protein where the RxLR leader of the P. infestans AVR3a was fused to monomeric red fluorescent protein. Therefore, we reexamined the ability of the reported P. sojae AVR1b RxLR leader to enter eukaryotic cells. Different relevant experiments were performed in three independent laboratories, using fluorescent reporter fusion constructs of AVR3a and Avr1b proteins in a side-by-side comparative study on plant tissue and human and animal cells. We report that we were unable to obtain conclusive evidence for specific RxLR-mediated translocation.

Policy-Based Management Natural Language Parser

NASA Technical Reports Server (NTRS)

James, Mark

2009-01-01

The Policy-Based Management Natural Language Parser (PBEM) is a rules-based approach to enterprise management that can be used to automate certain management tasks. This parser simplifies the management of a given endeavor by establishing policies to deal with situations that are likely to occur. Policies are operating rules that can be referred to as a means of maintaining order, security, consistency, or other ways of successfully furthering a goal or mission. PBEM provides a way of managing configuration of network elements, applications, and processes via a set of high-level rules or business policies rather than managing individual elements, thus switching the control to a higher level. This software allows unique management rules (or commands) to be specified and applied to a cross-section of the Global Information Grid (GIG). This software embodies a parser that is capable of recognizing and understanding conversational English. Because all possible dialect variants cannot be anticipated, a unique capability was developed that parses passed on conversation intent rather than the exact way the words are used. This software can increase productivity by enabling a user to converse with the system in conversational English to define network policies. PBEM can be used in both manned and unmanned science-gathering programs. Because policy statements can be domain-independent, this software can be applied equally to a wide variety of applications.

Bioaccumulation and harmful effects of microcystin-LR in the aquatic plants Lemna minor and Wolffia arrhiza and the filamentous alga Chladophora fracta.

PubMed

Mitrovic, Simon M; Allis, Orla; Furey, Ambrose; James, Kevin J

2005-07-01

Although the toxic effects of cyanotoxins on animals have been examined extensively, little research has focused on their effects on higher plants and macroalgae, and the potential for bioaccumulation in the food web through plants. Two aquatic plants, Lemna minor and Wolffia arrhiza, and one filamentous alga, Chladophora fracta, were exposed to the cyanotoxin microcystin-LR. Growth of L. minor (as weight and frond number) and root length were significantly reduced and peroxidase activity was significantly increased after 5 days of exposure to concentrations of 10 and 20 microg mL(-1) microcystin-LR. Growth of W. arrhiza (as frond number) was significantly reduced after 5 days of exposure to 15 microg mL(-1) microcystin-LR. Growth and peroxidase activity of C. fracta were not affected by microcystin-LR at concentrations up to 10 microg mL(-1). L. minor also accumulated microcystin-LR up to a concentration of 0.288 +/- 0.009 ng mg(-1) wet wt. plant material over the 5 days of the experiment, equivalent to an accumulation rate of 0.058 ng mg(-1) day(-1). C. fracta accumulated a microcystin-LR concentration of 0.042 +/- 0.015 ng mg(-1) wet wt. plant material over the 5 days of the experiment, equivalent to an accumulation rate of 0.008 ng mg(-1) day(-1).

Semi-automated ontology generation and evolution

NASA Astrophysics Data System (ADS)

Stirtzinger, Anthony P.; Anken, Craig S.

2009-05-01

Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural components referenced above and identify a potential technology transition path to Scott AFB's Tanker Airlift Control Center (TACC) which serves as the Air Operations Center (AOC) for the Air Mobility Command (AMC).

INITIATE: An Intelligent Adaptive Alert Environment.

PubMed

Jafarpour, Borna; Abidi, Samina Raza; Ahmad, Ahmad Marwan; Abidi, Syed Sibte Raza

2015-01-01

Exposure to a large volume of alerts generated by medical Alert Generating Systems (AGS) such as drug-drug interaction softwares or clinical decision support systems over-whelms users and causes alert fatigue in them. Some of alert fatigue effects are ignoring crucial alerts and longer response times. A common approach to avoid alert fatigue is to devise mechanisms in AGS to stop them from generating alerts that are deemed irrelevant. In this paper, we present a novel framework called INITIATE: an INtellIgent adapTIve AlerT Environment to avoid alert fatigue by managing alerts generated by one or more AGS. We have identified and categories the lifecycle of different alerts and have developed alert management logic as per the alerts' lifecycle. Our framework incorporates an ontology that represents the alert management strategy and an alert management engine that executes this strategy. Our alert management framework offers the following features: (1) Adaptability based on users' feedback; (2) Personalization and aggregation of messages; and (3) Connection to Electronic Medical Records by implementing a HL7 Clinical Document Architecture parser.

Rearfoot and midfoot or forefoot impacts in habitually shod runners.

PubMed

Boyer, Elizabeth R; Rooney, Brandon D; Derrick, Timothy R

2014-07-01

Shear loading rates (LR) have not been investigated in runners with a mid- or forefoot strike (FFS) versus rearfoot strike (RFS). The purpose of this study was to compare three-dimensional ground reaction forces (GRF) and LR during impact in habitual rearfoot strikers (hRF) and habitual forefoot strikers (hFF) strikers. Thirty competitive runners performed 10 overground running trials with both foot strike styles. Peak three-dimensional and resultant GRF and instantaneous LR during impact were compared. Vertical LR significantly decreased for hRF using an FFS (RFS = 148 ± 36 body weight [BW]·s(-1), FFS = 98 ± 31 BW·s(-1)) but was similar for hFF running with either foot strike (FFS = 136 ± 35 BW·s(-1), RFS = 135 ± 28 BW·s(-1)). Posterior impact forces were present during FFS but not during RFS, and posterior LR was significantly greater for both groups during FFS (-58 ± 17 vs -19 ± 6 BW·s(-1)). Medial impact forces were also present during FFS but not during RFS, and medial LR was significantly larger for both groups during FFS (-21 ± 7 vs -6 ± 6 BW·s(-1)). Interestingly, hFF had greater impact peaks and LR in all directions compared with hRF during FFS. This may be explained by hFF using a smaller strike index (hFF = 62% ± 9%, hRF = 67% ± 9%; P = 0.02), which was significantly inversely related to vertical LR and impact peak. Peak resultant and vertical LR are not ubiquitously lower when using a shod FFS versus RFS despite an absence of resultant and vertical impact peaks. Furthermore, there were impact peaks in the posterior and medial directions, leading also to greater LR in these directions during FFS. Therefore, transitioning from RFS to FFS in traditional running shoes may not offer long-term protection against impact-related running injuries because hFF running with an FFS demonstrated many GRF and LR similar to or greater than RFS.

Integration of nodal and BMP signals in the heart requires FoxH1 to create left-right differences in cell migration rates that direct cardiac asymmetry.

PubMed

Lenhart, Kari F; Holtzman, Nathalia G; Williams, Jessica R; Burdine, Rebecca D

2013-01-01

Failure to properly establish the left-right (L/R) axis is a major cause of congenital heart defects in humans, but how L/R patterning of the embryo leads to asymmetric cardiac morphogenesis is still unclear. We find that asymmetric Nodal signaling on the left and Bmp signaling act in parallel to establish zebrafish cardiac laterality by modulating cell migration velocities across the L/R axis. Moreover, we demonstrate that Nodal plays the crucial role in generating asymmetry in the heart and that Bmp signaling via Bmp4 is dispensable in the presence of asymmetric Nodal signaling. In addition, we identify a previously unappreciated role for the Nodal-transcription factor FoxH1 in mediating cell responsiveness to Bmp, further linking the control of these two pathways in the heart. The interplay between these TGFβ pathways is complex, with Nodal signaling potentially acting to limit the response to Bmp pathway activation and the dosage of Bmp signals being critical to limit migration rates. These findings have implications for understanding the complex genetic interactions that lead to congenital heart disease in humans.

Clinical and laboratory assessment of dehydration severity in children with acute gastroenteritis.

PubMed

Parkin, Patricia C; Macarthur, Colin; Khambalia, Amina; Goldman, Ran D; Friedman, Jeremy N

2010-03-01

To evaluate clinical and laboratory assessment of dehydration severity in children, 1 to 36 months, with acute gastroenteritis. Clinical and laboratory measures and weight change following rehydration were collected for enrolled children. Pediatric emergency department. Likelihood ratio (LR+) and 95% confidence interval (CI): for a clinical score of 0, the LR+ was 2.2 (95% CI = 0.9-5.3); for a clinical score of 1 to 4, the LR+ was 1.3 (95% CI = 0.90-1.74); for a clinical score of 5 to 8, the LR+ was 5.2 (95% CI = 2.2-12.8); for a venous pH <7.32, the LR+ was 7.2 (95% CI = 2.4-21.9); and for serum bicarbonate <18 mmol/L, the LR+ was 11.6 (95% CI = 3.5-38.0). Clinicians may find it useful to incorporate the Clinical Dehydration Scale and laboratory measures into clinical decision-making algorithms to assess dehydration severity in children with acute gastroenteritis.

Prospective evaluation of the ability of clinical scoring systems and physician-determined likelihood of appendicitis to obviate the need for CT.

PubMed

Golden, Sean K; Harringa, John B; Pickhardt, Perry J; Ebinger, Alexander; Svenson, James E; Zhao, Ying-Qi; Li, Zhanhai; Westergaard, Ryan P; Ehlenbach, William J; Repplinger, Michael D

2016-07-01

To determine whether clinical scoring systems or physician gestalt can obviate the need for computed tomography (CT) in patients with possible appendicitis. Prospective, observational study of patients with abdominal pain at an academic emergency department (ED) from February 2012 to February 2014. Patients over 11 years old who had a CT ordered for possible appendicitis were eligible. All parameters needed to calculate the scores were recorded on standardised forms prior to CT. Physicians also estimated the likelihood of appendicitis. Test characteristics were calculated using clinical follow-up as the reference standard. Receiver operating characteristic curves were drawn. Of the 287 patients (mean age (range), 31 (12-88) years; 60% women), the prevalence of appendicitis was 33%. The Alvarado score had a positive likelihood ratio (LR(+)) (95% CI) of 2.2 (1.7 to 3) and a negative likelihood ratio (LR(-)) of 0.6 (0.4 to 0.7). The modified Alvarado score (MAS) had LR(+) 2.4 (1.6 to 3.4) and LR(-) 0.7 (0.6 to 0.8). The Raja Isteri Pengiran Anak Saleha Appendicitis (RIPASA) score had LR(+) 1.3 (1.1 to 1.5) and LR(-) 0.5 (0.4 to 0.8). Physician-determined likelihood of appendicitis had LR(+) 1.3 (1.2 to 1.5) and LR(-) 0.3 (0.2 to 0.6). When combined with physician likelihoods, LR(+) and LR(-) was 3.67 and 0.48 (Alvarado), 2.33 and 0.45 (RIPASA), and 3.87 and 0.47 (MAS). The area under the curve was highest for physician-determined likelihood (0.72), but was not statistically significantly different from the clinical scores (RIPASA 0.67, Alvarado 0.72, MAS 0.7). Clinical scoring systems performed equally well as physician gestalt in predicting appendicitis. These scores do not obviate the need for imaging for possible appendicitis when a physician deems it necessary. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Corona Enhancement and Mosaic Architecture for Prognosis and Selection Between of Liver Resection Versus Transcatheter Arterial Chemoembolization in Single Hepatocellular Carcinomas >5 cm Without Extrahepatic Metastases: An Imaging-Based Retrospective Study.

PubMed

Li, Meng; Xin, Yongjie; Fu, Sirui; Liu, Zaiyi; Li, Yong; Hu, Baoshan; Chen, Shuting; Liang, Changhong; Lu, Ligong

2016-01-01

Corona enhancement and mosaic architecture are 2 radiologic features of hepatocellular carcinoma (HCC). However, neither their prognostic values nor their impacts on the selection of liver resection (LR) versus transcatheter arterial chemoembolization (TACE) as treatment modalities have been established.We retrospectively analyzed 275 patients with a single HCC lesion >5 cm without extrahepatic metastasis treated with LR or TACE. In LR patients, the overall survival (OS) and time to progression (TTP) were compared between corona enhancement negative (corona-) versus positive (corona+) and mosaic architecture negative (mosaic-) versus positive (mosaic+) patients. Furthermore, by the combination of corona and mosaic, LR patients were divided into negative for both corona and mosaic patterns (LR-/-), positive for only 1 feature (LR+/-), and positive for both (LR+/+); their OS and TTP were compared to those of the TACE group. Cox regression was performed to identify independent factors for OS.In the survival plots for LR, corona- had better OS and TTP than corona+, and mosaic- had better OS than mosaic+. There was no significant difference in TTP between the subgroups. On Cox regression analysis, corona enhancement, but not mosaic architecture, was a significant factor for OS, whereas neither were a significant factor for TTP. In TACE patients, neither corona nor mosaic patterns had significant correlations with OS or TTP. In the whole population, LR-/ and LR+/- subgroups had similar OS, which was better than the LR+/+ and TACE groups. Moreover, LR-/- and LR+/- patients had better TTP than TACE patients, but there were no differences between the LR-/- versus LR+/-, LR-/ versus LR+/+, LR+/- versus LR+/+, and LR+/+ versus TACE groups. On Cox regression analysis, the presence of corona/mosaic patterns was an independent prognostic factor for OS.Our results showed that, for patients with a single HCC >5 cm without extrahepatic metastasis, corona and mosaic patterns are indicators of limited LR efficacy. When both of the features are present, TACE can be used instead of LR with no negative influence on survival.

Adding a Medical Lexicon to an English Parser

PubMed Central

Szolovits, Peter

2003-01-01

We present a heuristic method to map lexical (syntactic) information from one lexicon to another, and apply the technique to augment the lexicon of the Link Grammar Parser with an enormous medical vocabulary drawn from the Specialist lexicon developed by the National Library of Medicine. This paper presents and justifies the mapping method and addresses technical problems that have to be overcome. It illustrates the utility of the method with respect to a large corpus of emergency department notes. PMID:14728251

Interactive effects of microcystin and ammonia on the reproductive performance and phenotypic traits of the rotifer Brachionus calyciflorus.

PubMed

Liang, Ye; Lu, Xuxin; Min, Yuanqi; Liu, Lulu; Yang, Jiaxin

2018-01-01

Elevated microcystin-LR (MC-LR) and ammonia (NH 3 -N) concentrations co-occur during the degradation of Microcystis blooms, and are toxic to aquatic organisms. The freshwater rotifer, Brachionus calyciflorus, was exposed to mixtures of MC-LR (0, 10, 30, and 100µgL -1 ) and NH 3 -N (0, 270, and 540µgL -1 ) to assess the combined effects of the two toxicants on reproductive performance and phenotype traits. Single solutions of MC-LR (100µgL -1 ) and NH 3 -N (540µgL -1 ) had negative effects on rotifer reproductive timing and fecundity. Pre- and post-reproductive periods fluctuated with MC-LR and NH 3 -N concentrations, while reproductive period and total offspring per female were reduced in mixtures of MC-LR and NH 3 -N (p < 0.05). Grazing rate of rotifers decreased with grazing time and concentrations of the two toxicants (p < 0.001). MC-LR in combination with NH 3 -N had negative effects on swimming speed and body length but positively stimulated posterolateral spine development (p < 0.001). MC-LR and NH 3 -N had synergetic interactive effects on pre-reproductive period, reproductive period, total offspring per female, grazing rate, swimming speed, and body length (p < 0.05). In contrast, these effects were antagonistic on post-reproductive period and posterolateral spine length (p > 0.05). These results indicate that MC-LR and NH 3 -N act synergistically and antagonistically in causing toxicity to B. calyciflorus regarding reproductive performance and the formation of defensive phenotypes. Copyright © 2017 Elsevier Inc. All rights reserved.

Increasing platelet concentrations in leukocyte-reduced platelet-rich plasma decrease collagen gene synthesis in tendons.

PubMed

Boswell, Stacie G; Schnabel, Lauren V; Mohammed, Hussni O; Sundman, Emily A; Minas, Tom; Fortier, Lisa A

2014-01-01

Platelet-rich plasma (PRP) is used for the treatment of tendinopathy. There are numerous PRP preparations, and the optimal combination of platelets and leukocytes is not known. Within leukocyte-reduced PRP (lrPRP), there is a plateau effect of platelet concentration, with increasing platelet concentrations being detrimental to extracellular matrix synthesis. Controlled laboratory study. Different formulations of lrPRP with respect to the platelet:leukocyte ratio were generated from venous blood of 8 horses. Explants of the superficial digital flexor tendon were cultured in lrPRP products for 96 hours. Platelet-derived growth factor-BB (PDGF-BB), tumor necrosis factor-α (TNF-α), transforming growth factor-β1 (TGF-β1), and interleukin-1β (IL-1β) concentrations were determined in the media by enzyme-linked immunosorbent assay. Gene expression in tendon tissue for collagen type I and III (COL1A1 and COL3A1, respectively), matrix metalloproteinase-3 and -13 (MMP-3 and MMP-13, respectively), cartilage oligomeric matrix protein (COMP), and IL-1β was determined. Data were divided into 3 groups of lrPRP based on the ratio of platelets:leukocytes and evaluated to determine the effect of platelet concentration. Complete blood counts verified leukocyte reduction and platelet enrichment in all PRP preparations. In the lrPRP preparation, the anabolic growth factors PDGF-BB and TGF-β1 were increased with increasing platelet concentrations, and the catabolic cytokine IL-1β was decreased with increasing platelet concentrations. Increasing the platelet concentration resulted in a significant reduction in COL1A1 and COL3A1 synthesis in tendons. Increasing the platelet concentration within lrPRP preparations results in the delivery of more anabolic growth factors and less proinflammatory cytokines, but the biological effect on tendons is diminished metabolism as indicated by a decrease in the synthesis of both COL1A1 and COL3A1. Together, this information suggests that minimizing leukocytes in PRP is more important than maximizing platelet numbers with respect to decreasing inflammation and enhancing matrix gene synthesis. This study suggests that reducing leukocytes to minimize catabolic signaling appears to be more important than increasing platelets in an effort to maximize anabolic signaling. Further, a maximum biological threshold of benefit was demonstrated with regard to the number of platelets beyond which further increases in platelet concentration did not result in further anabolic upregulation. In vivo investigations documenting the use of platelets for the treatment of tendinopathy are justified as well as further in vitro characterization of the ideal PRP product for the treatment of tendinopathy and other musculoskeletal applications.

Early embryonic programming of neuronal left/right asymmetry in C. elegans.

PubMed

Poole, Richard J; Hobert, Oliver

2006-12-05

Nervous systems are largely bilaterally symmetric on a morphological level but often display striking degrees of functional left/right (L/R) asymmetry. How L/R asymmetric functional features are superimposed onto an essentially bilaterally symmetric structure and how nervous-system laterality relates to the L/R asymmetry of internal organs are poorly understood. We address these questions here by using the establishment of L/R asymmetry in the ASE chemosensory neurons of C. elegans as a paradigm. This bilaterally symmetric neuron pair is functionally lateralized in that it senses a distinct class of chemosensory cues and expresses a putative chemoreceptor family in a L/R asymmetric manner. We show that the directionality of the asymmetry of the two postmitotic ASE neurons ASE left (ASEL) and ASE right (ASER) in adults is dependent on a L-/R-symmetry-breaking event at a very early embryonic stage, the six-cell stage, which also establishes the L/R asymmetric placement of internal organs. However, the L/R asymmetry of the ASE neurons per se is dependent on an even earlier anterior-posterior (A/P) Notch signal that specifies embryonic ABa/ABp blastomere identities at the four-cell stage. This Notch signal, which functions through two T box genes, acts genetically upstream of a miRNA-controlled bistable feedback loop that regulates the L/R asymmetric gene-expression program in the postmitotic ASE cells. Our results link adult neuronal laterality to the generation of the A/P axis at the two-cell stage and raise the possibility that neural asymmetries observed across the animal kingdom are similarly established by very early embryonic interactions.

Synthesis of visible light sensitized S, N and C co-doped polymorphic TiO2 for Microcystin-LR MC-LR removal

EPA Science Inventory

Microcystin-LR (MC-LR) is considered as one of the most widespread and toxic cyanotoxins, which had been discovered to be hepatotoxic, cytotoxic and neurotoxic. It is the only cyanotoxin that has been proposed by Word Health Organization (WHO) for a provisional guideline (1 ppb) ...

Protection of cerebral microcirculation, mitochondrial function, and electrocortical activity by small-volume resuscitation with terlipressin in a rat model of haemorrhagic shock.

PubMed

Ida, K K; Chisholm, K I; Malbouisson, L M S; Papkovsky, D B; Dyson, A; Singer, M; Duchen, M R; Smith, K J

2018-06-01

During early treatment of haemorrhagic shock, cerebral perfusion pressure can be restored by small-volume resuscitation with vasopressors. Whether this therapy is improved with additional fluid remains unknown. We assessed the value of terlipressin and lactated Ringer's solution (LR) on early recovery of microcirculation, tissue oxygenation, and mitochondrial and electrophysiological function in the rat cerebral cortex. Animals treated with LR replacing three times (3LR) the volume bled (n=26), terlipressin (n=27), terlipressin plus 1LR (n=26), 2LR (n=16), or 3LR (n=15) were compared with untreated (n=36) and sham-operated rats (n=17). In vivo confocal microscopy was used to assess cortical capillary perfusion, changes in tissue oxygen concentration, and mitochondrial membrane potential and redox state. Electrophysiological function was assessed by cortical somatosensory evoked potentials, spinal cord dorsum potential, and peripheral electromyography. Compared with sham treatment, haemorrhagic shock reduced the mean (SD) area of perfused vessels [82% (sd 10%) vs 38% (12%); P<0.001] and impaired oxygen concentration, mitochondrial redox state [99% (4%) vs 59% (15%) of baseline; P<0.001], and somatosensory evoked potentials [97% (13%) vs 27% (19%) of baseline]. Administration of terlipressin plus 1LR or 2LR was able to recover these measures, but terlipressin plus 3LR or 3LR alone were not as effective. Spinal cord dorsum potential was preserved in all groups, but no therapy protected electromyographic function. Resuscitation from haemorrhagic shock using terlipressin with small-volume LR was superior to high-volume LR, with regard to cerebral microcirculation, and mitochondrial and electrophysiological functions. Copyright © 2018 British Journal of Anaesthesia. Published by Elsevier Ltd. All rights reserved.

Effect of Lithospermi Radix on Contact Dermatitis Induced by Dinitrofluorobenzene in Mice

PubMed Central

Kim, Han-Na; Kim, Mi-Young; Choi, Chan-Hun; Kim, Byung-Joo; Kim, Kyung-Yoon; Kim, Gye-Yeop; Jeong, Hyun-Woo; Kim, Hyung-Woo

2012-01-01

Objective: The root of Lithospermum erythrorhizon Sieb. et Zucc. (Lithospermi Radix, LR) is a kind of heat clearing and blood cooling medicinal herbs. It can clear away heat and cool the blood, reduce toxins and disperse maculae. LR has long been used as efficacious therapy for inflammation, burns, frostbite and skin diseases such as eczema and psoriasis. Methods: In the present study, we investigate anti-allergic and anti-inflammatory effects of LR by using the 1-fluoro-2, 4- dinitrofluorobenzene (DNFB)-induced contact dermatitis mouse model. Results: Topical application of 10 mg/mL of LR effectively inhibited skin lesions induced by repeated paintings with DNFB. Topical application of LR also inhibited hyperplasia, edema, spongiosis and infiltrations of mononuclear cells. In addition, production levels of total immunoglobulin and IgG1 in serum were decreased by using LR in vivo. Conclusion: These data suggest that LR acts as an antiinflammatory agent, improving skin lesions in CD mice. PMID:25780635

Physiological response, blood chemistry profile and mucus secretion of red sea bream (Pagrus major) fed diets supplemented with Lactobacillus rhamnosus under low salinity stress.

PubMed

Dawood, Mahmoud A O; Koshio, Shunsuke; Ishikawa, Manabu; El-Sabagh, Mabrouk; Yokoyama, Saichiro; Wang, Wei-Long; Yukun, Zhang; Olivier, Adissin

2017-02-01

Environmental stressors caused by inadequate aquaculture management strategies suppress the immune response of fish and make them more susceptible to diseases. Therefore, efforts have been made to relieve stress in fish by using various functional feed additives in the diet, including probiotics. The present work evaluates the effects of Lactobacillus rhamnosus (LR) on physiological stress response, blood chemistry and mucus secretion of red sea bream (Pagrus major) under low salinity stress. Fish were fed four diets supplemented with LR at [0 (LR0), 1 × 10 2 (LR1), 1 × 10 4 (LR2) and 1 × 10 6 (LR3) cells g -1 ] for 56 days. Before stress, blood cortisol, urea nitrogen (BUN) and total bilirubin (T-BIL) showed no significant difference (P > 0.05), whereas plasma glucose and triglyceride (TG) of fish-fed LR2 and LR3 diets were significantly lower (P < 0.05) than those of the other groups. Plasma total cholesterol (T-CHO) of fish-fed LR3 diet was significantly (P < 0.05) lower than that of the other groups. Furthermore, total plasma protein, mucus myeloperoxidase activity and the amount of mucus secretion were significantly enhanced in LR-supplemented groups when compared with the control group (P < 0.05). After the application of the low salinity stress test, plasma cortisol, glucose, T-CHO and TG contents in all groups showed an increased trend significantly (P < 0.01) compared to the fish before the stress challenge. However, plasma total protein and the amount of secreted mucus showed a decreased trend in all groups. On the other hand, BUN, T-BIL and mucus myeloperoxidase activity showed no significant difference after exposure to the low salinity stress (P > 0.05). In addition, the fish that received LR-supplemented diets showed significantly higher tolerance against low salinity stress than the fish-fed LR-free diet (P < 0.05). The physiological status and the detected immune responses, including total plasma protein and mucus myeloperoxidase activity in red sea bream, will provide a more comprehensive outlook of the effects of probiotics to relieve stress in fish.

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly.

PubMed

Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G

2017-08-01

Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.

Software Development Of XML Parser Based On Algebraic Tools

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2011-12-01

In this paper, is presented one software development and implementation of an algebraic method for XML data processing, which accelerates XML parsing process. Therefore, the proposed in this article nontraditional approach for fast XML navigation with algebraic tools contributes to advanced efforts in the making of an easier user-friendly API for XML transformations. Here the proposed software for XML documents processing (parser) is easy to use and can manage files with strictly defined data structure. The purpose of the presented algorithm is to offer a new approach for search and restructuring hierarchical XML data. This approach permits fast XML documents processing, using algebraic model developed in details in previous works of the same authors. So proposed parsing mechanism is easy accessible to the web consumer who is able to control XML file processing, to search different elements (tags) in it, to delete and to add a new XML content as well. The presented various tests show higher rapidity and low consumption of resources in comparison with some existing commercial parsers.

Overview of the ArbiTER edge plasma eigenvalue code

NASA Astrophysics Data System (ADS)

Baver, Derek; Myra, James; Umansky, Maxim

2011-10-01

The Arbitrary Topology Equation Reader, or ArbiTER, is a flexible eigenvalue solver that is currently under development for plasma physics applications. The ArbiTER code builds on the equation parser framework of the existing 2DX code, extending it to include a topology parser. This will give the code the capability to model problems with complicated geometries (such as multiple X-points and scrape-off layers) or model equations with arbitrary numbers of dimensions (e.g. for kinetic analysis). In the equation parser framework, model equations are not included in the program's source code. Instead, an input file contains instructions for building a matrix from profile functions and elementary differential operators. The program then executes these instructions in a sequential manner. These instructions may also be translated into analytic form, thus giving the code transparency as well as flexibility. We will present an overview of how the ArbiTER code is to work, as well as preliminary results from early versions of this code. Work supported by the U.S. DOE.

Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat

USDA-ARS?s Scientific Manuscript database

The widely effective and linked rust resistance genes Yr47 and Lr52 were previously mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population t...

Inclusion probability for DNA mixtures is a subjective one-sided match statistic unrelated to identification information

PubMed Central

Perlin, Mark William

2015-01-01

Background: DNA mixtures of two or more people are a common type of forensic crime scene evidence. A match statistic that connects the evidence to a criminal defendant is usually needed for court. Jurors rely on this strength of match to help decide guilt or innocence. However, the reliability of unsophisticated match statistics for DNA mixtures has been questioned. Materials and Methods: The most prevalent match statistic for DNA mixtures is the combined probability of inclusion (CPI), used by crime labs for over 15 years. When testing 13 short tandem repeat (STR) genetic loci, the CPI-1 value is typically around a million, regardless of DNA mixture composition. However, actual identification information, as measured by a likelihood ratio (LR), spans a much broader range. This study examined probability of inclusion (PI) mixture statistics for 517 locus experiments drawn from 16 reported cases and compared them with LR locus information calculated independently on the same data. The log(PI-1) values were examined and compared with corresponding log(LR) values. Results: The LR and CPI methods were compared in case examples of false inclusion, false exclusion, a homicide, and criminal justice outcomes. Statistical analysis of crime laboratory STR data shows that inclusion match statistics exhibit a truncated normal distribution having zero center, with little correlation to actual identification information. By the law of large numbers (LLN), CPI-1 increases with the number of tested genetic loci, regardless of DNA mixture composition or match information. These statistical findings explain why CPI is relatively constant, with implications for DNA policy, criminal justice, cost of crime, and crime prevention. Conclusions: Forensic crime laboratories have generated CPI statistics on hundreds of thousands of DNA mixture evidence items. However, this commonly used match statistic behaves like a random generator of inclusionary values, following the LLN rather than measuring identification information. A quantitative CPI number adds little meaningful information beyond the analyst's initial qualitative assessment that a person's DNA is included in a mixture. Statistical methods for reporting on DNA mixture evidence should be scientifically validated before they are relied upon by criminal justice. PMID:26605124

Inclusion probability for DNA mixtures is a subjective one-sided match statistic unrelated to identification information.

PubMed

Perlin, Mark William

2015-01-01

DNA mixtures of two or more people are a common type of forensic crime scene evidence. A match statistic that connects the evidence to a criminal defendant is usually needed for court. Jurors rely on this strength of match to help decide guilt or innocence. However, the reliability of unsophisticated match statistics for DNA mixtures has been questioned. The most prevalent match statistic for DNA mixtures is the combined probability of inclusion (CPI), used by crime labs for over 15 years. When testing 13 short tandem repeat (STR) genetic loci, the CPI(-1) value is typically around a million, regardless of DNA mixture composition. However, actual identification information, as measured by a likelihood ratio (LR), spans a much broader range. This study examined probability of inclusion (PI) mixture statistics for 517 locus experiments drawn from 16 reported cases and compared them with LR locus information calculated independently on the same data. The log(PI(-1)) values were examined and compared with corresponding log(LR) values. The LR and CPI methods were compared in case examples of false inclusion, false exclusion, a homicide, and criminal justice outcomes. Statistical analysis of crime laboratory STR data shows that inclusion match statistics exhibit a truncated normal distribution having zero center, with little correlation to actual identification information. By the law of large numbers (LLN), CPI(-1) increases with the number of tested genetic loci, regardless of DNA mixture composition or match information. These statistical findings explain why CPI is relatively constant, with implications for DNA policy, criminal justice, cost of crime, and crime prevention. Forensic crime laboratories have generated CPI statistics on hundreds of thousands of DNA mixture evidence items. However, this commonly used match statistic behaves like a random generator of inclusionary values, following the LLN rather than measuring identification information. A quantitative CPI number adds little meaningful information beyond the analyst's initial qualitative assessment that a person's DNA is included in a mixture. Statistical methods for reporting on DNA mixture evidence should be scientifically validated before they are relied upon by criminal justice.

Draco,Version 6.x.x

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

Thompson, Kelly; Budge, Kent; Lowrie, Rob

2016-03-03

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible.

PubMed

Tyler, Brett M; Kale, Shiv D; Wang, Qunqing; Tao, Kai; Clark, Helen R; Drews, Kelly; Antignani, Vincenzo; Rumore, Amanda; Hayes, Tristan; Plett, Jonathan M; Fudal, Isabelle; Gu, Biao; Chen, Qinghe; Affeldt, Katharyn J; Berthier, Erwin; Fischer, Gregory J; Dou, Daolong; Shan, Weixing; Keller, Nancy P; Martin, Francis; Rouxel, Thierry; Lawrence, Christopher B

2013-06-01

A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent reexamination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells concluded that the RxLR domains of Phytophthora infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and nonhost plant and animal cells. Here, we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells and also into wheat leaf cells, at levels well above background nonspecific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the seven different labs that coauthored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected by Wawra et al. (2013).

Two-step superresolution approach for surveillance face image through radial basis function-partial least squares regression and locality-induced sparse representation

NASA Astrophysics Data System (ADS)

Jiang, Junjun; Hu, Ruimin; Han, Zhen; Wang, Zhongyuan; Chen, Jun

2013-10-01

Face superresolution (SR), or face hallucination, refers to the technique of generating a high-resolution (HR) face image from a low-resolution (LR) one with the help of a set of training examples. It aims at transcending the limitations of electronic imaging systems. Applications of face SR include video surveillance, in which the individual of interest is often far from cameras. A two-step method is proposed to infer a high-quality and HR face image from a low-quality and LR observation. First, we establish the nonlinear relationship between LR face images and HR ones, according to radial basis function and partial least squares (RBF-PLS) regression, to transform the LR face into the global face space. Then, a locality-induced sparse representation (LiSR) approach is presented to enhance the local facial details once all the global faces for each LR training face are constructed. A comparison of some state-of-the-art SR methods shows the superiority of the proposed two-step approach, RBF-PLS global face regression followed by LiSR-based local patch reconstruction. Experiments also demonstrate the effectiveness under both simulation conditions and some real conditions.

Uptake and biotransformation of pure commercial microcystin-LR versus microcystin-LR from a natural cyanobacterial bloom extract in the aquatic fungus Mucor hiemalis.

PubMed

Esterhuizen-Londt, Maranda; Hertel, Stefanie; Pflugmacher, Stephan

2017-10-01

To evaluate the remediation efficiency of Mucor hiemalis by comparing media elimination, uptake, and biotransformation of microcystin-LR with exposure to pure toxin versus a crude bloom extract. With exposure to the extract, the elimination rate of microcystin-LR from the media, which was 0.28 ng MC-LR l -1  h -1 , was significantly higher compared to that achieved with exposure to the pure toxin (0.16 ng MC-LR l -1  h -1 ) after 24 h. However, intracellular breakdown of microcystin-LR was significantly lower in the extract exposed pellets compared to the pure toxin treated fungal pellets over time. This coincided with reduced intracellular glutathione S-transferase activity with crude extract exposure which could be responsible for the detection of only the glutathione conjugate of microcystin-LR. This paper signifies the importance of using laboratory exposure scenarios which resemble conditions in nature to fully understand and evaluate remediation efficiency. There is merit in using M. hiemalis for mycoremediation of cyanotoxins in surface waters.

[Analysis of fragments of intergenome spacers of human body observed in chromosomes containing no nuclear organization].

PubMed

Kupriyanova, N S; Nechvolodov, K K; Korsunenko, A V

2014-01-01

Tandem repetitions of rDNA provide so-called nuclear organizations (NOR). On the other hand, rDNA-structures are observed in some NOR chromosomes. It was demonstrated that, in addition to ribosome biogenesis, nucleoli provided a number of functions: cell cycle regulation, stress-induced response, transcription regulation, which often induced cell cascades. The mechanisms of the induction of rDNA segments in NOR chromosomes are obscure and require further research. About 1/3 repetitions are associated with nucleoli and SINE/Alu repetitions, homogeneous repetition, and tandem repetition. Perhaps, relative position of nucleoli and chromosomes may facilitate/prevent interaction of chromosomes with rDNA clusters. The variability of two larger repetitions in the central part of rMGS, LR1, and LR2 similar by -90% and separated by several hundred pairs of bases from each other was studied in our previous works. This work was devoted to the search for the LR1-LR2 segments in other chromosomes, characterization of their terminal tips at rupture points and genome areas of incorporation of the LR1-LR2 segments.

The effect of intravenous lactated Ringer's solution versus 0.9% sodium chloride solution on serum osmolality in human volunteers.

PubMed

Williams, E L; Hildebrand, K L; McCormick, S A; Bedel, M J

1999-05-01

Animal studies have shown that large volumes of IV lactated Ringer's solution (LR) decrease serum osmolality, thereby increasing cerebral water. These studies have led to recommendations to limit LR to avoid cerebral edema in neurosurgical patients. Eighteen healthy human volunteers aged 20-48 yr received 50 mL/kg LR over 1 h on one occasion and 0.9% sodium chloride (NS) on another. Venous samples were taken at baseline (T1), at infusion end (T2), and 1 h after T2 (T3). Time until first urination was noted. With LR, serum osmolality decreased by 4+/-3 mOsm/kg from T1 to T2 and increased insignificantly with NS. At T3, osmolality returned almost to baseline in the LR group. Blood pH increased from T1 to T2 with LR by 0.04+/-0.04 and decreased with NS by 0.04+/-0.04. These pH changes persisted at T3. Subjective mental changes occurred only with NS. Abdominal discomfort was more common with NS. Time until first urination was longer with NS (106+/-11 min) than with LR (75+/-10 min) (P < 0.001). In healthy humans, an infusion of large volumes of LR, but not NS, transiently decreased serum osmolality, whereas acidosis associated with NS persisted and urinary output was slower with NS. Large volumes of lactated Ringer's solution administered to healthy humans produced small transient changes in serum osmolality. Large volumes of sodium chloride did not change osmolality but resulted in lower pH.

The Accuracy of the Physical Examination for the Diagnosis of Midlumbar and Low Lumbar Nerve Root Impingement

PubMed Central

Suri, Pradeep; Rainville, James; Katz, Jeffrey N.; Jouve, Cristin; Hartigan, Carol; Limke, Janet; Pena, Enrique; Li, Ling; Swaim, Bryan; Hunter, David J

2010-01-01

Study Design Cross-sectional study with prospective recruitment. Objective To determine the accuracy of the physical examination for the diagnosis of midlumbar nerve root impingement (L2, L3, or L4), low lumbar nerve root impingement (L5 or S1) and level-specific lumbar nerve root impingement on magnetic resonance imaging (MRI), using individual tests and combinations of tests. Summary of Background Data The sensitivity and specificity of the physical examination for the localization of nerve root impingement has not been previously studied. Methods Sensitivities, specificities and LRs were calculated for the ability of individual tests and test combinations to predict the presence or absence of nerve root impingement at midlumbar, low lumbar, and specific nerve root levels. Results LRs ≥5.0 indicate moderate to large changes from pre-test probability of nerve root impingement to post-test probability. For the diagnosis of midlumbar impingement, the femoral stretch test (FST), crossed femoral stretch test (CFST), medial ankle pinprick sensation, and patellar reflex testing demonstrated LRs ≥5.0 (LR ∞). LRs ≥5.0 were seen with the combinations of FST and either patellar reflex testing (LR 7.0; 95% CI 2.3–21), or the sit-to-stand test (LR ∞). For the diagnosis of low lumbar impingement, the Achilles reflex test demonstrated a LR ≥5.0 (LR 7.1; CI 0.96–53); test combinations did not increase LRs. For the diagnosis of level-specific impingement, LRs ≥5.0 were seen for anterior thigh sensation at L2 (LR 13; 95% CI 1.8–87); FST at L3 (LR 5.7 ; 95% CI 2.3–4.4); patellar reflex testing (LR 7.7; 95% CI 1.7–35), medial ankle sensation (LR ∞), or CFST (LR 13; 95% CI 1.8–87) at L4; and hip abductor strength at L5(LR 11; 95% CI 1.3–84). Test combinations increased LRs for level-specific root impingement at the L4 level only. Conclusions Individual physical examination tests may provide clinical information which substantially alters the likelihood that midlumbar impingement, low lumbar impingement, or level-specific impingement is present. Test combinations improve diagnostic accuracy for midlumbar impingement. PMID:20543768

Detection of novel mutations that cause autosomal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing

PubMed Central

Dias, Miguel de Sousa; Hernan, Imma; Pascual, Beatriz; Borràs, Emma; Mañé, Begoña; Gamundi, Maria José

2013-01-01

Purpose To devise an effective method for detecting mutations in 12 genes (CA4, CRX, IMPDH1, NR2E3, RP9, PRPF3, PRPF8, PRPF31, PRPH2, RHO, RP1, and TOPORS) commonly associated with autosomal dominant retinitis pigmentosa (adRP) that account for more than 95% of known mutations. Methods We used long-range PCR (LR-PCR) amplification and next-generation sequencing (NGS) performed in a GS Junior 454 benchtop sequencing platform. Twenty LR-PCR fragments, between 3,000 and 10,000 bp, containing all coding exons and flanking regions of the 12 genes, were obtained from DNA samples of patients with adRP. Sequencing libraries were prepared with an enzymatic (Fragmentase technology) method. Results Complete coverage of the coding and flanking sequences of the 12 genes assayed was obtained with NGS, with an average sequence depth of 380× (ranging from 128× to 1,077×). Five previous known mutations in the adRP genes were detected with a sequence variation percentage between 35% and 65%. We also performed a parallel sequence analysis of four samples, three of them new patients with index adRP, in which two novel mutations were detected in RHO (p.Asn73del) and PRPF31 (p.Ile109del). Conclusions The results demonstrate that genomic LR-PCR amplification together with NGS is an effective method for analyzing individual patient samples for mutations in a monogenic heterogeneous disease such as adRP. This approach proved effective for the parallel analysis of adRP and has been introduced as routine. Additionally, this approach could be extended to other heterogeneous genetic diseases. PMID:23559859

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

Woźny, Maciej, E-mail: maciej.wozny@uwm.edu.pl

To date, there has been no systematic approach comprehensively describing the sequence of pathological changes in fish during prolonged exposure to microcystin-LR (MC-LR). Towards this aim, juvenile whitefish individuals received an intraperitoneal injection with pure MC-LR, and the injection was repeated every week to maintain continuous exposure for 28 days. During the exposure period, growth and condition of the fish were assessed based on biometric measurements. Additionally, selected biochemical markers were analysed in the fishes' blood, and their livers were carefully examined for morphological, ultrastructural, and molecular changes. The higher dose of MC-LR (100 μg·kg{sup −1}) caused severe liver injurymore » at the beginning of the exposure period, whereas the lower dose (10 μg·kg{sup −1}) caused less, probably reversible injury, and its effects began to be observed later in the exposure period. These marked changes were accompanied by substantial MC-LR uptake by the liver. However, starting on the 7th day of exposure, cell debris began to be removed by phagocytes, then by 14th day, proliferation of liver cells had markedly increased, which led to reconstruction of the liver parenchyma at the end of the treatment. Surprisingly, despite weekly-repeated intraperitoneal injections, MC-LR did not accumulate over time of exposure which suggests its limited uptake in the later phase of exposure. In support, mRNA expression of the membrane transport protein oatp1d was decreased at the same time as the regenerative processes were observed. Our study shows that closing of active membrane transport may serve as one defence mechanism against further MC-LR intoxication. - Highlights: • The study presents pathological changes in whitefish during prolonged MC-LR exposure. • After early, severe injury, the damaged liver parenchyma of the fish regenerated. • Endoplasmic reticulum, cytoskeleton, and chromatin were the main targets for MC-LR. • MC-LR did not accumulate over time of exposure despite weekly-repeated injections. • Down-regulation of oatp1d expression may serve as a defence mechanism against MC-LR.« less

Adsorptive removal of microcystin-LR from surface and wastewater using tyre-based powdered activated carbon: Kinetics and isotherms.

PubMed

Mashile, Phodiso P; Mpupa, Anele; Nomngongo, Philiswa N

2018-04-01

Microcystin LR (MC-LR) is a highly toxic compound and it is known for its adverse health effect on both humans and animals. Due to the ineffectiveness of conventional water treatments methods, for the past decades, researchers have been developing cost-effective ways of removing MC-LR from water bodies. This study reports the application of powdered activated carbon (PAC) obtained from the waste tyre for the removal of MC-LR. The choice of the adsorbent was chosen due to its attractive properties. The prepared tyre-based PAC was found to have the large surface area (1111 m 2  g -1 ). The detection of MC-LR was achieved using high performance liquid chromatography (HPLC) coupled with a PDA detector. The experimental parameters (such as optimum pH, dosage and contact time) affecting the removal of MC-LR using tyre based-powdered activated carbon were optimized using response surface methodology (RSM). Maximum removal of MC-LR was achieved under the following optimum conditions; sample pH 4, carbon dosage concentration 10,000 mg L -1 and contact time of 34 min. Under optimum conditions, kinetic studies and adsorption isotherms reflected better fit for pseudo-second-order rate and Langmuir isotherm model, respectively. The optimized method was applied for the removal of MC-LR in wastewater sample. The effluent and influent sample contained initial concentrations ranging from 0.52 to 8.54 μg L -1 and the removal efficiency was 100%. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mapping of leaf rust resistance genes and molecular characterization of the 2NS/2AS translocation in the wheat cultivar Jagger

USDA-ARS?s Scientific Manuscript database

Winter wheat cultivar 'Jagger' was recently found to have an alien chromosomal segment 'VPM1' that should carry Lr37, a gene conferring resistance against leaf rust caused by Puccinia triticina, and this cultivar was also reported to have the wheat gene Lr17 against leaf rust. Both Lr17 and Lr37 wer...

40 CFR 272.951 - Louisiana State-administered program: Final authorization.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., 1997. Copies of the document can be obtained from EPA Region 6, 1445 Ross Avenue, Dallas, Texas 75202... November 20, 1988 LR 18:1375 December 20, 1992. LAC § 303.K.1 (previously LHWR § 3.2(k)(1)) July 20, 1984 LR 14:790 November 20, 1988. LAC § 901 (LHWR § 6.1) March 20, 1984 LR 20:1000 September 20, 1994. LAC...

The CMIP5 Model Documentation Questionnaire: Development of a Metadata Retrieval System for the METAFOR Common Information Model

NASA Astrophysics Data System (ADS)

Pascoe, Charlotte; Lawrence, Bryan; Moine, Marie-Pierre; Ford, Rupert; Devine, Gerry

2010-05-01

The EU METAFOR Project (http://metaforclimate.eu) has created a web-based model documentation questionnaire to collect metadata from the modelling groups that are running simulations in support of the Coupled Model Intercomparison Project - 5 (CMIP5). The CMIP5 model documentation questionnaire will retrieve information about the details of the models used, how the simulations were carried out, how the simulations conformed to the CMIP5 experiment requirements and details of the hardware used to perform the simulations. The metadata collected by the CMIP5 questionnaire will allow CMIP5 data to be compared in a scientifically meaningful way. This paper describes the life-cycle of the CMIP5 questionnaire development which starts with relatively unstructured input from domain specialists and ends with formal XML documents that comply with the METAFOR Common Information Model (CIM). Each development step is associated with a specific tool. (1) Mind maps are used to capture information requirements from domain experts and build a controlled vocabulary, (2) a python parser processes the XML files generated by the mind maps, (3) Django (python) is used to generate the dynamic structure and content of the web based questionnaire from processed xml and the METAFOR CIM, (4) Python parsers ensure that information entered into the CMIP5 questionnaire is output as CIM compliant xml, (5) CIM compliant output allows automatic information capture tools to harvest questionnaire content into databases such as the Earth System Grid (ESG) metadata catalogue. This paper will focus on how Django (python) and XML input files are used to generate the structure and content of the CMIP5 questionnaire. It will also address how the choice of development tools listed above provided a framework that enabled working scientists (who we would never ordinarily get to interact with UML and XML) to be part the iterative development process and ensure that the CMIP5 model documentation questionnaire reflects what scientists want to know about the models. Keywords: metadata, CMIP5, automatic information capture, tool development

Lithospermi radix extract inhibits histamine release and production of inflammatory cytokine in mast cells.

PubMed

Kim, Eun Kyoung; Kim, Eun-Young; Moon, Phil-Dong; Um, Jae-Young; Kim, Hyung-Min; Lee, Hyun-Sam; Sohn, Youngjoo; Park, Seong Kyu; Jung, Hyuk-Sang; Sohn, Nak-Won

2007-12-01

Lithospermi radix (LR, Borraginaceae, the root of Lithospermum erythrorhizon Siebold. et Zuccarinii) is used in herbal medicine to treat such conditions as eczema, skin burns and frostbite. This study investigates the effects of LR on the anti-allergy mechanism. LR inhibited the release of histamine from rat peritoneal mast cells by compound 48/80 in a dose-dependent manner. LR orally administered at 6.59 mg/100 g also inhibited the anti-DNP IgE-induced passive cutaneous anaphylaxis reaction. LR inhibited the PMA plus A23187-induced increase in IL-6, IL-8, and TNF-alpha expression in HMC-1 cells. In addition, LR also inhibited nuclear factor-kappa B (NF-kappaB) activation and I kappaB-alpha degradation. These results show that LR had an inhibitory effect on the atopic allergic reaction. Furthermore, the in vivo and in vitro anti-allergic effect of LR suggests possible therapeutic applications of this agent for inflammatory allergic diseases.

[Survey on the contamination of microcystin-LR in water supply of Shanghai city].

PubMed

Wu, He-yan; Zheng, Li-xing; Su, Jin; Shi, Wei

2005-03-01

To study the pollution level of microcystin-LR in water supply of Shanghai city and the removal efficacy for microcystin-LR through routine water treatment technique. High performance liquid chromatogram (HPLC) was applied to determine the concentration of microcystin-LR in source water, water samples after various water treatment procedures and tap water. The concentration of microcystin-LR varied with sampling seasons and sites and reached peak during summer and fall. The maximum of microcystin-LR was 2.38 microg/L in source water. Coagulation plus chlorine disinfection were found to be effective for the removal of microcystin-LR, while the remove rate through filtration was not significant. And it could also be detected in tap water as high as 1.27 microg/L. The source waters of Shanghai city were polluted by cyanobacteria toxins represented by microcystin-LR. The source water in suburb was more polluted. Routine water treatment techniques can not remove the toxins effectively.

Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS.

PubMed

Singh, Sukhwinder; Franks, C D; Huang, L; Brown-Guedira, G L; Marshall, D S; Gill, B S; Fritz, A

2004-02-01

The leaf rust resistance gene Lr41 in wheat germplasm KS90WGRC10 and a resistance gene in wheat breeding line WX93D246-R-1 were transferred to Triticum aestivum from Aegilops tauschii and Ae. cylindrica, respectively. The leaf rust resistance gene in WX93D246-R-1 was located on wheat chromosome 2D by monosomic analysis. Molecular marker analysis of F(2) plants from non-critical crosses determined that this gene is 11.2 cM distal to marker Xgwm210 on the short arm of 2D. No susceptible plants were detected in a population of 300 F(2) plants from a cross between WX93D246-R-1 and TA 4186 ( Lr39), suggesting that the gene in WX93D246-R-1 is the same as, or closely linked to, Lr39. In addition, no susceptible plants were detected in a population of 180 F(2) plants from the cross between KS90WGRC10 and WX93D246-R-1. The resistance gene in KS90WGRC10, Lr41, was previously reported to be located on wheat chromosome 1D. In this study, no genetic association was found between Lr41 and 51 markers located on chromosome 1D. A population of 110 F(3 )lines from a cross between KS90WGRC10 and TAM 107 was evaluated with polymorphic SSR markers from chromosome 2D and marker Xgdm35 was found to be 1.9 cM proximal to Lr41. When evaluated with diverse isolates of Puccinia triticina, similar reactions were observed on WX93D246-R-1, KS90WGRC10, and TA 4186. The results of mapping, allelism, and race specificity test indicate that these germplasms likely have the same gene for resistance to leaf rust.

Cytogenetic analysis and mapping of leaf rust resistance in Aegilops speltoides Tausch derived bread wheat line Selection2427 carrying putative gametocidal gene(s).

PubMed

Niranjana, M; Vinod; Sharma, J B; Mallick, Niharika; Tomar, S M S; Jha, S K

2017-12-01

Leaf rust (Puccinia triticina) is a major biotic stress affecting wheat yields worldwide. Host-plant resistance is the best method for controlling leaf rust. Aegilops speltoides is a good source of resistance against wheat rusts. To date, five Lr genes, Lr28, Lr35, Lr36, Lr47, and Lr51, have been transferred from Ae. speltoides to bread wheat. In Selection2427, a bread wheat introgresed line with Ae. speltoides as the donor parent, a dominant gene for leaf rust resistance was mapped to the long arm of chromosome 3B (LrS2427). None of the Lr genes introgressed from Ae. speltoides have been mapped to chromosome 3B. Since none of the designated seedling leaf rust resistance genes have been located on chromosome 3B, LrS2427 seems to be a novel gene. Selection2427 showed a unique property typical of gametocidal genes, that when crossed to other bread wheat cultivars, the F 1 showed partial pollen sterility and poor seed setting, whilst Selection2427 showed reasonable male and female fertility. Accidental co-transfer of gametocidal genes with LrS2427 may have occurred in Selection2427. Though LrS2427 did not show any segregation distortion and assorted independently of putative gametocidal gene(s), its utilization will be difficult due to the selfish behavior of gametocidal genes.

Characterization of in vitro effects of microcystin-LR on intestinal epithelial cells.

PubMed

Zhou, Yuan; Xu, Xiaoping; Yu, Beibei; Yu, Guang

2017-05-01

The intestinal epithelium is a single-cell layer that provides an important barrier against natural toxins. Microcystin-LR (MC-LR), a cyclic heptapeptide, is one of the best known toxins able to alter the functions of intestine. This study evaluated the toxic effects and the possible mechanisms of MC-LR on barrier function of the intestinal epithelial cells. Intestinal epithelial cells (IEC-6) were exposed to 0, 6.25, 12.5, 25 and 50 μM MC-LR. Cell viability significantly decreased, while the ratio of apoptotic cells increased after exposure to 12.5μM and higer concentration of MC-LR. As expected, the integrity of a polarized IEC-6 monolayer was affected by MC-LR exposure, as demonstrated by a decrease in the transepithelial electrical resistance (TEER) values, becoming most pronounced at 50μM, 24 h. No effects were detected on the protein expression levels of the tight junction protein claudin at 50μM. However, the expression of occludin and zonula occludens-1 (ZO-1) declined. Furthermore, MC-LR can immigrate into IEC-6 cells. The activity of protein phosphatases 2A (PP2A) decreased from the concentration of 12.5 μM, showing a dose-dependent decline. These results provide new information that strengthens the concept that the intestinal epithelium is important targets for toxic effects of water contaminants like MC-LR. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1539-1547, 2017. © 2016 Wiley Periodicals, Inc.

"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar.

PubMed

Mozzherin, Dmitry Y; Myltsev, Alexander A; Patterson, David J

2017-05-26

Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role. We refer to this as 'parsing' the name. Parsing categorizes name's elements into those that are stable and those that are prone to change. Names are matched first by combining them according to their stable elements. Matches are then refined by examining their varying elements. This two stage process dramatically improves the number and quality of matches. It is especially useful for the automatic data exchange within the context of "Big Data" in biology. We introduce Global Names Parser (gnparser). It is a Java tool written in Scala language (a language for Java Virtual Machine) to parse scientific names. It is based on a Parsing Expression Grammar. The parser can be applied to scientific names of any complexity. It assigns a semantic meaning (such as genus name, species epithet, rank, year of publication, authorship, annotations, etc.) to all elements of a name. It is able to work with nested structures as in the names of hybrids. gnparser performs with ≈99% accuracy and processes 30 million name-strings/hour per CPU thread. The gnparser library is compatible with Scala, Java, R, Jython, and JRuby. The parser can be used as a command line application, as a socket server, a web-app or as a RESTful HTTP-service. It is released under an Open source MIT license. Global Names Parser (gnparser) is a fast, high precision tool for biodiversity informaticians and biologists working with large numbers of scientific names. It can replace expensive and error-prone manual parsing and standardization of scientific names in many situations, and can quickly enhance the interoperability of distributed biological information.

History, Physical Examination, Laboratory Testing, and Emergency Department Ultrasonography for the Diagnosis of Acute Cholecystitis.

PubMed

Jain, Ashika; Mehta, Ninfa; Secko, Michael; Schechter, Joshua; Papanagnou, Dimitri; Pandya, Shreya; Sinert, Richard

2017-03-01

Acute cholecystitis (AC) is a common differential for patients presenting to the emergency department (ED) with abdominal pain. The diagnostic accuracy of history, physical examination, and bedside laboratory tests for AC have not been quantitatively described. We performed a systematic review to determine the utility of history and physical examination (H&P), laboratory studies, and ultrasonography (US) in diagnosing AC in the ED. We searched medical literature from January 1965 to March 2016 in PubMed, Embase, and SCOPUS using a strategy derived from the following formulation of our clinical question: patients-ED patients suspected of AC; interventions-H&P, laboratory studies, and US findings commonly used to diagnose AC; comparator-surgical pathology or definitive diagnostic radiologic study confirming AC; and outcome-the operating characteristics of the investigations in diagnosing AC were calculated. Sensitivity, specificity, and likelihood ratios (LRs) were calculated using Meta-DiSc with a random-effects model (95% CI). Study quality and risks for bias were assessed using the Quality Assessment Tool for Diagnostic Accuracy Studies. Separate PubMed, Embase, and SCOPUS searches retrieved studies for H&P (n = 734), laboratory findings (n = 74), and US (n = 492). Three H&P studies met inclusion/exclusion criteria with AC prevalence of 7%-64%. Fever had sensitivity ranging from 31% to 62% and specificity from 37% to 74%; positive LR [LR+] was 0.71-1.24, and negative LR [LR-] was 0.76-1.49. Jaundice sensitivity ranged from 11% to 14%, and specificity from 86% to 99%; LR+ was 0.80-13.81, and LR- was 0.87-1.03. Murphy's sign sensitivity was 62% (range = 53%-71%), and specificity was 96% (range = 95%-97%); LR+ was 15.64 (range = 11.48-21.31), and LR- was 0.40 (range = 0.32-0.50). Right upper quadrant pain had sensitivity ranging from 56% to 93% and specificity of 0% to 96%; LR+ ranged from 0.92 to 14.02, and LR- from 0.46 to 7.86. One laboratory study met criteria with a 26% prevalence of AC. Elevated bilirubin had a sensitivity of 40% (range = 12%-74%) and specificity of 93% (range = 77%-99%); LR+ was 5.80 (range = 1.25-26.99), and LR- was 0.64 (range = 0.39-1.08). Five US studies with a prevalence of AC of between 10% and 46%. US sensitivity was 86% (range = 78%-94%) and specificity was 71% (range = 66%-76%); LR+ was 3.23 (range = 1.74-6.00), and LR- was 0.18 (range = 0.10-0.33). Variable disease prevalence, coupled with limited sample sizes, increases the risk of selection bias. Individually, none of these investigations reliably rule out AC. Development of a clinical decision rule to include evaluation of H&P, laboratory data, and US are more likely to achieve a correct diagnosis of AC. © 2016 by the Society for Academic Emergency Medicine.

Corona Enhancement and Mosaic Architecture for Prognosis and Selection Between of Liver Resection Versus Transcatheter Arterial Chemoembolization in Single Hepatocellular Carcinomas >5 cm Without Extrahepatic Metastases

PubMed Central

Li, Meng; Xin, Yongjie; Fu, Sirui; Liu, Zaiyi; Li, Yong; Hu, Baoshan; Chen, Shuting; Liang, Changhong; Lu, Ligong

2016-01-01

Abstract Corona enhancement and mosaic architecture are 2 radiologic features of hepatocellular carcinoma (HCC). However, neither their prognostic values nor their impacts on the selection of liver resection (LR) versus transcatheter arterial chemoembolization (TACE) as treatment modalities have been established. We retrospectively analyzed 275 patients with a single HCC lesion >5 cm without extrahepatic metastasis treated with LR or TACE. In LR patients, the overall survival (OS) and time to progression (TTP) were compared between corona enhancement negative (corona−) versus positive (corona+) and mosaic architecture negative (mosaic−) versus positive (mosaic+) patients. Furthermore, by the combination of corona and mosaic, LR patients were divided into negative for both corona and mosaic patterns (LR−/−), positive for only 1 feature (LR+/−), and positive for both (LR+/+); their OS and TTP were compared to those of the TACE group. Cox regression was performed to identify independent factors for OS. In the survival plots for LR, corona− had better OS and TTP than corona+, and mosaic− had better OS than mosaic+. There was no significant difference in TTP between the subgroups. On Cox regression analysis, corona enhancement, but not mosaic architecture, was a significant factor for OS, whereas neither were a significant factor for TTP. In TACE patients, neither corona nor mosaic patterns had significant correlations with OS or TTP. In the whole population, LR−/ and LR+/− subgroups had similar OS, which was better than the LR+/+ and TACE groups. Moreover, LR−/− and LR+/− patients had better TTP than TACE patients, but there were no differences between the LR−/− versus LR+/−, LR−/ versus LR+/+, LR+/− versus LR+/+, and LR+/+ versus TACE groups. On Cox regression analysis, the presence of corona/mosaic patterns was an independent prognostic factor for OS. Our results showed that, for patients with a single HCC >5 cm without extrahepatic metastasis, corona and mosaic patterns are indicators of limited LR efficacy. When both of the features are present, TACE can be used instead of LR with no negative influence on survival. PMID:26765441

Detecting modification of biomedical events using a deep parsing approach.

PubMed

Mackinlay, Andrew; Martinez, David; Baldwin, Timothy

2012-04-30

This work describes a system for identifying event mentions in bio-molecular research abstracts that are either speculative (e.g. analysis of IkappaBalpha phosphorylation, where it is not specified whether phosphorylation did or did not occur) or negated (e.g. inhibition of IkappaBalpha phosphorylation, where phosphorylation did not occur). The data comes from a standard dataset created for the BioNLP 2009 Shared Task. The system uses a machine-learning approach, where the features used for classification are a combination of shallow features derived from the words of the sentences and more complex features based on the semantic outputs produced by a deep parser. To detect event modification, we use a Maximum Entropy learner with features extracted from the data relative to the trigger words of the events. The shallow features are bag-of-words features based on a small sliding context window of 3-4 tokens on either side of the trigger word. The deep parser features are derived from parses produced by the English Resource Grammar and the RASP parser. The outputs of these parsers are converted into the Minimal Recursion Semantics formalism, and from this, we extract features motivated by linguistics and the data itself. All of these features are combined to create training or test data for the machine learning algorithm. Over the test data, our methods produce approximately a 4% absolute increase in F-score for detection of event modification compared to a baseline based only on the shallow bag-of-words features. Our results indicate that grammar-based techniques can enhance the accuracy of methods for detecting event modification.

Highly sensitive detection and discrimination of LR and YR microcystins based on protein phosphatases and an artificial neural network.

PubMed

Covaci, O I; Sassolas, A; Alonso, G A; Muñoz, R; Radu, G L; Bucur, B; Marty, J-L

2012-08-01

The inhibition characteristics of three different protein phosphatases by three microcystin (MC) variants--LR, YR, and RR--were studied. The corresponding K (I) for each enzyme-MC couple was calculated. The toxicity of MC varies in the following order: MC-LR > MC-YR > MC-RR. The sensitivity of the enzymes increased in the following order: mutant PP2A < mutant PP1 < natural PP2A. The best limit of detection obtained was 21.2 pM MC-LR using the most sensible enzyme. Methanol, ethanol, and acetonitrile up to 2 % (v/v) may be used in inhibition measurements. An artificial neural network (ANN) was used to discriminate two MC variants--LR and YR--using the differences in inhibition percentages measured with mutant PP1 and natural PP2A. The ANN is able to analyze mixtures with concentrations ranging from 8 to 98 pM MC-LR and 31 to 373 pM MC-YR.

Does This Older Adult With Lower Extremity Pain Have the Clinical Syndrome of Lumbar Spinal Stenosis?

PubMed Central

Suri, Pradeep; Rainville, James; Kalichman, Leonid; Katz, Jeffrey N.

2012-01-01

Context The clinical syndrome of lumbar spinal stenosis (LSS) is a common diagnosis in older adults presenting with lower extremity pain. Objective To systematically review the accuracy of the clinical examination for the diagnosis of the clinical syndrome of LSS. Data Sources MEDLINE, EMBASE, and CINAHL searches of articles published from January 1966 to September 2010. Study Selection Studies were included if they contained adequate data on the accuracy of the history and physical examination for diagnosing the clinical syndrome of LSS, using a reference standard of expert opinion with radiographic or anatomic confirmation. Data Extraction Two authors independently reviewed each study to determine eligibility, extract data, and appraise levels of evidence. Data Synthesis Four studies evaluating 741 patients were identified. Among patients with lower extremity pain, the likelihood of the clinical syndrome of LSS was increased for individuals older than 70 years (likelihood ratio [LR], 2.0; 95% confidence interval [CI], 1.6–2.5), and was decreased for those younger than 60 years (LR, 0.40; 95% CI, 0.29–0.57). The most useful symptoms for increasing the likelihood of the clinical syndrome of LSS were having no pain when seated (LR, 7.4; 95% CI, 1.9–30), improvement of symptoms when bending forward (LR, 6.4; 95% CI, 4.1–9.9), the presence of bilateral buttock or leg pain (LR, 6.3; 95% CI, 3.1–13), and neurogenic claudication (LR, 3.7; 95% CI, 2.9–4.8). Absence of neurogenic claudication (LR, 0.23; 95% CI, 0.17–0.31) decreased the likelihood of the diagnosis. A wide-based gait (LR, 13; 95% CI, 1.9–95) and abnormal Romberg test result (LR, 4.2; 95% CI, 1.4–13) increased the likelihood of the clinical syndrome of LSS. A score of 7 or higher on a diagnostic support tool including history and examination findings increased the likelihood of the clinical syndrome of LSS (LR, 3.3; 95% CI, 2.7–4.0), while a score lower than 7 made the diagnosis much less likely (LR, 0.10; 95% CI, 0.06–0.16). Conclusions The diagnosis of the clinical syndrome of LSS requires the appropriate clinical picture and radiographic findings. Absence of pain when seated and improvement of symptoms when bending forward are the most useful individual findings. Combinations of findings are most useful for identifying patients who are unlikely to have the diagnosis. PMID:21156951

Tedizolid susceptibility in linezolid- and vancomycin-resistant Enterococcus faecium isolates.

PubMed

Klupp, E-M; Both, A; Belmar Campos, C; Büttner, H; König, C; Christopeit, M; Christner, M; Aepfelbacher, M; Rohde, H

2016-12-01

Vancomycin-resistant enterococci (VRE) are of ever-increasing importance, most notably in high-risk patient populations. Therapy options are often limited for these isolates, and apart from tigecycline and daptomycin, oxazolidinone linezolid is frequently administered. The broad usage of linezolid, however, has driven the emergence of linezolid-resistant VRE strains (LR-VRE), further shortening therapeutic options. Second-generation oxazolidinone tedizolid has the advantage of being active against a specific subset of LR-VRE, i.e. isolates expressing the plasmid-encoded chloramphenicol-florfenicol resistance (cfr) gene. Here we tested tedizolid activity in a collection of 30 LR Enterococcus faecium VRE (MIC range 32-256 mg/l) isolated between 2012 and 2015 from clinical and screening specimens. By pulsed field gel electrophoresis (PFGE) isolates were assigned to 16 clonal lineages. In three cases, linezolid-susceptible progenitor isolates of LR-VRE were isolated, thus demonstrating the de-novo emergence of the linezolid-resistant phenotype. PCR did not detect cfr, cfr(B) or novel oxazolidinone resistance gene optrA in LR-VRE. All isolates, however, carried mutations within the 23S rDNA. Compared to linezolid, tedizolid MICs were lower in all isolates (MIC range 2-32 mg/l), but remained above the FDA tedizolid breakpoint for E. faecalis at 0.5 mg/l. Thus, related to the predominant resistance mechanism, tedizolid is of limited value for treatment of most LR-VRE and represents a therapeutic option only for a limited subset of isolates.

The interactive effects of microcystin-LR and cylindrospermopsin on the growth rate of the freshwater algae Chlorella vulgaris.

PubMed

Pinheiro, Carlos; Azevedo, Joana; Campos, Alexandre; Vasconcelos, Vítor; Loureiro, Susana

2016-05-01

Microcystin-LR (MC-LR) and cylindrospermopsin (CYN) are the most representative cyanobacterial cyanotoxins. They have been simultaneously detected in aquatic systems, but their combined ecotoxicological effects to aquatic organisms, especially microalgae, is unknown. In this study, we examined the effects of these cyanotoxins individually and as a binary mixture on the growth rate of the freshwater algae Chlorella vulgaris. Using the MIXTOX tool, the reference model concentration addition (CA) was selected to evaluate the combined effects of MC-LR and CYN on the growth of the freshwater green algae due to its conservative prediction of mixture effect for putative similar or dissimilar acting chemicals. Deviations from the CA model such as synergism/antagonism, dose-ratio and dose-level dependency were also assessed. In single exposures, our results demonstrated that MC-LR and CYN had different impacts on the growth rates of C. vulgaris at the highest tested concentrations, being CYN the most toxic. In the mixture exposure trial, MC-LR and CYN showed a synergistic deviation from the conceptual model CA as the best descriptive model. MC-LR individually was not toxic even at high concentrations (37 mg L(-1)); however, the presence of MC-LR at much lower concentrations (0.4-16.7 mg L(-1)) increased the CYN toxicity. From these results, the combined exposure of MC-LR and CYN should be considered for risk assessment of mixtures as the toxicity may be underestimated when looking only at the single cyanotoxins and not their combination. This study also represents an important step to understand the interactions among MC-LR and CYN detected previously in aquatic systems.

Effects of microcystin-LR, cylindrospermopsin and a microcystin-LR/cylindrospermopsin mixture on growth, oxidative stress and mineral content in lettuce plants (Lactuca sativa L.).

PubMed

Freitas, Marisa; Azevedo, Joana; Pinto, Edgar; Neves, Joana; Campos, Alexandre; Vasconcelos, Vitor

2015-06-01

Toxic cyanobacterial blooms are documented worldwide as an emerging environmental concern. Recent studies support the hypothesis that microcystin-LR (MC-LR) and cylindrospermopsin (CYN) produce toxic effects in crop plants. Lettuce (Lactuca sativa L.) is an important commercial leafy vegetable that supplies essential elements for human nutrition; thus, the study of its sensitivity to MC-LR, CYN and a MC-LR/CYN mixture is of major relevance. This study aimed to assess the effects of environmentally relevant concentrations (1, 10 and 100 µg/L) of MC-LR, CYN and a MC-LR/CYN mixture on growth, antioxidant defense system and mineral content in lettuce plants. In almost all treatments, an increase in root fresh weight was obtained; however, the fresh weight of leaves was significantly decreased in plants exposed to 100 µg/L concentrations of each toxin and the toxin mixture. Overall, GST activity was significantly increased in roots, contrary to GPx activity, which decreased in roots and leaves. The mineral content in lettuce leaves changed due to its exposure to cyanotoxins; in general, the mineral content decreased with MC-LR and increased with CYN, and apparently these effects are time and concentration-dependent. The effects of the MC-LR/CYN mixture were almost always similar to the single cyanotoxins, although MC-LR seems to be more toxic than CYN. Our results suggest that lettuce plants in non-early stages of development are able to cope with lower concentrations of MC-LR, CYN and the MC-LR/CYN mixture; however, higher concentrations (100 µg/L) can affect both lettuce yield and nutritional quality. Copyright © 2015 Elsevier Inc. All rights reserved.

The Unification Space implemented as a localist neural net: predictions and error-tolerance in a constraint-based parser.

PubMed

Vosse, Theo; Kempen, Gerard

2009-12-01

We introduce a novel computer implementation of the Unification-Space parser (Vosse and Kempen in Cognition 75:105-143, 2000) in the form of a localist neural network whose dynamics is based on interactive activation and inhibition. The wiring of the network is determined by Performance Grammar (Kempen and Harbusch in Verb constructions in German and Dutch. Benjamins, Amsterdam, 2003), a lexicalist formalism with feature unification as binding operation. While the network is processing input word strings incrementally, the evolving shape of parse trees is represented in the form of changing patterns of activation in nodes that code for syntactic properties of words and phrases, and for the grammatical functions they fulfill. The system is capable, at least qualitatively and rudimentarily, of simulating several important dynamic aspects of human syntactic parsing, including garden-path phenomena and reanalysis, effects of complexity (various types of clause embeddings), fault-tolerance in case of unification failures and unknown words, and predictive parsing (expectation-based analysis, surprisal effects). English is the target language of the parser described.

Verification of STS markers for leaf rust resistance genes of wheat by seven European laboratories.

PubMed

Błaszczyk, Lidia; Chełkowski, Jerzy; Korzun, Victor; Kraic, Jan; Ordon, Frank; Ovesná, Jaroslava; Purnhauser, Laszlo; Tar, Melinda; Vida, Gyula

2004-01-01

A set of Thatcher near-isogenic lines and two breeding lines were used to examine sequence tagged site (STS) markers linked to leaf rust resistance genes Lr9, Lr10, Lr19, Lr24, Lr28, Lr29, Lr35, and a simple sequenced repeat (SSR) marker for Lr39. The selected STS markers for resistance genes Lr9, Lr10, Lr19, Lr24 and Lr28 were identified in seven accessions by seven European laboratories. Near-isogenic lines of the spring wheat Thatcher were used as positive controls. Markers for resistance genes Lr9, Lr10, Lr19, Lr24 were identified in all seven laboratories as amplification products of 1100 bp, 310 bp, 130 bp and 310 bp, respectively. The STS markers linked to resistance genes Lr9, Lr10, Lr19, Lr24, Lr29, Lr35 and the SSR marker for Lr39 were robust and highly specific for these genes and will be useful in marker-assisted selection in wheat. However, the amplification product of 378 bp that corresponded with resistance gene Lr28 was detected in all accessions including genotypes lacking this gene in all seven laboratories. This marker needs to be improved.

Microcystin-LR, a protein phosphatase inhibitor, induces alterations in mitotic chromatin and microtubule organization leading to the formation of micronuclei in Vicia faba

PubMed Central

Beyer, Dániel; Tándor, Ildikó; Kónya, Zoltán; Bátori, Róbert; Roszik, Janos; Vereb, György; Erdődi, Ferenc; Vasas, Gábor; M-Hamvas, Márta; Jambrovics, Károly; Máthé, Csaba

2012-01-01

Background and Aims Microcystin-LR (MCY-LR) is a cyanobacterial toxin, a specific inhibitor of type 1 and 2A protein phosphatases (PP1 and PP2A) with significant impact on aquatic ecosystems. It has the potential to alter regulation of the plant cell cycle. The aim of this study was improved understanding of the mitotic alterations induced by cyanotoxin in Vicia faba, a model organism for plant cell biology studies. Methods Vicia faba seedlings were treated over the long and short term with MCY-LR purified in our laboratory. Short-term treatments were performed on root meristems synchronized with hydroxylurea. Sections of lateral root tips were labelled for chromatin, phosphorylated histone H3 and β-tubulin via histochemical and immunohistochemical methods. Mitotic activity and the occurrence of mitotic alterations were detected and analysed by fluorescence microscopy. The phosphorylation state of histone H3 was studied by Western blotting. Key Results Long-term MCY-LR exposure of lateral root tip meristems increased the percentage of either early or late mitosis in a concentration-dependent manner. We observed hypercondensed chromosomes and altered sister chromatid segregation (lagging chromosomes) leading to the formation of micronuclei, accompanied by the formation of disrupted, multipolar and monopolar spindles, disrupted phragmoplasts and the hyperphosphorylation of histone H3 at Ser10. Short-term MCY-LR treatment of synchronized cells showed that PP1 and PP2A inhibition delayed the onset of anaphase at 1 µg mL−1 MCY-LR, accelerated cell cycle at 10 µg mL−1 MCY-LR and induced the formation of lagging chromosomes. In this case mitotic microtubule alterations were not detected, but histone H3 was hyperphosphorylated. Conclusions MCY-LR delayed metaphase–anaphase transition. Consequently, it induced aberrant chromatid segregation and micronucleus formation that could be associated with both H3 hyperphosphorylation and altered microtubule organization. However, these two phenomena seemed to be independent. The toxin may be a useful tool in the study of plant cell cycle regulation. PMID:22819947

Microcystin-LR, a protein phosphatase inhibitor, induces alterations in mitotic chromatin and microtubule organization leading to the formation of micronuclei in Vicia faba.

PubMed

Beyer, Dániel; Tándor, Ildikó; Kónya, Zoltán; Bátori, Róbert; Roszik, Janos; Vereb, György; Erdodi, Ferenc; Vasas, Gábor; M-Hamvas, Márta; Jambrovics, Károly; Máthé, Csaba

2012-09-01

Microcystin-LR (MCY-LR) is a cyanobacterial toxin, a specific inhibitor of type 1 and 2A protein phosphatases (PP1 and PP2A) with significant impact on aquatic ecosystems. It has the potential to alter regulation of the plant cell cycle. The aim of this study was improved understanding of the mitotic alterations induced by cyanotoxin in Vicia faba, a model organism for plant cell biology studies. Vicia faba seedlings were treated over the long and short term with MCY-LR purified in our laboratory. Short-term treatments were performed on root meristems synchronized with hydroxylurea. Sections of lateral root tips were labelled for chromatin, phosphorylated histone H3 and β-tubulin via histochemical and immunohistochemical methods. Mitotic activity and the occurrence of mitotic alterations were detected and analysed by fluorescence microscopy. The phosphorylation state of histone H3 was studied by Western blotting. Long-term MCY-LR exposure of lateral root tip meristems increased the percentage of either early or late mitosis in a concentration-dependent manner. We observed hypercondensed chromosomes and altered sister chromatid segregation (lagging chromosomes) leading to the formation of micronuclei, accompanied by the formation of disrupted, multipolar and monopolar spindles, disrupted phragmoplasts and the hyperphosphorylation of histone H3 at Ser10. Short-term MCY-LR treatment of synchronized cells showed that PP1 and PP2A inhibition delayed the onset of anaphase at 1 µg mL(-1) MCY-LR, accelerated cell cycle at 10 µg mL(-1) MCY-LR and induced the formation of lagging chromosomes. In this case mitotic microtubule alterations were not detected, but histone H3 was hyperphosphorylated. MCY-LR delayed metaphase-anaphase transition. Consequently, it induced aberrant chromatid segregation and micronucleus formation that could be associated with both H3 hyperphosphorylation and altered microtubule organization. However, these two phenomena seemed to be independent. The toxin may be a useful tool in the study of plant cell cycle regulation.

A new leaf rust resistance gene Lr79 mapped in chromosome 3BL from the durum wheat landrace Aus26582.

PubMed

Qureshi, Naeela; Bariana, Harbans; Kumran, Vikas Venu; Muruga, Sivasamy; Forrest, Kerrie L; Hayden, Mathew J; Bansal, Urmil

2018-05-01

A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection. Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3. LrAW2 was located in chromosome 6BS and this study focused on characterisation of LrAW3 using RILs lacking LrAW2. LrAW3 was incorporated into the DArTseq map of Aus26582/Bansi and was located in chromosome 3BL. Markers linked with LrAW3 were developed from the chromosome survey sequence contig 3B_10474240 in which closely-linked DArTseq markers 1128708 and 3948563 were located. Although bulk segregant analysis (BSA) with the 90 K Infinium array identified 51 SNPs associated with LrAW3, only one SNP-derived KASP marker mapped close to the locus. Deletion bin mapping of LrAW3-linked markers located LrAW3 between bins 3BL11-0.85-0.90 and 3BL7-0.63. Since no other all stage leaf rust resistance gene is located in chromosome 3BL, LrAW3 represented a new locus and was designated Lr79. Marker sun786 mapped 1.8 cM distal to Lr79 and Aus26582 was null for this locus. However, the marker can be reliably scored as it also amplifies a monomorphic fragment that serves as an internal control to differentiate the null status of Aus26582 from reaction failure. This marker was validated among a set of durum and common wheat cultivars and was shown to be useful for marker-assisted selection of Lr79 at both ploidy levels.

Removal of cyanotoxins from surface water resources using reusable molecularly imprinted polymer adsorbents.

PubMed

Krupadam, Reddithota J; Patel, Govind P; Balasubramanian, Rajasekhar

2012-06-01

Microcystins (MCs; cyclic heptapeptides) are produced by freshwater cyanobacteria and cause public health concern in potable water supplies. There are more than 60 types of MCs identified to date, of which MC-LR is the most common found worldwide. For MC-LR, the WHO has established a threshold value of 1 μg L(-1) for drinking water. The present MCs removal methods such as coagulation, flocculation, adsorption, and filtration showed low efficiency for removing dissolved MC fraction from surface waters to the stipulated limit prescribed by WHO based on MC health impacts. The search for cost-effective and efficient removal method is still warranted for remediation of dissolved MC-LR-contaminated water resources. Molecularly imprinted polymer (MIP) adsorbent has been prepared using non-covalent imprinting approach. Using MC-LR as a template, itaconic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linking monomer, a MIP has been synthesized. Computer simulations were used to design effective binding sites for MC-LR binding in aqueous solutions. Batch binding adsorption assay was followed to determine binding capacity of MIP under the influence of environmental parameters such as total dissolved solids and pH. The adsorptive removal of MC-LR from lake water has been investigated using MIPs. The MIP showed excellent adsorption potential toward MC-LR in aqueous solutions with a binding capacity of 3.64 μg mg(-1) which is about 60% and 70% more than the commercially used powdered activated carbon (PAC) and resin XAD, respectively. Environmental parameters such as total organic carbon (represented as chemical oxygen demand (COD)) and total dissolved solids (TDS) showed no significant interference up to 300 mg L(-1) for MC-LR removal from lake water samples. It was found that the binding sites on PAC and XAD have more affinity toward COD and TDS than the MC-LR. Further, the adsorption capacity of the MIP was evaluated rigorously by its repeated contact with fresh lake water, and it was found that the adsorption capacity of the MIP did not change even after seven adsorption/desorption cycles. The contaminated water of MC-LR (1.0 μg L(-1)) of 3,640 L could be treated by 1 g of MIP with an estimated cost of US $1.5. The adsorption capacity of the MIP is 40% more than commercially used PAC and resins and also the polymer showed reusable potential which is one of the important criteria in selection of cyanotoxins remediation methods.

IgG1-iS18 impedes the adhesive and invasive potential of early and late stage malignant melanoma cells.

PubMed

Munien, Carmelle; Rebelo, Thalia M; Ferreira, Eloise; Weiss, Stefan F T

2017-02-15

The 37kDa/67kDa laminin receptor (LRP/LR) is a non-integrin laminin receptor which is overexpressed in tumorigenic cells and supports progression of cancer via promoting metastasis, angiogenesis and telomerase activity and impediment of apoptosis. The present study investigates the role of LRP/LR on the metastatic potential of early (A375) and late (A375SM) stage malignant melanoma cells. Flow cytometry revealed that both early and late stage malignant melanoma cells display high levels of LRP/LR on their cell surface. Flow cytometry and western blot analysis showed that late stage malignant melanoma cells display significantly higher total and cell surface LRP/LR levels in comparison to early stage malignant melanoma cells and the poorly invasive breast cancer (MCF-7) control cell line. Targeting LRP/LR using the LRP/LR specific antibody IgG1-iS18 resulted in a significant reduction of the adhesive potential to laminin-1 and the invasive potential through the 'ECM-simulating' Matrigel™ of both early and late stage malignant melanoma cells. Furthermore, Pearson's correlation coefficient confirmed that increased LRP levels correlate with the increased invasive and adhesive potential in early and late stage melanoma cells. Thus, blocking LRP/LR using the IgG1-iS18 antibody may therefore be a promising therapeutic strategy for early and late stage malignant melanoma treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

pLR: a lentiviral backbone series to stable transduction of bicistronic genes and exchange of promoters.

PubMed

Vargas, José Eduardo; Salton, Gabrielle; Sodré de Castro Laino, Andressa; Pires, Tiago Dalberto; Bonamino, Martin; Lenz, Guido; Delgado-Cañedo, Andrés

2012-11-01

Gene transfer based on lentiviral vectors allow the integration of exogenous genes into the genome of a target cell, turning these vectors into one of the most used methods for stable transgene expression in mammalian cells, in vitro and in vivo. Currently, there are no lentivectors that allow the cloning of different genes to be regulated by different promoters. Also, there are none that permit the analysis of the expression through an IRES (internal ribosome entry site)-- reporter gene system. In this work, we have generated a series of lentivectors containing: (1) a malleable structure to allow the cloning of different target genes in a multicloning site (mcs); (2) unique site to exchange promoters, and (3) IRES followed by one of two reporter genes: eGFP or DsRed. The series of the produced vectors were named pLR (for lentivirus and RSV promoter) and were fairly efficient with a strong fluorescence of the reporter genes in direct transfection and viral transduction experiments. This being said, the pLR series have been found to be powerful biotechnological tools for stable gene transfer and expression. Copyright © 2012 Elsevier Inc. All rights reserved.

Estrogenic potency of MC-LR is induced via stimulating steroidogenesis: In vitro and in vivo evidence.

PubMed

Hou, Jie; Su, Yujing; Lin, Wang; Guo, Honghui; Li, Li; Anderson, Donald M; Li, Dapeng; Tang, Rong; Chi, Wei; Zhang, Xi

2018-05-14

Waterborne microcystin-LR (MC-LR) has been reported to disrupt sex hormones, while its estrogenic potency remains controversial. We hypothesized that MC-LR could induce estrogenic effects via disrupting sex hormone synthesis, and verified this hypothesis by in vitro and in vivo assays. Effects of MC-LR (1, 10, 100, 500, 1000 and 5000 μg/L) on steroidogenesis were assessed in the H295R cells after 48 h. The contents of 17β-estradiol (E2) and testosterone (T) increased in a non-dose-dependent manner, which showed positive correlations with the expression of steroidogenic genes. In the in vivo assay, adult male zebrafish were exposed to 0.3, 1, 3, 10 and 30 μg/L MC-LR for 30 d. Similarly, E2 and T contents in the testis were increased, accompanied by extensive up-regulation of steroidogenic genes, especially cyp19a. Meanwhile, the percentage of spermatid in the testis declined. In the liver, the vtg1 gene was significantly up-regulated while both the transcriptional and protein levels of the estrogenic receptor (ER) declined. These results indicate that MC-LR induced non-dose-dependent estrogenic effects at environmental concentrations, which may result from steroidogenesis stimulation via a non-ER-mediated pathway. Our findings support a paradigm shift in the risk assessment of MC-LR from traditional toxicity to estrogenic risk, particularly at low concentrations, and emphasize the potential threat to the male reproductive capacity of wildlife in bloom areas. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microcystin-LR Induced Reactive Oxygen Species Mediate Cytoskeletal Disruption and Apoptosis of Hepatocytes in Cyprinus carpio L.

PubMed Central

Jiang, Jinlin; Shan, Zhengjun; Xu, Weili; Wang, Xiaorong; Zhou, Junying; Kong, Deyang; Xu, Jing

2013-01-01

Microcystins (MCs) are a group of cyclic hepatotoxic peptides produced by cyanobacteria. Microcystin-LR (MC-LR) contains Leucine (L) and Arginine (R) in the variable positions, and is one of the most common and potently toxic peptides. MC-LR can inhibit protein phosphatase type 1 and type 2A (PP1 and PP2A) activities and induce excessive production of reactive oxygen species (ROS). The underlying mechanism of the inhibition of PP1 and PP2A has been extensively studied. The over-production of ROS is considered to be another main mechanism behind MC-LR toxicity; however, the detailed toxicological mechanism involved in over-production of ROS in carp (Cyprinus carpio L.) remains largely unclear. In our present study, the hydroxyl radical (•OH) was significantly induced in the liver of carp after a relatively short-term exposure to MC-LR. The elevated reactive oxygen species (ROS) production may play an important role in the disruption of microtubule structure. Pre-injection of the antioxidant N-acetyl-cysteine (NAC) provided significant protection to the cytoskeleton, however buthionine sulfoximine (BSO) exacerbated cytoskeletal destruction. In addition, the elevated ROS formation induced the expression of apoptosis-related genes, including p38, JNKa, and bcl-2. A significant increase in apoptotic cells was observed at 12 - 48 hours. Our study further supports evidence that ROS are involved in MC-LR induced damage to liver cells in carp, and indicates the need for further study of the molecular mechanisms behind MC-LR toxicity. PMID:24376844

Does this adult patient have a blunt intra-abdominal injury?

PubMed

Nishijima, Daniel K; Simel, David L; Wisner, David H; Holmes, James F

2012-04-11

Blunt abdominal trauma often presents a substantial diagnostic challenge. Well-informed clinical examination can identify patients who require further diagnostic evaluation for intra-abdominal injuries after blunt abdominal trauma. To systematically assess the precision and accuracy of symptoms, signs, laboratory tests, and bedside imaging studies to identify intra-abdominal injuries in patients with blunt abdominal trauma. We conducted a structured search of MEDLINE (1950-January 2012) and EMBASE (1980-January 2012) to identify English-language studies examining the identification of intra-abdominal injuries. A separate, structured search was conducted for studies evaluating bedside ultrasonography. We included studies of diagnostic accuracy for intra-abdominal injury that compared at least 1 finding with a reference standard of abdominal computed tomography, diagnostic peritoneal lavage, laparotomy, autopsy, and/or clinical course for intra-abdominal injury. Twelve studies on clinical findings and 22 studies on bedside ultrasonography met inclusion criteria for data extraction. Critical appraisal and data extraction were independently performed by 2 authors. The prevalence of intra-abdominal injury in adult emergency department patients with blunt abdominal trauma among all evidence level 1 and 2 studies was 13% (95% CI, 10%-17%), with 4.7% (95% CI, 2.5%-8.6%) requiring therapeutic surgery or angiographic embolization of injuries. The presence of a seat belt sign (likelihood ratio [LR] range, 5.6-9.9), rebound tenderness (LR, 6.5; 95% CI, 1.8-24), hypotension (LR, 5.2; 95% CI, 3.5-7.5), abdominal distention (LR, 3.8; 95% CI, 1.9-7.6), or guarding (LR, 3.7; 95% CI, 2.3-5.9) suggest an intra-abdominal injury. The absence of abdominal tenderness to palpation does not rule out an intra-abdominal injury (summary LR, 0.61; 95% CI, 0.46-0.80). The presence of intraperitoneal fluid or organ injury on bedside ultrasound assessment is more accurate than any history and physical examination findings (adjusted summary LR, 30; 95% CI, 20-46); conversely, a normal ultrasound result decreases the chance of injury detection (adjusted summary LR, 0.26; 95% CI, 0.19-0.34). Test results increasing the likelihood of intra-abdominal injury include a base deficit less than -6 mEq/L (LR, 18; 95% CI, 11-30), elevated liver transaminases (LR range, 2.5-5.2), hematuria (LR range, 3.7-4.1), anemia (LR range, 2.2-3.3), and abnormal chest radiograph (LR range, 2.5-3.8). Symptoms and signs may be most useful in combination, particularly in identification of patients who do not need further diagnostic workup. Bedside ultrasonography has the highest accuracy of all individual findings, but a normal result does not rule out an intra-abdominal injury. Combinations of clinical findings may be most useful to determine which patients do not require further evaluation, but the ideal combination of variables for identifying patients without intra-abdominal injury requires further study.

Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory.

PubMed

Zhang, Long; Zhou, Qing-Xin; Song, Man; Chen, Xiao-Long; Xu, Xi-Hui; Chen, Kai; Li, Shun-Peng; Jiang, Jian-Dong

2015-12-01

Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).

Contrast ultrasound LI-RADS LR-5 identifies hepatocellular carcinoma in cirrhosis in a multicenter restropective study of 1,006 nodules.

PubMed

Terzi, Eleonora; Iavarone, Massimo; Pompili, Maurizio; Veronese, Letizia; Cabibbo, Giuseppe; Fraquelli, Mirella; Riccardi, Laura; De Bonis, Ludovico; Sangiovanni, Angelo; Leoni, Simona; Zocco, Maria Assunta; Rossi, Sandro; Alessi, Nicola; Wilson, Stephanie R; Piscaglia, Fabio

2018-03-01

The use of contrast enhanced ultrasound (CEUS) for the diagnosis of hepatocellular carcinoma (HCC) in cirrhosis was questioned because of the risk of a false positive diagnosis in cases of cholangiocarcinoma. The American College of Radiology has recently released a scheme (CEUS Liver Imaging Reporting and Data System [LI-RADS®]) to classify lesions at risk of HCC investigated by CEUS. The aim of the present study was to validate this LI-RADS scheme for the diagnosis of HCC. A total of 1,006 nodules from 848 patients with chronic liver disease at risk of HCC were collected in five Italian centers and retrospectively analyzed. Nodules were classified as LR-5, (HCC) if ≥1 cm with arterial phase hyperenhancement, and late washout (onset ≥60 s after contrast injection) of mild degree. Rim enhancement and/or early and/or marked washout qualified lesions as LR-M (malignant, but not specific for HCC). Other combinations qualified lesions at intermediate risk for HCC (LR-3) or probable HCC (LR-4). Diagnostic reference standard was CT/MRI diagnosis of HCC (n = 506) or histology (n = 500). The median nodule size was 2 cm. Of 1,006 nodules, 820 (81%) were HCC, 40 (4%) were cholangiocarcinoma, 116 (11%) regenerative nodules (±dysplastic). The LR-5 category (52% of all nodules) was 98.5% predictive of HCC, with no risk of misdiagnosis for pure cholangiocarcinoma. Sensitivity for HCC was 62%. All LR-M nodules were malignant and the majority of non-hepatocellular origin. Over 75% of cholangiocarcinomas were LR-M. The LR-3 category included 203 lesions (HCC 96 [47%]) and the LR-4 202 (HCC 173 [87%]). The CEUS LI-RADS class LR-5 is highly specific for HCC, enabling its use for a confident non-invasive diagnosis. This is a retrospective study of approximately 1,000 focal lesions at risk for hepatocellular carcinoma (HCC). Herein, we demonstrate that the refined definition of the typical contrast enhanced ultrasound pattern of HCC introduced by the Liver Imaging Reporting and Data System (LI-RADS®) practically abolishes the risk of misdiagnosis of other malignant entities (e.g. cholangiocarcinoma) for HCC with negligible reduction in sensitivity. These data support the use of contrast enhanced ultrasound to diagnose HCC in cirrhosis. Copyright © 2017 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Microcystin-leucine arginine mediates apoptosis and engulfment of Leydig cell by testicular macrophages resulting in reduced serum testosterone levels.

PubMed

Chen, Yabing; Wang, Jing; Chen, Xiang; Li, Dongmei; Han, Xiaodong

2018-06-01

Microcystin-leucine arginine (MC-LR) causes decline of serum testosterone levels resulting in impaired spermatogenesis; however, the underlying molecular mechanisms are not fully understood. In this study, we aimed to investigate the effects of MC-LR exposure on the number of Leydig cells (LCs) in testis. Following chronic low dose exposure to MC-LR, the number of LCs was markedly decreased while macrophages were significantly increased. Then, we established a co-culture system to study the interaction between macrophages and LCs in the presence of MC-LR. No significant apoptosis of LCs cultured alone was observed after MC-LR (< 5 000 nM) treatment; however, apoptosis was robustly increased when LCs were co-cultured with macrophages in the presence of MC-LR. Further studies identified that MC-LR could stimulate macrophage to produce TNF-α, and secreted TNF-α induced LC apoptosis by binding to the tumor necrosis factor receptor 1 (TNFR1) on the LCs and thus activating reactive oxygen species (ROS)-p38MAPK signaling pathway. Furthermore, we also examined increased expression of Axl receptor and growth arrest-specific 6 (Gas6) in macrophages after MC-LR treatment. GAS6 mediates phagocytosis of apoptotic LCs by binding to the Axl receptor on macrophages and phosphatidylserine (PtdSer) on apoptotic LCs. Together, these results suggested that reduced serum testosterone levels may be associated with decrease of LCs as a result of LC apoptosis and phagocytosis by immune cells in MC-LR-treated mice. Copyright © 2018 Elsevier B.V. All rights reserved.

Likelihood ratios for the prediction of preterm delivery with biomarkers.

PubMed

Hee, Lene

2011-11-01

To conduct a literature search for selected biomarkers on preterm delivery and estimate their likelihood ratios (LR). Structured review. Low and high-risk populations and women with symptoms of preterm delivery. METHODS. Publications were identified in PubMed. LR on selected biomarkers for preterm delivery. In asymptomatic women with low risk of preterm delivery, the following biomarkers gave major shifts in probability (LR above 5): twins (LR+ 10), Ureaplasma urealyticum in amniotic fluid (LR+ of 10), cervical length <25mm (LR+ 6), salival estriol (LR+ 5) and various combined tests. In asymptomatic women with high risk of preterm delivery, short cervical length (LR+ 11, LR- 0.7), high serum tumor necrosis factor-alpha (LR+ 10, LR- 0.6) gave major shifts in probability. In women with symptoms of preterm delivery, major shifts in probability can be obtained from the following amniotic fluid biomarkers: high matrix metalloproteinase-8 (LR+ 23, LR- 0.6), Ureaplasma urealyticum (LR+ 19, LR- 0.8), high interleukin (IL)-6 (LR+ 9, LR- 0.2), IL-8 (LR+10, LR- 0.2) and tumor necrosis factor-alpha (LR+ 8, LR- 0.4). In serum IL-6 (LR+ 12, LR- 0.2), Cluster of Differentiation 163 (LR+9, LR-0.8) and various combined tests. Vaginal fetal fibronectin (LR+ 3 and LR- 0.5) and short cervical length (LR+ 2, LR- 0.3) gave LRs of some importance (LR below 5). Several biomarkers have been identified for assessment of risk of preterm delivery. Their clinical relevance depends on the efficacy of the interventions which can be offered to these patients. © 2011 The Author Acta Obstetricia et Gynecologica Scandinavica© 2011 Nordic Federation of Societies of Obstetrics and Gynecology.

Pre-operative prediction of surgical morbidity in children: comparison of five statistical models.

PubMed

Cooper, Jennifer N; Wei, Lai; Fernandez, Soledad A; Minneci, Peter C; Deans, Katherine J

2015-02-01

The accurate prediction of surgical risk is important to patients and physicians. Logistic regression (LR) models are typically used to estimate these risks. However, in the fields of data mining and machine-learning, many alternative classification and prediction algorithms have been developed. This study aimed to compare the performance of LR to several data mining algorithms for predicting 30-day surgical morbidity in children. We used the 2012 National Surgical Quality Improvement Program-Pediatric dataset to compare the performance of (1) a LR model that assumed linearity and additivity (simple LR model) (2) a LR model incorporating restricted cubic splines and interactions (flexible LR model) (3) a support vector machine, (4) a random forest and (5) boosted classification trees for predicting surgical morbidity. The ensemble-based methods showed significantly higher accuracy, sensitivity, specificity, PPV, and NPV than the simple LR model. However, none of the models performed better than the flexible LR model in terms of the aforementioned measures or in model calibration or discrimination. Support vector machines, random forests, and boosted classification trees do not show better performance than LR for predicting pediatric surgical morbidity. After further validation, the flexible LR model derived in this study could be used to assist with clinical decision-making based on patient-specific surgical risks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sparse Representations-Based Super-Resolution of Key-Frames Extracted from Frames-Sequences Generated by a Visual Sensor Network

PubMed Central

Sajjad, Muhammad; Mehmood, Irfan; Baik, Sung Wook

2014-01-01

Visual sensor networks (VSNs) usually generate a low-resolution (LR) frame-sequence due to energy and processing constraints. These LR-frames are not very appropriate for use in certain surveillance applications. It is very important to enhance the resolution of the captured LR-frames using resolution enhancement schemes. In this paper, an effective framework for a super-resolution (SR) scheme is proposed that enhances the resolution of LR key-frames extracted from frame-sequences captured by visual-sensors. In a VSN, a visual processing hub (VPH) collects a huge amount of visual data from camera sensors. In the proposed framework, at the VPH, key-frames are extracted using our recent key-frame extraction technique and are streamed to the base station (BS) after compression. A novel effective SR scheme is applied at BS to produce a high-resolution (HR) output from the received key-frames. The proposed SR scheme uses optimized orthogonal matching pursuit (OOMP) for sparse-representation recovery in SR. OOMP does better in terms of detecting true sparsity than orthogonal matching pursuit (OMP). This property of the OOMP helps produce a HR image which is closer to the original image. The K-SVD dictionary learning procedure is incorporated for dictionary learning. Batch-OMP improves the dictionary learning process by removing the limitation in handling a large set of observed signals. Experimental results validate the effectiveness of the proposed scheme and show its superiority over other state-of-the-art schemes. PMID:24566632

Sparse representations-based super-resolution of key-frames extracted from frames-sequences generated by a visual sensor network.

PubMed

Sajjad, Muhammad; Mehmood, Irfan; Baik, Sung Wook

2014-02-21

Visual sensor networks (VSNs) usually generate a low-resolution (LR) frame-sequence due to energy and processing constraints. These LR-frames are not very appropriate for use in certain surveillance applications. It is very important to enhance the resolution of the captured LR-frames using resolution enhancement schemes. In this paper, an effective framework for a super-resolution (SR) scheme is proposed that enhances the resolution of LR key-frames extracted from frame-sequences captured by visual-sensors. In a VSN, a visual processing hub (VPH) collects a huge amount of visual data from camera sensors. In the proposed framework, at the VPH, key-frames are extracted using our recent key-frame extraction technique and are streamed to the base station (BS) after compression. A novel effective SR scheme is applied at BS to produce a high-resolution (HR) output from the received key-frames. The proposed SR scheme uses optimized orthogonal matching pursuit (OOMP) for sparse-representation recovery in SR. OOMP does better in terms of detecting true sparsity than orthogonal matching pursuit (OMP). This property of the OOMP helps produce a HR image which is closer to the original image. The K-SVD dictionary learning procedure is incorporated for dictionary learning. Batch-OMP improves the dictionary learning process by removing the limitation in handling a large set of observed signals. Experimental results validate the effectiveness of the proposed scheme and show its superiority over other state-of-the-art schemes.

Completion of the Viking Labeled Release experiment on Mars

NASA Technical Reports Server (NTRS)

Levin, G. V.; Straat, P. A.

1979-01-01

The final Labeled Release (LR) cycle on each Viking lander tested a surface sample that had been stored for several months at approximately 10 C prior to the onset of the active sequence. At each lander site, activity was strongly diminished. This thermal sensitivity of the active agent on the surface of Mars is consistent with a biological explanation of the LR experiment. At the end of one of these cycles, the incubation mixture was heated to 50 C to release any radioactive gas trapped in the sample matrix. The results suggest that more than one carbon substrate is involved in the LR reaction on Mars. The thermal data from the stored samples, coupled with data from previous cycles, have formed the basis for evaluation of the thermal decomposition of the Mars active agent. The slope of the resulting Arrhenius plot has been used to test the fit of other flight data and to calculate the activation energy for thermal decomposition of the Mars agent. The results and their interpretation still leave unresolved the question of whether the Mars LR data were generated by biological or chemical activity.

Completion of the Viking labeled release experiment on Mars.

PubMed

Levin, G V; Straat, P A

1979-12-01

The final Labeled Release (LR) cycle on each Viking lander tested a surface sample that had been stored for several months at approximately 10 degrees C prior to the onset of the active sequence. At each lander site, activity was strongly diminished. This thermal sensitivity of the active agent on the surface of Mars is consistent with a biological explanation of the LR experiment. At the end of one of these cycles, the incubation mixture was heated to 50 degrees C to release any radioactive gas trapped in the sample matrix. The results suggest that more than one carbon substrate is involved in the LR reaction on Mars. The thermal data from the stored samples, coupled with data from previous cycles, have formed the basis for evaluation of the thermal decomposition of the Mars active agent. The slope of the resulting Arrhenius plot has been used to test the fit of other flight data and to calculate the activation energy for thermal decomposition of the Mars agent. The results and their interpretation still leave unresolved the question of whether the Mars LR data were generated by biological or chemical activity.

Degradation of microcystin-LR by highly efficient AgBr/Ag3PO4/TiO2 heterojunction photocatalyst under simulated solar light irradiation

NASA Astrophysics Data System (ADS)

Wang, Xin; Utsumi, Motoo; Yang, Yingnan; Li, Dawei; Zhao, Yingxin; Zhang, Zhenya; Feng, Chuanping; Sugiura, Norio; Cheng, Jay Jiayang

2015-01-01

A novel photocatalyst AgBr/Ag3PO4/TiO2 was developed by a simple facile in situ deposition method and used for degradation of mirocystin-LR. TiO2 (P25) as a cost effective chemical was used to improve the stability of AgBr/Ag3PO4 under simulated solar light irradiation. The photocatalytic activity tests for this heterojunction were conducted under simulated solar light irradiation using methyl orange as targeted pollutant. The results indicated that the optimal Ag to Ti molar ratio for the photocatalytic activity of the resulting heterojunction AgBr/Ag3PO4/TiO2 was 1.5 (named as 1.5 BrPTi), which possessed higher photocatalytic capacity than AgBr/Ag3PO4. The 1.5 BrPTi heterojunction was also more stable than AgBr/Ag3PO4 in photocatalysis. This highly efficient and relatively stable photocatalyst was further tested for degradation of the hepatotoxin microcystin-LR (MC-LR). The results suggested that MC-LR was much more easily degraded by 1.5 BrPTi than by AgBr/Ag3PO4. The quenching effects of different scavengers proved that reactive h+ and •OH played important roles for MC-LR degradation.

77 FR 6150 - Notice of Sunshine Act Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-07

... Status of Outreach and Educational Efforts with External Stakeholders Related to the Safety Culture...). a. Entergy Nuclear Generation Co. and Entergy Nuclear Operations, Inc (Pilgrim Nuclear Power Station). Docket No. 50-293-LR (Tentative). b. Southern Nuclear Operating Co. (Vogtle Electric Generating Plant...

In Vitro Evaluation of Swine-Derived Lactobacillus reuteri: Probiotic Properties and Effects on Intestinal Porcine Epithelial Cells Challenged with Enterotoxigenic Escherichia coli K88.

PubMed

Wang, Zhilin; Wang, Li; Chen, Zhuang; Ma, Xianyong; Yang, Xuefen; Zhang, Jian; Jiang, Zongyong

2016-06-28

Probiotics are considered as the best effective alternatives to antibiotics. The aim of this study was to characterize the probiotic potential of lactobacilli for use in swine farming by using in vitro evaluation methods. A total of 106 lactic acid bacterial isolates, originating from porcine feces, were first screened for the capacity to survive stresses considered important for putative probiotic strains. Sixteen isolates showed notable acid and bile resistance, antibacterial activity, and adherence to intestinal porcine epithelial cells (IPEC-1). One isolate, LR1, identified as Lactobacillus reuteri, was selected for extensive study of its probiotic and functional properties in IPEC-1 cell models. L. reuteri LR1 exhibited good adhesion to IPEC-1 cells and could inhibit the adhesion of enterotoxigenic Escherichia coli (ETEC) to IPEC-1 cells. L. reuteri LR1 could also modulate transcript and protein expression of cytokines involved in inflammation in IPEC-1 cells; the Lactobacillus strain inhibited the ETEC-induced expression of proinflammatory transcripts (IL-6 and TNF-α) and protein (IL-6), and increased the level of anti-inflammatory cytokine (IL-10). Measurement of the permeation of FD-4 showed that L. reuteri LR1 could maintain barrier integrity in monolayer IPEC-1 cells exposed to ETEC. Immunolocalization experiments showed L. reuteri LR1 could also prevent ETEC-induced tight junction ZO-1 disruption. Together, these results indicate that L. reuteri LR1 exhibits desirable probiotic properties and could be a potential probiotic for use in swine production.

Liver Resection versus Radiofrequency Ablation plus Transcatheter Arterial Chemoembolization in Cirrhotic Patients with Solitary Large Hepatocellular Carcinoma.

PubMed

Saviano, Antonio; Iezzi, Roberto; Giuliante, Felice; Salvatore, Lucia; Mele, Caterina; Posa, Alessandro; Ardito, Francesco; De Gaetano, Anna Maria; Pompili, Maurizio

2017-11-01

To compare liver resection (LR) with single-step, balloon-occluded radiofrequency (RF) ablation plus drug-eluting embolics transarterial chemoembolization in cirrhotic patients with single hepatocellular carcinoma (HCC) ≥ 3 cm. From 2010 to 2014, 25 patients with compensated cirrhosis and single HCC ≥ 3 cm (median size 4.5 cm; range, 3.0-6.8 cm) not suitable for LR or liver transplantation were treated with RF ablation plus transarterial chemoembolization in a prospective observational single-center pilot study; all patients had complete tumor necrosis after treatment. A retrospective control group included 29 patients (median HCC size 4.0 cm; range, 3.0-7.4 cm) who underwent LR. RF ablation plus transarterial chemoembolization group included more patients with severe portal hypertension (65.5% vs 35.0%, P = .017). Primary endpoints were overall survival (OS) and tumor recurrence (TR) rates. One death and 1 major complication (4%) were observed in LR group. No major complications were reported in RF ablation plus transarterial chemoembolization group (P = .463). OS rates at 1 and 3 years were 91.8% and 79.3% in LR group and 89.4% and 48.2% in RF ablation plus transarterial chemoembolization group (P = 0.117). TR rates at 1 and 3 years were 29.5% and 45.0% in LR group and 42.4% and 76.0% in RF ablation plus transarterial chemoembolization group (P = .034). Local tumor progression (LTP) rates at 3 years were significantly lower in LR group (21.8% vs 58.1%, P = .005). Similar results were found in patients with HCC ≤ 5 cm (TR rates 35.4% vs 75.1%, P = .016; LTP 16.0% vs 55.7%, P = .013). LR achieved lower TR and LTP rates than RF ablation plus transarterial chemoembolization, but 3-years OS rates were not statistically different between the 2 groups. RF ablation plus transarterial chemoembolization is an effective treatment option in patients with compensated cirrhosis and solitary HCC ≥ 3 cm unsuitable for LR. Copyright © 2017 SIR. Published by Elsevier Inc. All rights reserved.

Prevalence of Low Cardiovascular Risk Profile Among Diverse Hispanic/Latino Adults in the United States by Age, Sex, and Level of Acculturation: The Hispanic Community Health Study/Study of Latinos.

PubMed

Daviglus, Martha L; Pirzada, Amber; Durazo-Arvizu, Ramon; Chen, Jinsong; Allison, Matthew; Avilés-Santa, Larissa; Cai, Jianwen; González, Hector M; Kaplan, Robert C; Schneiderman, Neil; Sorlie, Paul D; Talavera, Gregory A; Wassertheil-Smoller, Sylvia; Stamler, Jeremiah

2016-08-20

Favorable levels of all readily measurable major cardiovascular disease risk factors (ie, low risk [LR]) are associated with lower risks of cardiovascular disease morbidity and mortality. Data are not available on LR prevalence among Hispanic/Latino adults of diverse ethnic backgrounds. This study aimed to describe the prevalence of a low cardiovascular disease risk profile among Hispanic/Latino adults in the United States and to examine cross-sectional associations of LR with measures of acculturation. The multicenter, prospective, population-based Hispanic Community Health Study/Study of Latinos examined 16 415 men and women aged 18 to 74 years at baseline (2008-2011) with diverse Hispanic/Latino backgrounds. Analyses involved 14 757 adults (mean age 41.3 years; 60.6% women). LR was defined using national guidelines for favorable levels of serum cholesterol, blood pressure, and body mass index and by not having diabetes mellitus and not currently smoking. Age-adjusted LR prevalence was low (8.4% overall; 5.1% for men, 11.2% for women) and varied by background (4.2% in men of Mexican heritage versus 15.0% in women of Cuban heritage). Lower acculturation (assessed using proxy measures) was significantly associated with higher odds of a LR profile among women only: Age-adjusted odds ratios of having LR were 1.64 (95% CI 1.24-2.17) for foreign-born versus US-born women and 1.96 (95% CI 1.49-2.58) for women residing in the United States <10 versus ≥10 years. Among diverse US Hispanic/Latino adults, the prevalence of a LR profile is low. Lower acculturation is associated with higher odds of a LR profile among women but not men. Comprehensive public health strategies are needed to improve the cardiovascular health of US Hispanic/Latino adults. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Kupffer's vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left-right development of the brain, heart and gut.

PubMed

Essner, Jeffrey J; Amack, Jeffrey D; Nyholm, Molly K; Harris, Erin B; Yost, H Joseph

2005-03-01

Monocilia have been proposed to establish the left-right (LR) body axis in vertebrate embryos by creating a directional fluid flow that triggers asymmetric gene expression. In zebrafish, dorsal forerunner cells (DFCs) express a conserved ciliary dynein gene (left-right dynein-related1, lrdr1) and form a ciliated epithelium inside a fluid-filled organ called Kupffer's vesicle (KV). Here, videomicroscopy demonstrates that cilia inside KV are motile and create a directional fluid flow just prior to the onset of asymmetric gene expression in lateral cells. Laser ablation of DFCs and surgical disruption of KV provide direct evidence that ciliated KV cells are required during early somitogenesis for subsequent LR patterning in the brain, heart and gut. Antisense morpholinos against lrdr1 disrupt KV fluid flow and perturb LR development. Furthermore, lrdr1 morpholinos targeted to DFC/KV cells demonstrate that Lrdr1 functions in these ciliated cells to control LR patterning. This provides the first direct evidence, in any vertebrate, that impairing cilia function in derivatives of the dorsal organizer, and not in other cells that express ciliogenic genes, alters LR development. Finally, genetic analysis reveals novel roles for the T-box transcription factor no tail and the Nodal signaling pathway as upstream regulators of lrdr1 expression and KV morphogenesis. We propose that KV is a transient embryonic 'organ of asymmetry' that directs LR development by establishing a directional fluid flow. These results suggest that cilia are an essential component of a conserved mechanism that controls the transition from bilateral symmetry to LR asymmetry in vertebrates.

Refined estimates of local recurrence risks by DCIS score adjusting for clinicopathological features: a combined analysis of ECOG-ACRIN E5194 and Ontario DCIS cohort studies.

PubMed

Rakovitch, E; Gray, R; Baehner, F L; Sutradhar, R; Crager, M; Gu, S; Nofech-Mozes, S; Badve, S S; Hanna, W; Hughes, L L; Wood, W C; Davidson, N E; Paszat, L; Shak, S; Sparano, J A; Solin, L J

2018-06-01

Better tools are needed to estimate local recurrence (LR) risk after breast-conserving surgery (BCS) for DCIS. The DCIS score (DS) was validated as a predictor of LR in E5194 and Ontario DCIS cohort (ODC) after BCS. We combined data from E5194 and ODC adjusting for clinicopathological factors to provide refined estimates of the 10-year risk of LR after treatment by BCS alone. Data from E5194 and ODC were combined. Patients with positive margins or multifocality were excluded. Identical Cox regression models were fit for each study. Patient-specific meta-analysis was used to calculate precision-weighted estimates of 10-year LR risk by DS, age, tumor size and year of diagnosis. The combined cohort includes 773 patients. The DS and age at diagnosis, tumor size and year of diagnosis provided independent prognostic information on the 10-year LR risk (p ≤ 0.009). Hazard ratios from E5194 and ODC cohorts were similar for the DS (2.48, 1.95 per 50 units), tumor size ≤ 1 versus  > 1-2.5 cm (1.45, 1.47), age ≥ 50 versus < 50 year (0.61, 0.84) and year ≥ 2000 (0.67, 0.49). Utilization of DS combined with tumor size and age at diagnosis predicted more women with very low (≤ 8%) or higher (> 15%) 10-year LR risk after BCS alone compared to utilization of DS alone or clinicopathological factors alone. The combined analysis provides refined estimates of 10-year LR risk after BCS for DCIS. Adding information on tumor size and age at diagnosis to the DS adjusting for year of diagnosis provides improved LR risk estimates to guide treatment decision making.

Effects of the naturally-occurring contaminant microcystins on the Azolla filiculoides-Anabaena azollae symbiosis.

PubMed

Pereira, A L; Monteiro, B; Azevedo, J; Campos, A; Osório, H; Vasconcelos, V

2015-08-01

Harmful algal blooms (HABs) contaminate aquatic ecosystems and are responsible for animal poisoning worldwide. We conducted a toxicity test with the aquatic fern and the biofertilizer, Azolla filiculoides. The sporophytes were exposed to three concentrations (0.01, 0.1 and 1μgmL(-1)) of a microcystin (MC) cyanobacterial crude extract and purified MC-LR. The growth of A. filiculoides decreased only at 1μgmL(-1) crude extract concentration while with MC-LR it decreased at all the tested concentrations, indicating that the presence of other compounds in the crude extract altered toxicity and stimulated the fern growth at lower concentrations (0.01 and 0.1μgmL(-1)). Both phycoerythrocyanin and allophycocyanin levels decreased in all the concentrations of crude extract and MC-LR. The phycocyanin had a marked increase at 0.1μgmL(-1) crude extract concentration and a marked decrease at 1μgmL(-1) MC-LR concentration. These changes in the phycobiliprotein content indicate a shift in the antenna pigments of the cyanobionts of A. filiculoides. The changes in two oxidative stress enzymes, glutathione reductase for the crude extract assay and glutathione peroxidase for MC-LR assay, points towards the induction of stress defense responses. The low bioconcentration factor in both crude extract and MC-LR treatments can suggest the low uptake of microcystins, and indicates that the aquatic fern can be used as a biofertilizer and as animal feed but is not suitable for MC phytoremediation. Copyright © 2015 Elsevier Inc. All rights reserved.

Layered Lithium-Rich Oxide Nanoparticles Doped with Spinel Phase: Acidic Sucrose-Assistant Synthesis and Excellent Performance as Cathode of Lithium Ion Battery.

PubMed

Chen, Min; Chen, Dongrui; Liao, Youhao; Zhong, Xiaoxin; Li, Weishan; Zhang, Yuegang

2016-02-01

Nanolayered lithium-rich oxide doped with spinel phase is synthesized by acidic sucrose-assistant sol-gel combustion and evaluated as the cathode of a high-energy-density lithium ion battery. Physical characterizations indicate that the as-synthesized oxide (LR-SN) is composed of uniform and separated nanoparticles of about 200 nm, which are doped with about 7% spinel phase, compared to the large aggregated ones of the product (LR) synthesized under the same condition but without any assistance. Charge/discharge demonstrates that LR-SN exhibits excellent rate capability and cyclic stability: delivering an average discharge capacity of 246 mAh g(-1) at 0.2 C (1C = 250 mA g(-1)) and earning a capacity retention of 92% after 100 cycles at 4 C in the lithium anode-based half cell, compared to the 227 mA g(-1) and the 63% of LR, respectively. Even in the graphite anode-based full cell, LR-SN still delivers a capacity of as high as 253 mAh g(-1) at 0.1 C, corresponding to a specific energy density of 801 Wh kg(-1), which are the best among those that have been reported in the literature. The separated nanoparticles of the LR-SN provide large sites for charge transfer, while the spinel phase doped in the nanoparticles facilitates lithium ion diffusion and maintains the stability of the layered structure during cycling.

Detecting modification of biomedical events using a deep parsing approach

PubMed Central

2012-01-01

Background This work describes a system for identifying event mentions in bio-molecular research abstracts that are either speculative (e.g. analysis of IkappaBalpha phosphorylation, where it is not specified whether phosphorylation did or did not occur) or negated (e.g. inhibition of IkappaBalpha phosphorylation, where phosphorylation did not occur). The data comes from a standard dataset created for the BioNLP 2009 Shared Task. The system uses a machine-learning approach, where the features used for classification are a combination of shallow features derived from the words of the sentences and more complex features based on the semantic outputs produced by a deep parser. Method To detect event modification, we use a Maximum Entropy learner with features extracted from the data relative to the trigger words of the events. The shallow features are bag-of-words features based on a small sliding context window of 3-4 tokens on either side of the trigger word. The deep parser features are derived from parses produced by the English Resource Grammar and the RASP parser. The outputs of these parsers are converted into the Minimal Recursion Semantics formalism, and from this, we extract features motivated by linguistics and the data itself. All of these features are combined to create training or test data for the machine learning algorithm. Results Over the test data, our methods produce approximately a 4% absolute increase in F-score for detection of event modification compared to a baseline based only on the shallow bag-of-words features. Conclusions Our results indicate that grammar-based techniques can enhance the accuracy of methods for detecting event modification. PMID:22595089

Interpretation of FTIR spectra of polymers and Raman spectra of car paints by means of likelihood ratio approach supported by wavelet transform for reducing data dimensionality.

PubMed

Martyna, Agnieszka; Michalska, Aleksandra; Zadora, Grzegorz

2015-05-01

The problem of interpretation of common provenance of the samples within the infrared spectra database of polypropylene samples from car body parts and plastic containers as well as Raman spectra databases of blue solid and metallic automotive paints was under investigation. The research involved statistical tools such as likelihood ratio (LR) approach for expressing the evidential value of observed similarities and differences in the recorded spectra. Since the LR models can be easily proposed for databases described by a few variables, research focused on the problem of spectra dimensionality reduction characterised by more than a thousand variables. The objective of the studies was to combine the chemometric tools easily dealing with multidimensionality with an LR approach. The final variables used for LR models' construction were derived from the discrete wavelet transform (DWT) as a data dimensionality reduction technique supported by methods for variance analysis and corresponded with chemical information, i.e. typical absorption bands for polypropylene and peaks associated with pigments present in the car paints. Univariate and multivariate LR models were proposed, aiming at obtaining more information about the chemical structure of the samples. Their performance was controlled by estimating the levels of false positive and false negative answers and using the empirical cross entropy approach. The results for most of the LR models were satisfactory and enabled solving the stated comparison problems. The results prove that the variables generated from DWT preserve signal characteristic, being a sparse representation of the original signal by keeping its shape and relevant chemical information.

Rapid Isolation of a Single-Chain Antibody against the Cyanobacterial Toxin Microcystin-LR by Phage Display and Its Use in the Immunoaffinity Concentration of Microcystins from Water

PubMed Central

McElhiney, Jacqui; Drever, Mathew; Lawton, Linda A.; Porter, Andy J.

2002-01-01

A naïve (unimmunized) human semisynthetic phage display library was employed to isolate recombinant antibody fragments against the cyanobacterial hepatotoxin microcystin-LR. Selected antibody scFv genes were cloned into a soluble expression vector and expressed in Escherichia coli for characterization against purified microcystin-LR by competition enzyme-linked immunosorbent assay (ELISA). The most sensitive single-chain antibody (scAb) isolated was capable of detecting microcystin-LR at levels below the World Health Organization limit in drinking water (1 μg liter−1) and cross-reacted with three other purified microcystin variants (microcystin-RR, -LW, and -LF) and the related cyanotoxin nodularin. Extracts of the cyanobacterium Microcystis aeruginosa were assayed by ELISA, and quantifications of microcystins in toxic samples showed good correlation with analysis by high-performance liquid chromatography. Immobilized scAb was also used to prepare immunoaffinity columns, which were assessed for the ability to concentrate microcystin-LR from water for subsequent analysis by high-performance liquid chromatography. Anti-microcystin-LR scAb was immobilized on columns via a hexahistidine tag, ensuring maximum exposure of antigen binding sites, and the performance of the columns was evaluated by directly applying 150 ml of distilled water spiked with 4 μg of purified microcystin-LR. The procedure was simple, and a recovery rate of 94% was achieved following elution in 1 ml of 100% methanol. Large-scale, low-cost production of anti-microcystin-LR scAb in E. coli is an exciting prospect for the development of biosensors and on-line monitoring systems for microcystins and will also facilitate a range of immunoaffinity applications for the cleanup and concentration of these toxins from environmental samples. PMID:12406716

LumenRECON Guidewire: Pilot Study of a Novel, Nonimaging Technology for Accurate Vessel Sizing and Delivery of Therapy in Femoropopliteal Disease.

PubMed

Nair, Pradeep K; Carr, Jeffrey G; Bigelow, Brian; Bhatt, Deepak L; Berwick, Zachary C; Adams, George

2018-01-01

Proper vessel sizing during endovascular interventions is crucial to avoid adverse procedural and clinical outcomes. LumenRECON (LR) is a novel, nonimaging, 0.035-inch wire-based technology that uses the physics-based principle of Ohm's law to provide a simple, real-time luminal size while also providing a platform for therapy delivery. This study evaluated the accuracy, reliability, and safety of the LR system in patients presenting for a femoropopliteal artery intervention. This multicenter, prospective pilot study of 24 patients presenting for peripheral intervention compared LR measurements of femoropopliteal artery size to angiographic visual estimation, duplex ultrasound, quantitative angiography, and intravascular ultrasound. The primary effectiveness and safety end point was comparison against core laboratory adjudicated intravascular ultrasound values and major adverse events, respectively. Additional preclinical studies were also performed in vitro and in vivo in swine to determine the accuracy of the LR guidewire system. No intra- or postprocedure device-related adverse events occurred. A balloon or stent was successfully delivered in 12 patients (50%) over the LR wire. Differences in repeatability between successive LR measurements was 2.5±0.40% ( R 2 =0.96) with no significant bias. Differences in measurements of LR to other modalities were 0.5±1.7%, 5.0±1.8%, -1.5±2.0%, and 6.8±3.4% for intravascular ultrasound core laboratory, quantitative angiography, angiographic, and duplex ultrasound, respectively. This study demonstrates that through a physics-based principle, LR provides a real-time, safe, reproducible, and accurate vessel size of the femoropopliteal artery during intervention and can additionally serve as a conduit for therapy delivery over its wire-based platform. © 2018 American Heart Association, Inc.

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

Byun, Eui-Baek; Choi, Han-Gyu; Sung, Nak-Yun

Highlights: Black-Right-Pointing-Pointer Expressions of CD80, CD86, and MHC class I/II were inhibited by EGCG via 67LR. Black-Right-Pointing-Pointer EGCG-treated DCs inhibited LPS-induced pro-inflammatory cytokines via 67LR. Black-Right-Pointing-Pointer EGCG-treated DCs inhibited MAPKs activation and NF-{kappa}B p65 translocation via 67LR. Black-Right-Pointing-Pointer EGCG elevated the expression of the Tollip protein through 67LR in DCs. -- Abstract: Epigallocatechin-3-gallate (EGCG), a major active polyphenol of green tea, has been shown to down-regulate inflammatory responses in dendritic cells (DCs); however, the underlying mechanism has not been understood. Recently, we identified the 67-kDa laminin receptor (67LR) as a cell-surface EGCG receptor. In this study, we showed the molecularmore » basis for the down-regulation of toll-like receptor 4 (TLR4) signal transduction by EGCG in DCs. The expressions of CD80, CD86, and MHC class I and II, which are molecules essential for antigen presentation by DCs, were inhibited by EGCG via 67LR. In addition, EGCG-treated DCs inhibited lipopolysaccharide (LPS)-induced production of pro-inflammatory cytokines (tumor necrosis factor [TNF]-{alpha}, interleukin [IL]-1{beta}, and IL-6) and activation of mitogen-activated protein kinases (MAPKs), e.g., extracellular signal-regulated kinase 1/2 (ERK1/2), p38, c-Jun N-terminal kinase (JNK), and nuclear factor {kappa}B (NF-{kappa}B) p65 translocation through 67LR. Interestingly, we also found that EGCG markedly elevated the expression of the Tollip protein, a negative regulator of TLR signaling, through 67LR. These novel findings provide new insight into the understanding of negative regulatory mechanisms of the TLR4 signaling pathway and consequent inflammatory responses that are implicated in the development and progression of many chronic diseases.« less

Fluid resuscitation with lactated Ringer’s solution vs normal saline in acute pancreatitis: A triple-blind, randomized, controlled trial

PubMed Central

Herrera-Marante, Iván; González-Camacho, Verónica; Bonjoch, Laia; Quesada-Vázquez, Noé; Almenta-Saavedra, Isabel; Miralles-Maciá, Cayetano; Acevedo-Piedra, Nelly G; Roger-Ibáñez, Manuela; Sánchez-Marin, Claudia; Osuna-Ligero, Rosa; Gracia, Ángel; Llorens, Pere; Zapater, Pedro; Singh, Vikesh K; Moreu-Martín, Rocío; Closa, Daniel

2017-01-01

Background Little is known regarding the optimal type of fluid resuscitation in acute pancreatitis (AP). Objective The objective of this article was to compare the effect of lactated Ringer’s solution (LR) vs normal saline (NS) in the inflammatory response in AP. Methods We conducted a triple-blind, randomized, controlled trial. Patients ≥ 18 admitted with AP were eligible. Patients were randomized to receive LR or NS. Primary outcome variables were number of systemic inflammatory response syndrome (SIRS) criteria at 24 hours, 48 hours and 72 hours and blood C-reactive protein (CRP) levels at 48 hours and 72 hours. In vitro complementary experiments were performed to further explore the interaction between pH, lactate and inflammation. Results Nineteen patients receiving LR and 21 receiving NS were analyzed. The median (p25–p75) number of SIRS criteria at 48 hours were 1 (1–2) for NS vs 1 (0–1) for LR, p = 0.060. CRP levels (mg/l) were as follows: at 48 hours NS 166 (78–281) vs LR 28 (3–124), p = 0.037; at 72 hours NS 217 (59–323) vs LR 25 (3–169), p = 0.043. In vitro, LR inhibited the induction of inflammatory phenotype of macrophages and NF-κB activation. This effect was not observed when using Ringer’s solution without lactate, suggesting a direct anti-inflammatory effect of lactate. Conclusions Lactated Ringer’s is associated with an anti-inflammatory effect in patients with acute pancreatitis. PMID:29435315

A perfluorochemical loss/restoration (L/R) system for tidal liquid ventilation.

PubMed

Libros, R; Philips, C M; Wolfson, M R; Shaffer, T H

2000-01-01

Tidal liquid ventilation is the transport of dissolved respiratory gases via volume exchange of perfluorochemical (PFC) liquid to and from the PFC-filled lung. All gas-liquid surface tension is eliminated, increasing compliance and providing lung protection due to lower inflation pressures. Tidal liquid ventilation is achieved by cycling fluid from a reservoir to and from the lung by a ventilator. Current approaches are microprocessor-based with feedback control. During inspiration, warmed oxygenated PFC liquid is pumped from a fluid reservoir/gas exchanger into the lung. PFC fluid is conserved by condensing (60-80% efficiency) vapor in the expired gas. A feedback-control system was developed to automatically replace PFC lost due to condenser inefficiency. This loss/restoration (L/R) system consists of a PFC-vapor thermal detector (+/- 2.5%), pneumatics, amplifiers, a gas flow detector (+/- 1%), a PFC pump (+/- 5%), and a controller. Gravimetric studies of perflubron loss from a flask due to evaporation were compared with experimental L/R results and found to be within +/- 1.4%. In addition, when L/R studies were conducted with a previously reported liquid ventilation system over a four-hour period, the L/R system maintained system perflubron volume to within +/- 1% of prime volume and 11.5% of replacement volume, and the difference between experimental PFC loss and that of the L/R system was 1.8 mL/hr. These studies suggest that the PFC L/R system may have significant economic (appropriate dosing for PFC loss) as well as physiologic (maintenance of PFC inventory in the lungs and liquid ventilator) impact on liquid ventilation procedures.

Ultrasound-based logistic regression model LR2 versus magnetic resonance imaging for discriminating between benign and malignant adnexal masses: a prospective study.

PubMed

Shimada, Kanane; Matsumoto, Koji; Mimura, Takashi; Ishikawa, Tetsuya; Munechika, Jiro; Ohgiya, Yoshimitsu; Kushima, Miki; Hirose, Yusuke; Asami, Yuka; Iitsuka, Chiaki; Miyamoto, Shingo; Onuki, Mamiko; Tsunoda, Hajime; Matsuoka, Ryu; Ichizuka, Kiyotake; Sekizawa, Akihiko

2018-06-01

The diagnostic performances of the International Ovarian Tumor Analysis (IOTA) ultrasound-based logistic regression model (LR2) and magnetic resonance imaging (MRI) in discriminating between benign and malignant adnexal masses have not been directly compared in a single study. Using the IOTA LR2 model and subjective interpretation of MRI findings by experienced radiologists, 265 consecutive patients with adnexal masses were preoperatively evaluated in two hospitals between February 2014 and December 2015. Definitive histological diagnosis of excised tissues was used as a gold standard. From the 265 study subjects, 54 (20.4%) tumors were histologically diagnosed as malignant (including 11 borderline and 3 metastatic tumors). Preoperative diagnoses of malignant tumors showed 91.7% total agreement between IOTA LR2 and MRI, with a kappa value of 0.77 [95% confidence interval (CI), 0.68-0.86]. Sensitivity of IOTA LR2 (0.94, 95% CI, 0.85-0.98) for predicting malignant tumors was similar to that of MRI (0.96, 95% CI, 0.87-0.99; P = 0.99), whereas specificity of IOTA LR2 (0.98, 95% CI, 0.95-0.99) was significantly higher than that of MRI (0.91, 95% CI, 0.87-0.95; P = 0.002). Combined IOTA LR2 and MRI results gave the greatest sensitivity (1.00, 95% CI, 0.93-1.00) and had similar specificity (0.91, 95% CI, 0.86-0.94) to MRI. The IOTA LR2 model had a similar sensitivity to MRI for discriminating between benign and malignant tumors and a higher specificity compared with MRI. Our findings suggest that the IOTA LR2 model, either alone or in conjunction with MRI, should be included in preoperative evaluation of adnexal masses.

A Novel Technique for Clinical Assessment of Laryngeal Nerve Conduction: Normal and Abnormal Results

PubMed Central

Sulica, Lucian; Carey, Bridget; Branski, Ryan C.

2014-01-01

Objectives/Hypothesis To describe a novel conduction study of the laryngeal nerves, including normal values and abnormal findings. Study Design Prospective nonrandomized. Methods Seventeen healthy adult volunteers, as well as three patients with clinically identified laryngeal neuropathy, underwent low-level brief electrical stimulation of the laryngeal mucosa by means of a wire inserted via a transnasal flexible laryngoscope. Bilateral hookwire electrodes recorded the result in the laryngeal adductor muscles. Results This study yields an early response ipsilateral to the side of stimulation (LR1), which is uniform and consistent (right 5 13.2 6 0.80 msec; left 5 15.2 6 1.20 msec), and late bilateral responses (ipsilateral LR2 [LR2i] and contralateral LR2 [LR2c]), which exhibit greater variation in latency and morphology (right LR2i 5 50.5 6 3.38 msec; left LR2i 5 52.2 msec; right LR2c 5 50.7 6 4.26; left LR2c 5 50.6 6 4.07). Findings in abnormal patients differ significantly from normal, consistent with the distribution of neuropathy. Conclusions We describe a novel, clinically applicable conduction study of laryngeal nerves. Normative electrodiagnostic values and variations of the reflex responses of the laryngeal adductor muscles in response to irritative stimulation of the laryngeal mucosa (Laryngeal Closure Reflex) are proposed. By enabling the determination of electrophysiological parameters of the superior laryngeal and recurrent laryngeal branches of cranial nerve X (CN X), this procedure, which is used as an adjunct to laryngeal electromyography, may provide earlier and more accurate information regarding the extent and grade of nerve injury. Because injury grade relates directly to prognosis, the information derived from this test may have clinical relevance in determining optimal treatment. Level of Evidence 4. PMID:23835889

Postulation of rust resistance genes in Nordic spring wheat genotypes and identification of widely effective sources of resistance against the Australian rust flora.

PubMed

Randhawa, Mandeep; Bansal, Urmil; Lillemo, Morten; Miah, Hanif; Bariana, Harbans

2016-11-01

Wild relatives, landraces and cultivars from different geographical regions have been demonstrated as the sources of genetic variation for resistance to rust diseases. This study involved assessment of diversity for resistance to three rust diseases among a set of Nordic spring wheat cultivars. These cultivars were tested at the seedling stage against several pathotypes of three rust pathogens in the greenhouse. All stage stem rust resistance genes Sr7b, Sr8a, Sr12, Sr15, Sr17, Sr23 and Sr30, and leaf rust resistance genes Lr1, Lr3a, Lr13, Lr14a, Lr16 and Lr20 were postulated either singly or in different combinations among these cultivars. A high proportion of cultivars were identified to carry linked rust resistance genes Sr15 and Lr20. Although 51 cultivars showed variation against Puccinia striiformis f. sp. tritici (Pst) pathotypes used in this study, results were not clearly contrasting to enable postulation of stripe rust resistance genes in these genotypes. Stripe rust resistance gene Yr27 was postulated in four cultivars and Yr1 was present in cultivar Zebra. Cultivar Tjalve produced low stripe rust response against all Pst pathotypes indicating the presence either of a widely effective resistance gene or combination of genes with compensating pathogenic specificities. Several cultivars carried moderate to high level of APR to leaf rust and stripe rust. Seedling stem rust susceptible cultivar Aston exhibited moderately resistant to moderately susceptible response, whereas other cultivars belonging to this class were rated moderately susceptible or higher. Molecular markers linked with APR genes Yr48, Lr34/Yr18/Sr57, Lr68 and Sr2 detected the presence of these genes in some genotypes.

Process optimization for microcystin-LR degradation by Response Surface Methodology and mechanism analysis in gas-liquid hybrid discharge system.

PubMed

Zhang, Yi; Wei, Hanyu; Xin, Qing; Wang, Mingang; Wang, Qi; Wang, Qiang; Cong, Yanqing

2016-12-01

A gas-liquid hybrid discharge system was applied to microcystin-LR (MC-LR) degradation. MC-LR degradation was completed after 1 min under a pulsed high voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 160 L/h. The Box-Behnken Design was proposed in Response Surface Methodology to evaluate the influence of pulsed high voltage, electrode distance and oxygen flow rate on MC-LR removal efficiency. Multiple regression analysis, focused on multivariable factors, was employed and a reduced cubic model was developed. The ANOVA analysis shows that the model is significant and the model prediction on MC-LR removal was also validated with experimental data. The optimum conditions for the process are obtained at pulsed voltage of 16 kV, gas-liquid interface gap of 10 mm and oxygen flow rate of 120 L/h with ta removal efficiency of MC-LR of 96.6%. The addition of catalysts (TiO 2 or Fe 2+ ) in the gas-liquid hybrid discharge system was found to enhance the removal of MC-LR. The intermediates of MC-LR degradation were analyzed by liquid chromatography/mass spectrometry. The degradation pathway proposed envisaged the oxidation of hydroxyl radicals and ozone, and attack of high-energy electrons on the unsaturated double bonds of Adda and Mdha, with MC-LR finally decomposing into small molecular products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synonym set extraction from the biomedical literature by lexical pattern discovery.

PubMed

McCrae, John; Collier, Nigel

2008-03-24

Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by Hearst 1, but it is still not clear how to automatically construct such patterns for different semantic relations and domains. In particular it is not certain which patterns are useful for capturing synonymy. The assumption of extant resources such as parsers is also a limiting factor for many languages, so it is desirable to find patterns that do not use syntactical analysis. Finally to give a more consistent and applicable result it is desirable to use these patterns to form synonym sets in a sound way. We present a method that automatically generates regular expression patterns by expanding seed patterns in a heuristic search and then develops a feature vector based on the occurrence of term pairs in each developed pattern. This allows for a binary classifications of term pairs as synonymous or non-synonymous. We then model this result as a probability graph to find synonym sets, which is equivalent to the well-studied problem of finding an optimal set cover. We achieved 73.2% precision and 29.7% recall by our method, out-performing hand-made resources such as MeSH and Wikipedia. We conclude that automatic methods can play a practical role in developing new thesauri or expanding on existing ones, and this can be done with only a small amount of training data and no need for resources such as parsers. We also concluded that the accuracy can be improved by grouping into synonym sets.

Strategies to diagnose ovarian cancer: new evidence from phase 3 of the multicentre international IOTA study.

PubMed

Testa, A; Kaijser, J; Wynants, L; Fischerova, D; Van Holsbeke, C; Franchi, D; Savelli, L; Epstein, E; Czekierdowski, A; Guerriero, S; Fruscio, R; Leone, F P G; Vergote, I; Bourne, T; Valentin, L; Van Calster, B; Timmerman, D

2014-08-12

To compare different ultrasound-based international ovarian tumour analysis (IOTA) strategies and risk of malignancy index (RMI) for ovarian cancer diagnosis using a meta-analysis approach of centre-specific data from IOTA3. This prospective multicentre diagnostic accuracy study included 2403 patients with 1423 benign and 980 malignant adnexal masses from 2009 until 2012. All patients underwent standardised transvaginal ultrasonography. Test performance of RMI, subjective assessment (SA) of ultrasound findings, two IOTA risk models (LR1 and LR2), and strategies involving combinations of IOTA simple rules (SRs), simple descriptors (SDs) and LR2 with and without SA was estimated using a meta-analysis approach. Reference standard was histology after surgery. The areas under the receiver operator characteristic curves of LR1, LR2, SA and RMI were 0.930 (0.917-0.942), 0.918 (0.905-0.930), 0.914 (0.886-0.936) and 0.875 (0.853-0.894). Diagnostic one-step and two-step strategies using LR1, LR2, SR and SD achieved summary estimates for sensitivity 90-96%, specificity 74-79% and diagnostic odds ratio (DOR) 32.8-50.5. Adding SA when IOTA methods yielded equivocal results improved performance (DOR 57.6-75.7). Risk of Malignancy Index had sensitivity 67%, specificity 91% and DOR 17.5. This study shows all IOTA strategies had excellent diagnostic performance in comparison with RMI. The IOTA strategy chosen may be determined by clinical preference.

Patterns of Local Recurrence and Dose Fractionation of Adjuvant Radiation Therapy in 462 Patients With Soft Tissue Sarcoma of Extremity and Trunk Wall

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

Jebsen, Nina L., E-mail: nina.louise.jebsen@helse-bergen.no; Department of Oncology, Haukeland University Hospital, Bergen; Engellau, Jacob

2013-08-01

Purpose: To study the impact of dose fractionation of adjuvant radiation therapy (RT) on local recurrence (LR) and the relation of LR to radiation fields. Methods and Materials: LR rates were analyzed in 462 adult patients with soft tissue sarcoma who underwent surgical excision and adjuvant RT at five Scandinavian sarcoma centers from 1998 to 2009. Medical records were reviewed for dose fractionation parameters and to determine the location of the LR relative to the radiation portals. Results: Fifty-five of 462 patients developed a LR (11.9%). Negative prognostic factors included intralesional surgical margin (hazard ratio [HR]: 7.83, 95% confidence intervalmore » [CI]: 3.08-20.0), high malignancy grade (HR: 5.82, 95% CI: 1.31-25.8), age at diagnosis (HR per 10 years: 1.27, 95% CI: 1.03-1.56), and malignant peripheral nerve sheath tumor histological subtype (HR: 6.66, 95% CI: 2.56-17.3). RT dose was tailored to margin status. No correlation between RT dose and LR rate was found in multiple Cox regression analysis. The majority (65%) of LRs occurred within the primary RT volume. Conclusions: No significant dose–response effect of adjuvant RT was demonstrated. Interestingly, patients given 45-Gy accelerated RT (1.8 Gy twice daily/2.5 weeks) had the best local outcome. A total dose of 50 Gy in 25 fractions seemed adequate following wide margin surgery. The risk of LR was associated with histopathologic subtype, which should be included in the treatment algorithm of adjuvant RT in soft tissue sarcoma.« less

Lesion size affects diagnostic performance of IOTA logistic regression models, IOTA simple rules and risk of malignancy index in discriminating between benign and malignant adnexal masses.

PubMed

Di Legge, A; Testa, A C; Ameye, L; Van Calster, B; Lissoni, A A; Leone, F P G; Savelli, L; Franchi, D; Czekierdowski, A; Trio, D; Van Holsbeke, C; Ferrazzi, E; Scambia, G; Timmerman, D; Valentin, L

2012-09-01

To estimate the ability to discriminate between benign and malignant adnexal masses of different size using: subjective assessment, two International Ovarian Tumor Analysis (IOTA) logistic regression models (LR1 and LR2), the IOTA simple rules and the risk of malignancy index (RMI). We used a multicenter IOTA database of 2445 patients with at least one adnexal mass, i.e. the database previously used to prospectively validate the diagnostic performance of LR1 and LR2. The masses were categorized into three subgroups according to their largest diameter: small tumors (diameter < 4 cm; n = 396), medium-sized tumors (diameter, 4-9.9 cm; n = 1457) and large tumors (diameter ≥ 10 cm, n = 592). Subjective assessment, LR1 and LR2, IOTA simple rules and the RMI were applied to each of the three groups. Sensitivity, specificity, positive and negative likelihood ratio (LR+, LR-), diagnostic odds ratio (DOR) and area under the receiver-operating characteristics curve (AUC) were used to describe diagnostic performance. A moving window technique was applied to estimate the effect of tumor size as a continuous variable on the AUC. The reference standard was the histological diagnosis of the surgically removed adnexal mass. The frequency of invasive malignancy was 10% in small tumors, 19% in medium-sized tumors and 40% in large tumors; 11% of the large tumors were borderline tumors vs 3% and 4%, respectively, of the small and medium-sized tumors. The type of benign histology also differed among the three subgroups. For all methods, sensitivity with regard to malignancy was lowest in small tumors (56-84% vs 67-93% in medium-sized tumors and 74-95% in large tumors) while specificity was lowest in large tumors (60-87%vs 83-95% in medium-sized tumors and 83-96% in small tumors ). The DOR and the AUC value were highest in medium-sized tumors and the AUC was largest in tumors with a largest diameter of 7-11 cm. Tumor size affects the performance of subjective assessment, LR1 and LR2, the IOTA simple rules and the RMI in discriminating correctly between benign and malignant adnexal masses. The likely explanation, at least in part, is the difference in histology among tumors of different size. Copyright © 2012 ISUOG. Published by John Wiley & Sons, Ltd.

Selective oxidation of key functional groups in cyanotoxins during drinking water ozonation.

PubMed

Onstad, Gretchen D; Strauch, Sabine; Meriluoto, Jussi; Codd, Geoffrey A; Von Gunten, Urs

2007-06-15

Chemical kinetics were determined for the reactions of ozone and hydroxyl radicals with the three cyanotoxins microcystin-LR (MC-LR), cylindrospermopsin (CYN) and anatoxin-a (ANTX). The second-order rate constants (k(O3)) at pH 8 were 4.1 +/- 0.1 x 10(5) M(-1) s(-1) for MC-LR, approximately 3.4 x 10(5) M(-1) s(-1) for CYN, and approximately 6.4 x 10(4) M(-1) s(-1) for ANTX. The reaction of ozone with MC-LR exhibits a k(O3) similar to that of the conjugated diene in sorbic acid (9.6 +/- 0.3 x 10(5) M(-1) s(-1)) at pH 8. The pH dependence and value of k(O3) for CYN at pH > 8 (approximately 2.5 +/- 0.1 x 10(6) M(-1) s(-1)) are similar to deprotonated amines of 6-methyluracil. The k(O3) of ANTX at pH > 9 (approximately 8.7 +/- 2.2 x 10(5) M(-1) s(-1)) agrees with that of neutral diethylamine, and the value at pH < 8 (2.8 +/- 0.2 x 10(4) M(-1) s(-1)) corresponds to an olefin. Second-order rate constants for reaction with OH radicals (*OH), k(OH) for cyanotoxins were measured at pH 7 to be 1.1 +/- 0.01 x 10(10) M(-1) s(-1) for MC-LR, 5.5 +/- 0.01 x 10(9) M(-1) s(-1) for CYN, and 3.0 +/- 0.02 x 10(9) M(-1) s(-1) for ANTX. Natural waters from Switzerland and Finland were examined for the influence of variations of dissolved organic matter, SUVA254, and alkalinity on cyanotoxin oxidation. For a Swiss water (1.6 mg/L DOC), 0.2, 0.4, and 0.8 mg/L ozone doses were required for 95% oxidation of MC-LR, CYN, and ANTX, respectively. For the Finnish water (13.1 mg/L DOC), >2 mg/L ozone dose was required for each toxin. The contribution of hydroxyl radicals to toxin oxidation during ozonation of natural water was greatest for ANTX > CYN > MC-LR. Overall, the order of reactivity of cyanotoxins during ozonation of natural waters corresponds to the relative magnitudes of the second-order rate constants for their reaction with ozone and *OH. Ozone primarily attacks the structural moieties responsible for the toxic effects of MC-LR, CYN, and ANTX, suggesting that ozone selectively detoxifies these cyanotoxins.

Risk factors for locoregional disease recurrence after breast-conserving therapy in patients with breast cancer treated with neoadjuvant chemotherapy: An international collaboration and individual patient meta-analysis.

PubMed

Valachis, Antonios; Mamounas, Eleftherios P; Mittendorf, Elizabeth A; Hayashi, Naoki; Ishitobi, Makoto; Natoli, Clara; Fitzal, Florian; Rubio, Isabel T; Tiezzi, Daniel G; Shin, Hee-Chul; Anderson, Stewart J; Hunt, Kelly K; Matsuda, Naoko; Ohsumi, Shozo; Totomi, Athina; Nilsson, Cecilia

2018-05-03

Several studies have reported a high risk of local disease recurrence (LR) and locoregional disease recurrence (LRR) in patients with breast cancer after neoadjuvant chemotherapy (NCT) and breast-conserving therapy (BCT). The objective of the current study was to identify potential risk factors for LR and LRR after NCT and BCT. Individual patient data sets from 9 studies were pooled. The outcomes of interest were the occurrence of LR and/or LRR. A 1-stage meta-analytic approach was used. Cox proportional hazards regression models were applied to identify factors that were predictive of LR and LRR, respectively. A total of 9 studies (4125 patients) provided their data sets. The 10-year LR rate was 6.5%, whereas the 10-year LRR rate was 10.3%. Four factors were found to be associated with a higher risk of LR: 1) estrogen receptor-negative disease; 2) cN + disease; 3) a lack of pathologic complete response in axilla (pN0); and 4) pN2 to pN3 disease. The predictive score for LR determined 3 risk groups: a low-risk, intermediate-risk, and high-risk group with 10-year LR rates of 4.0%, 7.9%, and 20.4%, respectively. Two additional factors were found to be associated with an increased risk of LRR: cT3 to cT4 disease and a lack of pathologic complete response in the breast. The predictive score for LRR determined 3 risk groups; a low-risk, intermediate-risk, and high-risk group with 10-year LRR rates of 3.2%, 10.1%, and 24.1%, respectively. BCT after NCT appears to be an oncologically safe procedure for a large percentage of patients with breast cancer. Two easy-to-use clinical scores were developed that can help clinicians to identify patients at higher risk of LR and LRR after NCT and BCT and individualize the postoperative treatment plan and follow-up. Cancer 2018. © 2018 American Cancer Society. © 2018 American Cancer Society.

Late Relapse of Classical Hodgkin Lymphoma: An Analysis of the German Hodgkin Study Group HD7 to HD12 Trials.

PubMed

Bröckelmann, Paul J; Goergen, Helen; Kohnhorst, Charlotte; von Tresckow, Bastian; Moccia, Alden; Markova, Jana; Meissner, Julia; Kerkhoff, Andrea; Ludwig, Wolf-Dieter; Fuchs, Michael; Borchmann, Peter; Engert, Andreas

2017-05-01

Purpose Clinical characteristics, therapeutic approaches, and prognosis of late relapse (LR) in patients with classic Hodgkin lymphoma (cHL) are poorly understood. We performed a comprehensive analysis of LR of Hodgkin lymphoma (LR-HL). Methods To estimate the incidence of LR-HL, we retrospectively analyzed 6,840 patients with cHL included in the German Hodgkin Study Group trials HD7 to HD12. Patients who experienced a relapse > 5 years into remission were compared with patients in continued remission for > 5 years and with those who experienced a relapse ≤ 5 years after first diagnosis. Results With a median observation time of 10.3 years, 141 incidences of LR-HL were observed. Cumulative incidences at 10, 15, and 20 years rose linearly and were 2.5%, 4.3%, and 6.9%, respectively. The standardized incidence ratio for HL with respect to age- and sex-matched German reference data was 84.5 (95% CI, 71.2 to 99.7). LR-HL was more frequently observed in patients with early-stage favorable than unfavorable or advanced stage at first diagnosis (15-year cumulative incidence, 5.3% v 3.9% and 3.9%, respectively; P = .01). Overall survival from first diagnosis was worse after LR compared with nonrelapse survivors (10-year estimate, 95.8% v 86.1%; hazard ratio, 2.5; 95% CI, 1.7 to 3.5; P < .001). In patients with LR-HL, survival was better compared with 466 patients with earlier relapse (hazard ratio, 0.6; 95% CI, 0.4 to 0.9, P = .01). Forty-four percent and 49% of patients with LR-HL and earlier relapse, respectively, received stem cell transplantations. Conclusion Apart from treatment-associated adverse effects, survivors after initially successful therapy for cHL are at an 85-fold risk for recurrence of disease compared with the general German population. After risk-adapted treatment strategies, especially in early-stage favorable HL, regular clinical follow-up is recommended for timely detection of LR-HL. With adequate treatment, prognosis of LR-HL is better compared with early relapses.

Effect of Laser Remelting on Friction-Wear Behaviors of Cold Sprayed Al Coatings in 3.5% NaCl Solution

PubMed Central

Jing, Zhang; Dejun, Kong

2018-01-01

A cold sprayed Al coating on S355 structural steel was processed using a laser remelting (LR). The surface and cross-section morphologies, chemical compositions, and phases of as-obtained Al coating before and after LR were analyzed using a scanning electronic microscope (SEM), energy dispersive spectrometer (EDS), and X-ray diffractometer (XRD), respectively, and their hardness was measured using a micro-hardness tester. The friction-wear behaviors of Al coating before and after LR in 3.5% NaCl solution were conducted to simulate the sand and gravel scouring on its surface in seawater, the effects of wear loads and speeds on the tribological properties of Al coating were analyzed, and the wear mechanisms under different wear loads and speeds were also discussed. The results show that the Al coating after LR is primarily composed of an Al phase and its hardness is 104.66 HV, increasing 54.70 HV than the cold sprayed Al coating. The average coefficient of friction (COF) of cold sprayed Al coating at the wear load of 0.5, 1.0 and 1.5 N is 0.285, 0.239, and 0.435, respectively, while that after LR is 0.243, 0.227, and 0.327, respectively, decreased by 14.73%, 5.02% and 24.83% compared to the cold sprayed Al coating. The wear rate of cold sprayed Al coating at the wear load of 0.5, 1.0 and 1.5 N is 1.60 × 10−4, 2.36 × 10−4, and 2.40 × 10−4 mm3/m·N, respectively, while that after LR is 1.59 × 10−4, 1.70 × 10−4, and 1.94 × 10–4 mm3/m·N, respectively, decreased by 1%, 32%, and 23%, respectively, indicating that LR has high anti-friction performance. Under the wear load action of 1.0 N, the average COF of laser remelted Al coating at the wear speeds of 300, 400 and 500 times/min is 0.294, 0.279, and 0.239, respectively, and the corresponding wear rate is 1.06 × 10−4, 1.24 × 10−4, and 1.70 × 10−4 mm3/m·N, respectively. The wear mechanism of cold sprayed Al coating is primarily corrosion wear at the loads of 0.5 and 1.0 N, and that at the load of 1.5 N is abrasive wear and fatigue wear; while that after LR is abrasive wear and fatigue wear, with no corrosion wear, showing that LR improves its corrosion and wear resistance. PMID:29439485

Effect of Laser Remelting on Friction-Wear Behaviors of Cold Sprayed Al Coatings in 3.5% NaCl Solution.

PubMed

Jing, Zhang; Dejun, Kong

2018-02-11

A cold sprayed Al coating on S355 structural steel was processed using a laser remelting (LR). The surface and cross-section morphologies, chemical compositions, and phases of as-obtained Al coating before and after LR were analyzed using a scanning electronic microscope (SEM), energy dispersive spectrometer (EDS), and X-ray diffractometer (XRD), respectively, and their hardness was measured using a micro-hardness tester. The friction-wear behaviors of Al coating before and after LR in 3.5% NaCl solution were conducted to simulate the sand and gravel scouring on its surface in seawater, the effects of wear loads and speeds on the tribological properties of Al coating were analyzed, and the wear mechanisms under different wear loads and speeds were also discussed. The results show that the Al coating after LR is primarily composed of an Al phase and its hardness is 104.66 HV, increasing 54.70 HV than the cold sprayed Al coating. The average coefficient of friction (COF) of cold sprayed Al coating at the wear load of 0.5, 1.0 and 1.5 N is 0.285, 0.239, and 0.435, respectively, while that after LR is 0.243, 0.227, and 0.327, respectively, decreased by 14.73%, 5.02% and 24.83% compared to the cold sprayed Al coating. The wear rate of cold sprayed Al coating at the wear load of 0.5, 1.0 and 1.5 N is 1.60 × 10 -4 , 2.36 × 10 -4 , and 2.40 × 10 -4 mm³/m·N, respectively, while that after LR is 1.59 × 10 -4 , 1.70 × 10 -4 , and 1.94 × 10 -4 mm³/m·N, respectively, decreased by 1%, 32%, and 23%, respectively, indicating that LR has high anti-friction performance. Under the wear load action of 1.0 N, the average COF of laser remelted Al coating at the wear speeds of 300, 400 and 500 times/min is 0.294, 0.279, and 0.239, respectively, and the corresponding wear rate is 1.06 × 10 -4 , 1.24 × 10 -4 , and 1.70 × 10 -4 mm³/m·N, respectively. The wear mechanism of cold sprayed Al coating is primarily corrosion wear at the loads of 0.5 and 1.0 N, and that at the load of 1.5 N is abrasive wear and fatigue wear; while that after LR is abrasive wear and fatigue wear, with no corrosion wear, showing that LR improves its corrosion and wear resistance.

The JCMT Gould Belt Survey: a quantitative comparison between SCUBA-2 data reduction methods

NASA Astrophysics Data System (ADS)

Mairs, S.; Johnstone, D.; Kirk, H.; Graves, S.; Buckle, J.; Beaulieu, S. F.; Berry, D. S.; Broekhoven-Fiene, H.; Currie, M. J.; Fich, M.; Hatchell, J.; Jenness, T.; Mottram, J. C.; Nutter, D.; Pattle, K.; Pineda, J. E.; Salji, C.; di Francesco, J.; Hogerheijde, M. R.; Ward-Thompson, D.; JCMT Gould Belt survey Team

2015-12-01

Performing ground-based submillimetre observations is a difficult task as the measurements are subject to absorption and emission from water vapour in the Earth's atmosphere and time variation in weather and instrument stability. Removing these features and other artefacts from the data is a vital process which affects the characteristics of the recovered astronomical structure we seek to study. In this paper, we explore two data reduction methods for data taken with the Submillimetre Common-User Bolometer Array-2 (SCUBA-2) at the James Clerk Maxwell Telescope (JCMT). The JCMT Legacy Reduction 1 (JCMT LR1) and The Gould Belt Legacy Survey Legacy Release 1 (GBS LR1) reduction both use the same software (STARLINK) but differ in their choice of data reduction parameters. We find that the JCMT LR1 reduction is suitable for determining whether or not compact emission is present in a given region and the GBS LR1 reduction is tuned in a robust way to uncover more extended emission, which better serves more in-depth physical analyses of star-forming regions. Using the GBS LR1 method, we find that compact sources are recovered well, even at a peak brightness of only three times the noise, whereas the reconstruction of larger objects requires much care when drawing boundaries around the expected astronomical signal in the data reduction process. Incorrect boundaries can lead to false structure identification or it can cause structure to be missed. In the JCMT LR1 reduction, the extent of the true structure of objects larger than a point source is never fully recovered.

Applying Semantic-based Probabilistic Context-Free Grammar to Medical Language Processing – A Preliminary Study on Parsing Medication Sentences

PubMed Central

Xu, Hua; AbdelRahman, Samir; Lu, Yanxin; Denny, Joshua C.; Doan, Son

2011-01-01

Semantic-based sublanguage grammars have been shown to be an efficient method for medical language processing. However, given the complexity of the medical domain, parsers using such grammars inevitably encounter ambiguous sentences, which could be interpreted by different groups of production rules and consequently result in two or more parse trees. One possible solution, which has not been extensively explored previously, is to augment productions in medical sublanguage grammars with probabilities to resolve the ambiguity. In this study, we associated probabilities with production rules in a semantic-based grammar for medication findings and evaluated its performance on reducing parsing ambiguity. Using the existing data set from 2009 i2b2 NLP (Natural Language Processing) challenge for medication extraction, we developed a semantic-based CFG (Context Free Grammar) for parsing medication sentences and manually created a Treebank of 4,564 medication sentences from discharge summaries. Using the Treebank, we derived a semantic-based PCFG (probabilistic Context Free Grammar) for parsing medication sentences. Our evaluation using a 10-fold cross validation showed that the PCFG parser dramatically improved parsing performance when compared to the CFG parser. PMID:21856440

Combined toxicity of microcystin-LR and copper on lettuce (Lactuca sativa L.).

PubMed

Cao, Qing; Steinman, Alan D; Wan, Xiang; Xie, Liqiang

2018-05-10

Microcystins and copper commonly co-exist in the natural environment, but their combined toxicity remains unclear, especially in terrestrial plants. The present study investigated the toxicity effects of microcystin-LR (0, 5, 50, 500, 1000 μg L -1 ) and copper (0, 50, 500, 1000, 2000 μg L -1 ), both individually and in mixture, on the germination, growth and oxidative response of lettuce. The bioaccumulation of microcystin-LR and copper was also evaluated. Results showed that the decrease in lettuce germination induced by copper alone was not significantly different from that induced by the mixture, and the combined toxicity assessment showed a simple additive effect. Lettuce growth was not significantly reduced by microcystin-LR alone, whereas it was significantly reduced by copper alone and the mixture when copper concentration was higher than 500 μg L -1 . High concentrations of microcystin-LR (1000 μg L -1 ) and copper (≥50 μg L -1 ),as well as their mixture (≥50 + 500 μg L -1 ), induced oxidative stress in lettuce. A synergistic effect on the growth and antioxidative system of lettuce was observed when exposed to low concentrations of the mixture (≤50 + 500 μg L -1 ), whereas an antagonistic effect was observed at high concentrations (≥1000 + 2000 μg L -1 ). Moreover, the interaction of microcystin-LR and copper can increase their accumulation in lettuce. Our results suggest that the toxicity effects of microcystin-LR and copper are exacerbated when they co-exist in the natural environment at low concentrations, which not only negatively affects plant growth but also poses a potential risk to human health via the food chain. Copyright © 2018. Published by Elsevier Ltd.

Accuracy and precision of the signs and symptoms of streptococcal pharyngitis in children: a systematic review.

PubMed

Shaikh, Nader; Swaminathan, Nithya; Hooper, Emma G

2012-03-01

To conduct a systematic review to determine whether clinical findings can be used to rule in or to rule out streptococcal pharyngitis in children. Two authors independently searched MEDLINE and EMBASE. We included articles if they contained data on the accuracy of symptoms or signs of streptococcal pharyngitis, individually or combined into prediction rules, in children 3-18 years of age. Thirty-eight articles with data on individual symptoms and signs and 15 articles with data on prediction rules met all inclusion criteria. In children with sore throat, the presence of a scarlatiniform rash (likelihood ratio [LR], 3.91; 95% CI, 2.00-7.62), palatal petechiae (LR, 2.69; CI, 1.92-3.77), pharyngeal exudates (LR, 1.85; CI, 1.58-2.16), vomiting (LR, 1.79; CI, 1.58-2.16), and tender cervical nodes (LR, 1.72; CI, 1.54-1.93) were moderately useful in identifying those with streptococcal pharyngitis. Nevertheless, no individual symptoms or signs were effective in ruling in or ruling out streptococcal pharyngitis. Symptoms and signs, either individually or combined into prediction rules, cannot be used to definitively diagnose or rule out streptococcal pharyngitis. Copyright © 2012 Mosby, Inc. All rights reserved.

Atmospheric correction of HJ-1 CCD imagery over turbid lake waters.

PubMed

Zhang, Minwei; Tang, Junwu; Dong, Qing; Duan, Hongtao; Shen, Qian

2014-04-07

We have presented an atmospheric correction algorithm for HJ-1 CCD imagery over Lakes Taihu and Chaohu with highly turbid waters. The Rayleigh scattering radiance (Lr) is calculated using the hyperspectral Lr with a wavelength interval 1nm. The hyperspectral Lr is interpolated from Lr in the central wavelengths of MODIS bands, which are converted from the band response-averaged Lr calculated using the Rayleigh look up tables (LUTs) in SeaDAS6.1. The scattering radiance due to aerosol (La) is interpolated from La at MODIS band 869nm, which is derived from MODIS imagery using a shortwave infrared atmospheric correction scheme. The accuracy of the atmospheric correction algorithm is firstly evaluated by comparing the CCD measured remote sensing reflectance (Rrs) with MODIS measurements, which are validated by the in situ data. The CCD measured Rrs is further validated by the in situ data for a total of 30 observation stations within ± 1h time window of satellite overpass and field measurements. The validation shows the mean relative errors about 0.341, 0.259, 0.293 and 0.803 at blue, green, red and near infrared bands.

Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.).

PubMed

Terracciano, Irma; Maccaferri, Marco; Bassi, Filippo; Mantovani, Paola; Sanguineti, Maria C; Salvi, Silvio; Simková, Hana; Doležel, Jaroslav; Massi, Andrea; Ammar, Karim; Kolmer, James; Tuberosa, Roberto

2013-04-01

Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar(®) markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.

11. Battery Richmond, emplacement no. 1, showing (LR): sealed location ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

11. Battery Richmond, emplacement no. 1, showing (L-R): sealed location of delivery table for projectile hoist, recess for powder hoist - Forth Wadsworth Battery Richmond, Fort Wadsworth, Staten Island, New York County, NY

LR: Compact connectivity representation for triangle meshes

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

Gurung, T; Luffel, M; Lindstrom, P

2011-01-28

We propose LR (Laced Ring) - a simple data structure for representing the connectivity of manifold triangle meshes. LR provides the option to store on average either 1.08 references per triangle or 26.2 bits per triangle. Its construction, from an input mesh that supports constant-time adjacency queries, has linear space and time complexity, and involves ordering most vertices along a nearly-Hamiltonian cycle. LR is best suited for applications that process meshes with fixed connectivity, as any changes to the connectivity require the data structure to be rebuilt. We provide an implementation of the set of standard random-access, constant-time operators formore » traversing a mesh, and show that LR often saves both space and traversal time over competing representations.« less

[Prolonged mechanical ventilation probability model].

PubMed

Añón, J M; Gómez-Tello, V; González-Higueras, E; Oñoro, J J; Córcoles, V; Quintana, M; López-Martínez, J; Marina, L; Choperena, G; García-Fernández, A M; Martín-Delgado, C; Gordo, F; Díaz-Alersi, R; Montejo, J C; Lorenzo, A García de; Pérez-Arriaga, M; Madero, R

2012-10-01

To design a probability model for prolonged mechanical ventilation (PMV) using variables obtained during the first 24 hours of the start of MV. An observational, prospective, multicenter cohort study. Thirteen Spanish medical-surgical intensive care units. Adult patients requiring mechanical ventilation for more than 24 hours. None. APACHE II, SOFA, demographic data, clinical data, reason for mechanical ventilation, comorbidity, and functional condition. A multivariate risk model was constructed. The model contemplated a dependent variable with three possible conditions: 1. Early mortality; 2. Early extubation; and 3. PMV. Of the 1661 included patients, 67.9% (n=1127) were men. Age: 62.1±16.2 years. APACHE II: 20.3±7.5. Total SOFA: 8.4±3.5. The APACHE II and SOFA scores were higher in patients ventilated for 7 or more days (p=0.04 and p=0.0001, respectively). Noninvasive ventilation failure was related to PMV (p=0.005). A multivariate model for the three above exposed outcomes was generated. The overall accuracy of the model in the training and validation sample was 0.763 (95%IC: 0.729-0.804) and 0.751 (95%IC: 0.672-0.816), respectively. The likelihood ratios (LRs) for early extubation, involving a cutoff point of 0.65, in the training sample were LR (+): 2.37 (95%CI: 1.77-3.19) and LR (-): 0.47 (95%CI: 0.41-0.55). The LRs for the early mortality model, for a cutoff point of 0.73, in the training sample, were LR (+): 2.64 (95%CI: 2.01-3.4) and LR (-): 0.39 (95%CI: 0.30-0.51). The proposed model could be a helpful tool in decision making. However, because of its moderate accuracy, it should be considered as a first approach, and the results should be corroborated by further studies involving larger samples and the use of standardized criteria. Copyright © 2011 Elsevier España, S.L. y SEMICYUC. All rights reserved.

Knockdown of the partner protein OsNAR2.1 for high-affinity nitrate transport represses lateral root formation in a nitrate-dependent manner

PubMed Central

Huang, Shuangjie; Chen, Si; Liang, Zhihao; Zhang, Chenming; Yan, Ming; Chen, Jingguang; Xu, Guohua; Fan, Xiaorong; Zhang, Yali

2015-01-01

The morphological plasticity of root systems is critical for plant survival, and understanding the mechanisms underlying root adaptation to nitrogen (N) fluctuation is critical for sustainable agriculture; however, the molecular mechanism of N-dependent root growth in rice remains unclear. This study aimed to identify the role of the complementary high-affinity NO3− transport protein OsNAR2.1 in NO3−-regulated rice root growth. Comparisons with wild-type (WT) plants showed that knockdown of OsNAR2.1 inhibited lateral root (LR) formation under low NO3− concentrations, but not under low NH4+ concentrations. 15N-labelling NO3− supplies (provided at concentrations of 0–10 mM) demonstrated that (i) defects in LR formation in mutants subjected to low external NO3− concentrations resulted from impaired NO3− uptake, and (ii) the mutants had significantly fewer LRs than the WT plants when root N contents were similar between genotypes. LR formation in osnar2.1 mutants was less sensitive to localised NO3− supply than LR formation in WT plants, suggesting that OsNAR2.1 may be involved in a NO3−-signalling pathway that controls LR formation. Knockdown of OsNAR2.1 inhibited LR formation by decreasing auxin transport from shoots to roots. Thus, OsNAR2.1 probably functions in both NO3− uptake and NO3−-signalling. PMID:26644084

In-situ electrochemical Fe(VI) for removal of microcystin-LR from drinking water: comparing dosing of the ferrate ion by electrochemical and chemical means.

PubMed

Dubrawski, K L; Cataldo, M; Dubrawski, Z; Mazumder, A; Wilkinson, D P; Mohseni, M

2018-06-01

Harmful algal blooms (HAB) release microtoxins that contaminate drinking water supplies and risk the health of millions annually. Crystalline ferrate(VI) is a powerful oxidant capable of removing algal microtoxins. We investigate in-situ electrochemically produced ferrate from common carbon steel as an on-demand alternative to crystalline ferrate for the removal of microcystin-LR (MC-LR) and compare the removal efficacy for both electrochemical (EC) and chemical dosing methodologies. We report that a very low dose of EC-ferrate in deionized water (0.5 mg FeO 4 2- L -1 ) oxidizes MC-LR (MC-LR 0 = 10 μg L -1 ) to below the guideline limit (1.0 μg L -1 ) within 10 minutes' contact time. With bicarbonate or natural organic matter (NOM), doses of 2.0-5.0 mg FeO 4 2- L -1 are required, with lower efficacy of EC-ferrate than crystalline ferrate due to loss of EC-ferrate by water oxidation. To evaluate the EC-ferrate process to concurrently oxidize micropollutants, coagulate NOM, and disinfect drinking water, we spiked NOM-containing real water with MC-LR and Escherichia coli, finding that EC-ferrate is effective at 10.0 mg FeO 4 2- L -1 under normal operation or 2.0 mg FeO 4 2- L -1 if the test water has initial pH optimized. We suggest in-situ EC-ferrate may be appropriate for sporadic HAB events in small water systems as a primary or back-up technology.

Local recurrence after laparoscopic radiofrequency ablation of malignant liver tumors: Results of a contemporary series.

PubMed

Takahashi, Hideo; Akyuz, Muhammet; Aksoy, Erol; Karabulut, Koray; Berber, Eren

2017-06-01

The aims of this study were to determine the incidence of Local recurrence (LR) in patients at long-term follow-up after laparoscopic RFA (LRFA) and also to determine the risk factors for LR from a contemporary series. Patients undergoing LRFA between 2005 and 2014 by a single surgeon were reviewed. Demographic and perioperative data were analyzed from a prospective database. LRFA was performed on 316 patients with 901 lesions. Median follow-up was 25 months, with 76% of whom completed at least one year of follow-up. The LR rate was 18.4%. The LR in patients followed for less than 12 months was 13.8%, 20.3% for 12 months, and 19.7% for 18 months (P = 0.02). One-fourth of the LRs developed after the 1st year. Morbidity was 8.9% and mortality 0.3%. Tumor type, size, ablation margin, and surgeon experience affected LR, with tumor type, size, and ablation margin being independent. This study shows that 14% of malignant liver tumors will develop LR within a year after LRFA. Additional 4% of the lesions will demonstrate recurrence within 1 cm of the ablation zone, mostly as part of a multifocal recurrence. Ablation margin is the only parameter that the surgeon can manipulate to decrease LR. © 2017 Wiley Periodicals, Inc.

Degradation of [Dha7]MC-LR by a Microcystin Degrading Bacterium Isolated from Lake Rotoiti, New Zealand

PubMed Central

Somdee, Theerasak; Ruck, John; Lys, Isabelle; Allison, Margaret; Page, Rachel

2013-01-01

For the first time a microcystin-degrading bacterium (NV-3 isolate) has been isolated and characterized from a NZ lake. Cyanobacterial blooms in New Zealand (NZ) waters contain microcystin (MC) hepatotoxins at concentrations which are a risk to animal and human health. Degradation of MCs by naturally occurring bacteria is an attractive bioremediation option for removing MCs from drinking and recreational water sources. The NV-3 isolate was identified by 16S rRNA sequence analysis and found to have 100% nucleotide sequence homology with the Sphingomonas MC-degrading bacterial strain MD-1 from Japan. The NV-3 isolate (concentration of 1.0 × 108 CFU/mL) at 30°C degraded a mixture of [Dha7]MC-LR and MC-LR (concentration 25 μg/mL) at a maximum rate of 8.33 μg/mL/day. The intermediate by-products of [Dha7]MC-LR degradation were detected and similar to MC-LR degradation by-products. The presence of three genes (mlrA, mlrB, and mlrC), that encode three enzymes involved in the degradation of MC-LR, were identified in the NV-3 isolate. This study confirmed that degradation of [Dha7]MC-LR by the Sphingomonas isolate NV-3 occurred by a similar mechanism previously described for MC-LR by Sphingomonas strain MJ-PV (ACM-3962). This has important implications for potential bioremediation of toxic blooms containing a variety of MCs in NZ waters. PMID:23936728

Effects of cyanobacterial biomass and purified microcystins on malformations in Xenopus laevis: teratogenesis assay (FETAX).

PubMed

Dvoráková, Dagmar; Dvoráková, Katerina; Bláha, Ludek; Marsálek, Blahoslav; Knotková, Zora

2002-12-01

Xenopus laevis (African clawed frog) embryos in a 96-h teratogenesis assay (FETAX) were exposed to 0-250 microg/L and 500 microg/L of purified microcystin-LR (MCYST-LR) for the estimation of lethality, as well as to equivalent concentrations of biomass containing MCYST-LR (natural water bloom dominated by Microcystis aeruginosa) and biomass without MCYST-LR (bloom dominated by Microcystis wesenbergii). The highest tested concentrations of purified MCYST-LR caused up to 30% lethality after a 96-h exposure, corresponding to a LC(25) of 380 microg/L. Cyanobacterial biomass containing MCYST-LR caused significant lethality up to 50% at the highest tested concentrations (300 mg/L, i.e., 250 microg/L of MCYST-LR). The estimated 96-h LC(25) values varied from 125 mg/L (biomass containing MCYST-LR) up to 232 mg/L (biomass without MCYST-LR). A statistically significant increase in the number of malformed embryos was observed after exposure to cyanobacterial samples. Purified MCYST-LR at and above 25 microg/L significantly increased the number of malformations, with 53% of surviving embryos malformed in the highest tested concentration, 250 microg/L (EC(25) = 27 microg/L). Exposure to the highest concentration of MCYST-LR containing biomass resulted in more than 60% of the embryos being malformed and an EC(25) of 52 mg/L (i.e., 43 microg of MCYST-LR/L). Cyanobacterial biomass with no natural microcystin also induced substantial malformations-about 50% aberrant embryos at the highest concentration, 300 mg/L (EC(25) = 75 mg/L). External additions of purified MCYST-LR to the biomass that was originally without microcystins resulted in a slight additional increase in the rate of malformations (80% at the highest concentration, 300 mg of biomass plus 250 microg of MCYST-LR per liter). A comparison of lethality and effects on malformations (teratogenic index, TI = LC(25)/EC(25)) showed that all samples had significant teratogenic potential in the FETAX assay (TI(MCYST-LR) = 14; TI for biomass with and without microcystin ranged between 2.4 and 3.1, respectively). We conclude that cyanobacterial water blooms can significantly alter the normal development of amphibian embryos. Copyright 2002 Wiley Periodicals, Inc.

Mechanisms of left-right asymmetry and patterning: driver, mediator and responder.

PubMed

Hamada, Hiroshi; Tam, Patrick P L

2014-01-01

The establishment of a left-right (LR) organizer in the form of the ventral node is an absolute prerequisite for patterning the tissues on contralateral sides of the body of the mouse embryo. The experimental findings to date are consistent with a mechanistic paradigm that the laterality information, which is generated in the ventral node, elicits asymmetric molecular activity and cellular behaviour in the perinodal tissues. This information is then relayed to the cells in the lateral plate mesoderm (LPM) when the left-specific signal is processed and translated into LR body asymmetry. Here, we reflect on our current knowledge and speculate on the following: (a) what are the requisite anatomical and functional attributes of an LR organizer, (b) what asymmetric information is emanated from this organizer, and (c) how this information is transferred across the paraxial tissue compartment and elicits a molecular response specifically in the LPM.

A Comparison Study of the Effectiveness of the Lexia Reading Programme

ERIC Educational Resources Information Center

Ness, Mike; Couperus, Josh; Willey, Matthew

2013-01-01

This study evaluates the efficacy of the Lexia Reading (LR) programme with a cohort of 37 students in a Decile 1 primary school. The students were randomly assigned to experimental (who used LR) and control groups (who did not use LR). The WIAT-II was used to provide pre and post measures of literacy skills. Results indicated that students who…

Intramuscular Distribution of the Abducens Nerve in the Lateral Rectus Muscle for the Management of Strabismus.

PubMed

Shin, Hyun Jin; Lee, Shin-Hyo; Shin, Kang-Jae; Koh, Ki-Seok; Song, Wu-Chul

2018-06-01

To elucidate the intramuscular distribution and branching patterns of the abducens nerve in the lateral rectus (LR) muscle so as to provide anatomical confirmation of the presence of compartmentalization, including for use in clinical applications such as botulinum toxin injections. Thirty whole-mount human cadaver specimens were dissected and then Sihler's stain was applied. The basic dimensions of the LR and its intramuscular nerve distribution were investigated. The distances from the muscle insertion to the point at which the abducens nerve enters the LR and to the terminal nerve plexus were also measured. The LR was 46.0 mm long. The abducens nerve enters the muscle on the posterior one-third of the LR and then typically divides into a few branches (average of 1.8). This supports a segregated abducens nerve selectively innervating compartments of the LR. The intramuscular nerve distribution showed a Y-shaped ramification with root-like arborization. The intramuscular nerve course finished around the middle of the LR (24.8 mm posterior to the insertion point) to form the terminal nerve plexus. This region should be considered the optimal target site for botulinum toxin injections. We have also identified the presence of an overlapping zone and communicating nerve branches between the neighboring LR compartments. Sihler's staining is a useful technique for visualizing the entire nerve network of the LR. Improving the knowledge of the nerve distribution patterns is important not only for researchers but also clinicians to understand the functions of the LR and the diverse pathophysiology of strabismus.

Elimination of microcystin-LR and residual Mn species using permanganate and powdered activated carbon: Oxidation products and pathways.

PubMed

Jeong, Boyoung; Oh, Min-Seok; Park, Hyun-Mee; Park, Chanhyuk; Kim, Eun-Ju; Hong, Seok Won

2017-05-01

The oxidation of microcystin-LR (MC-LR) in deionized water (DI) and river water using potassium permanganate (KMnO 4 ) at a neutral pH and at 23 ± 2 °C was investigated. These two aqueous systems (i.e., DI and river water) gave comparable second-order rate constants (289.9 and 285.5 M -1 s -1 (r 2  > 0.99), respectively), which confirmed the effectiveness of this oxidation process for the treatment of natural surface water. The presence of either humic or fulvic acid reduced the removal efficiency of MC-LR, with the latter exhibiting a greater inhibitory effect. Monitoring of MC-LR and residual Mn 2+ levels with adding KMnO 4 (1 mg/L) and powdered activated carbon (PAC, 5-20 mg L -1 ) before and during coagulation, respectively, revealed that 60 min of permanganate pre-oxidation followed by coagulant addition with PAC was the most effective approach for reducing both levels below limits stated by WHO guidelines. The MC-LR degradation products were the result of oxidation occurring at the diene and aromatic moieties of the Adda (3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid) side-chain, in addition to amine bond hydrolysis of the Mdha (N-methyldehydroalanine) moiety. Several toxic by-products with an intact Adda chain were observed during the reaction, but completely disappeared after 60 min. This further supports the conclusion that sufficient contact time with permanganate (i.e., >60 min) is essential to reducing the residual toxicity and maximizing the efficiency of MC-LR oxidation when treating raw water. Copyright © 2017 Elsevier Ltd. All rights reserved.

Empirical Properties of Multilingual Phone-To-Word Transduction

DTIC Science & Technology

2008-01-01

model are described next. Intended words I’m sorry we’ll blame him Intended phones aI m S a r i: w i: l b l ei m H I m Corrupted phones aI m S a r i...w i: D l ei m H I m Recovered words I’m sorry we blame him Table 1. Steps in the noisy channel model 3. DATABASE AND ACOUSTIC MODELS 3.1. CallHome In...respectively that take speci c values such as rs and ls. Then M (L;R) = X L,R P (L,R) log P (L,R) P (L)P (R) ≈ X s log P (rs, ls) P (rs)P (ls) = X s log P

MAXIMIZING GROWTH AND SEXUAL MATURATION OF SHEEPSHEAD MINNOWS IN SUPPORT OF MULTI-GENERATION TEST DEVELOPMENT

EPA Science Inventory

Hemmer, R.L., G.M. Cripe and L.R. Goodman. In press. Maximizing Growth and Sexual Maturation of Sheepshead Minnows (Cyprinodon variegatus) in Support of Multi-Generation Test Development (Abstract). To be presented at the SETAC Fourth World Congress, 14-18 November 2004, Portland...

Fast estimation of Colles' fracture load of the distal section of the radius by homogenized finite element analysis based on HR-pQCT.

PubMed

Hosseini, Hadi S; Dünki, Andreas; Fabech, Jonas; Stauber, Martin; Vilayphiou, Nicolas; Pahr, Dieter; Pretterklieber, Michael; Wandel, Jasmin; Rietbergen, Bert van; Zysset, Philippe K

2017-04-01

Fractures of the distal section of the radius (Colles' fractures) occur earlier in life than other osteoporotic fractures. Therefore, they can be interpreted as a warning signal for later, more deleterious fractures of vertebral bodies or the femoral neck. In the past decade, the advent of HR-pQCT allowed a detailed architectural analysis of the distal radius and an automated but time-consuming estimation of its strength with linear micro-finite element (μFE) analysis. Recently, a second generation of HR-pQCT scanner (XtremeCT II, SCANCO Medical, Switzerland) with a resolution beyond 61 μm became available for even more refined biomechanical investigations in vivo. This raises the question how biomechanical outcome variables compare between the original (LR) and the new (HR) scanner resolution. Accordingly, the aim of this work was to validate experimentally a patient-specific homogenized finite element (hFE) analysis of the distal section of the human radius for the fast prediction of Colles' fracture load based on the last generation HR-pQCT. Fourteen pairs of fresh frozen forearms (mean age = 77.5±9) were scanned intact using the high (61 μm) and the low (82 μm) resolution protocols that correspond to the new and original HR-pQCT systems. From each forearm, the 20mm most distal section of the radius were dissected out, scanned with μCT at 16.4 μm and tested experimentally under compression up to failure for assessment of stiffness and ultimate load. Linear and nonlinear hFE models together with linear micro finite element (μFE) models were then generated based on the μCT and HR-pQCT reconstructions to predict the aforementioned mechanical properties of 24 sections. Precision errors of the short term reproducibility of the FE analyses were measured based on the repeated scans of 12 sections. The calculated failure loads correlated strongly with those measured in the experiments: accounting for donor as a random factor, the nonlinear hFE provided a marginal coefficient of determination (R m 2 ) of 0.957 for the high resolution (HR) and 0.948 for the low resolution (LR) protocols, the linear hFE with R m 2 of 0.957 for the HR and 0.947 for the LR protocols. Linear μFE predictions of the ultimate load were similar with an R m 2 of 0.950 for the HR and 0.954 for the LR protocols, respectively. Nonlinear hFE strength computation led to precision errors of 2.2 and 2.3% which were higher than the ones calculated based on the linear hFE (1.6 and 1.9%) and linear μFE (1.2 and 1.6%) for the HR and LR protocols respectively. Computation of the fracture load with nonlinear hFE demanded in average 6h of CPU time which was 3 times faster than with linear μFE, while computation with linear hFE took only a few minutes. This study delivers an extensive experimental and numerical validation for the application of an accurate and fast hFE diagnostic tool to help in identifying individuals who may be at risk of an osteoporotic wrist fracture and to follow up pharmacological and other treatments in such patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Variability Of Microcystin-LR Standards Available From Commercial Vendors

EPA Science Inventory

VARIABILITY OF MICROCYSTIN-LR STANDARDS AVAILABLE FROM COMMERCIAL VENDORS II: TOXICOLOGICAL EVALUATION Donna Hill1, Neil Chernoff1, Thao Le2, Johnsie R. Lang2, Judy Schmid1 1 NHEERL, U.S. Environmental Protection Agency, Research Triangle Park, NC 2 Oak Ridge Institute for Sci...

Strategies to diagnose ovarian cancer: new evidence from phase 3 of the multicentre international IOTA study

PubMed Central

Testa, A; Kaijser, J; Wynants, L; Fischerova, D; Van Holsbeke, C; Franchi, D; Savelli, L; Epstein, E; Czekierdowski, A; Guerriero, S; Fruscio, R; Leone, F P G; Vergote, I; Bourne, T; Valentin, L; Van Calster, B; Timmerman, D

2014-01-01

Background: To compare different ultrasound-based international ovarian tumour analysis (IOTA) strategies and risk of malignancy index (RMI) for ovarian cancer diagnosis using a meta-analysis approach of centre-specific data from IOTA3. Methods: This prospective multicentre diagnostic accuracy study included 2403 patients with 1423 benign and 980 malignant adnexal masses from 2009 until 2012. All patients underwent standardised transvaginal ultrasonography. Test performance of RMI, subjective assessment (SA) of ultrasound findings, two IOTA risk models (LR1 and LR2), and strategies involving combinations of IOTA simple rules (SRs), simple descriptors (SDs) and LR2 with and without SA was estimated using a meta-analysis approach. Reference standard was histology after surgery. Results: The areas under the receiver operator characteristic curves of LR1, LR2, SA and RMI were 0.930 (0.917–0.942), 0.918 (0.905–0.930), 0.914 (0.886–0.936) and 0.875 (0.853–0.894). Diagnostic one-step and two-step strategies using LR1, LR2, SR and SD achieved summary estimates for sensitivity 90–96%, specificity 74–79% and diagnostic odds ratio (DOR) 32.8–50.5. Adding SA when IOTA methods yielded equivocal results improved performance (DOR 57.6–75.7). Risk of Malignancy Index had sensitivity 67%, specificity 91% and DOR 17.5. Conclusions: This study shows all IOTA strategies had excellent diagnostic performance in comparison with RMI. The IOTA strategy chosen may be determined by clinical preference. PMID:24937676

Effects of Porphyromonas gingivalis LPS and LR12 peptide on TREM-1 expression by monocytes.

PubMed

Dubar, Marie; Carrasco, Kevin; Gibot, Sebastien; Bisson, Catherine

2018-05-19

Periodontal disease involves the activation of host immune response, acting not only as defender of periodontal tissues against bacterial aggression but also as mediator of tissue destruction. Triggering receptor expressed on myeloid cells 1 (TREM-1) is an immune receptor that synergizes with Toll-like receptors in amplifying the inflammatory response mediated by microbial molecules. To investigate the role of P. gingivalis lipopolysaccharide (LPS) and the effect of LR12, a TREM-1 inhibitory peptide, on the expression of membrane-bound and soluble form of TREM-1 on human primary monocytes, as well as the production of proinflammatory cytokines. Cells were stimulated with 1 μg/ml of LPS with or without LR12. PCR, flow cytometry and ELISA were used to determine TREM-1 expressions and cytokines release by monocytes. P. gingivalis LPS can induce a significant increase in TREM-1 expression (mRNA, membrane-bound and soluble form, p < 0.001) as well as cytokines (IL-1β, TNFα) and chemokines (IL-8) production by monocytes. This monocytes' activation was partly prevented by LR12. TREM-1 inhibitors such as LR12 could be interesting for the modulation of the excessive inflammatory response that occurs during periodontal disease. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Registration of spring wheat sources of the resistance genes Lr53, Lr56, Lr59 and Lr62

USDA-ARS?s Scientific Manuscript database

Spring wheat (Triticum aestivum L.) germplasm with the alien derived leaf rust (caused by Puccinia triticina Erikss) resistance genes, Lr53, Lr56, Lr59, and Lr62 has been developed with infrastructure and financial support provided consecutively by the University of Stellenbosch (South Africa), the ...

δ opioid receptor antagonist, ICI 174,864, is suitable for the early treatment of uncontrolled hemorrhagic shock in rats.

PubMed

Liu, Liangming; Tian, Kunlun; Zhu, Yu; Ding, Xiaoli; Li, Tao

2013-08-01

Fluid resuscitation is the essential step for early treatment of traumatic hemorrhagic shock. However, its implementation is greatly limited before hospital or during evacuation. The authors investigated whether δ opioid receptor antagonist ICI 174,864 was suitable for the early treatment of traumatic hemorrhagic shock. With uncontrolled hemorrhagic-shock rats, the antishock effects of six dosages of ICI 174,864 (0.1, 0.3, 0.5, 1, 3, and 5 mg/kg) infused with or without a small volume of lactated Ringer's solution (LR) before bleeding controlled or bleeding cessation at different times were observed. ICI 174,864 (0.1-3 mg/kg) with or without 1/4 volume of LR infusion showed dose-dependent increase in the mean arterial blood pressure, and significantly prolonged the survival time and 8-h survival rate, as compared with ICI 174,864 plus 1/2 volume of LR infusion. The best effect was shown with 3 mg/kg of ICI 174,864. Bleeding cessation at 1, 2, or 3 h during infusion of ICI 174,864 (3 mg/kg) plus 1/4 volume of LR improved subsequent treatment (70% 24-h survival rate vs. 50 and 10% 24-h survival rate in hypotensive resuscitation and LR group, respectively). There was significant improvement in hemodynamic parameters, oxygen delivery, and tissue perfusion of hemorrhagic-shock rats with 3 mg/kg of ICI 174,864 plus 1/4 volume of LR infusion. δ Opioid receptor antagonist ICI 174,864 alone or with small volume of fluid infusion has good beneficial effect on uncontrolled hemorrhagic shock. Its early application can "buy" time for subsequent treatment of traumatic shock.

Xyce parallel electronic simulator reference guide, Version 6.0.1.

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

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

2014-01-01

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .

Single Image Super-Resolution Using Global Regression Based on Multiple Local Linear Mappings.

PubMed

Choi, Jae-Seok; Kim, Munchurl

2017-03-01

Super-resolution (SR) has become more vital, because of its capability to generate high-quality ultra-high definition (UHD) high-resolution (HR) images from low-resolution (LR) input images. Conventional SR methods entail high computational complexity, which makes them difficult to be implemented for up-scaling of full-high-definition input images into UHD-resolution images. Nevertheless, our previous super-interpolation (SI) method showed a good compromise between Peak-Signal-to-Noise Ratio (PSNR) performances and computational complexity. However, since SI only utilizes simple linear mappings, it may fail to precisely reconstruct HR patches with complex texture. In this paper, we present a novel SR method, which inherits the large-to-small patch conversion scheme from SI but uses global regression based on local linear mappings (GLM). Thus, our new SR method is called GLM-SI. In GLM-SI, each LR input patch is divided into 25 overlapped subpatches. Next, based on the local properties of these subpatches, 25 different local linear mappings are applied to the current LR input patch to generate 25 HR patch candidates, which are then regressed into one final HR patch using a global regressor. The local linear mappings are learned cluster-wise in our off-line training phase. The main contribution of this paper is as follows: Previously, linear-mapping-based conventional SR methods, including SI only used one simple yet coarse linear mapping to each patch to reconstruct its HR version. On the contrary, for each LR input patch, our GLM-SI is the first to apply a combination of multiple local linear mappings, where each local linear mapping is found according to local properties of the current LR patch. Therefore, it can better approximate nonlinear LR-to-HR mappings for HR patches with complex texture. Experiment results show that the proposed GLM-SI method outperforms most of the state-of-the-art methods, and shows comparable PSNR performance with much lower computational complexity when compared with a super-resolution method based on convolutional neural nets (SRCNN15). Compared with the previous SI method that is limited with a scale factor of 2, GLM-SI shows superior performance with average 0.79 dB higher in PSNR, and can be used for scale factors of 3 or higher.

Microcystin-LR nanobody screening from an alpaca phage display nanobody library and its expression and application.

PubMed

Xu, Chongxin; Yang, Ying; Liu, Liwen; Li, Jianhong; Liu, Xiaoqin; Zhang, Xiao; Liu, Yuan; Zhang, Cunzheng; Liu, Xianjin

2018-04-30

Microcystin-LR (MC-LR) is a type of biotoxin that pollutes the ecological environment and food. The study aimed to obtain new nanobodies from phage nanobody library for determination of MC-LR. The toxin was conjugated to keyhole limpet haemocyanin (KLH) and bovine serum albumin (BSA), respectively, then the conjugates were used as coated antigens for enrichment (coated MC-LR-KLH) and screening (coated MC-LR-BSA) of MC-LR phage nanobodies from an alpaca phage display nanobody library. The antigen-specific phage particles were enriched effectively with four rounds of biopanning. At the last round of enrichment, total 20 positive monoclonal phage nanobodies were obtained from the library, which were analyzed after monoclonal phage enzyme linked immunosorbent assay (ELISA), colony PCR and DNA sequencing. The most three positive nanobody genes, ANAb12, ANAb9 and ANAb7 were cloned into pET26b vector, then the nanobodies were expressed in Escherichia coli BL21 respectively. After being purified, the molecular weight (M.W.) of all nanobodies were approximate 15kDa with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The purified nanobodies, ANAb12, ANAb9 and ANAb7 were used to establish the indirect competitive ELISA (IC-ELISA) for MC-LR, and their half-maximum inhibition concentrations (IC 50 ) were 0.87, 1.17 and 1.47μg/L, their detection limits (IC 10 ) were 0.06, 0.08 and 0.12μg/L, respectively. All of them showed strong cross-reactivity (CRs) of 82.7-116.9% for MC-RR, MC-YR and MC-WR, and weak CRs of less than 4.56% for MC-LW, less than 0.1% for MC-LY and MC-LF. It was found that all the IC-ELISAs for MC-LR spiked in tap water samples detection were with good accuracy, stability and repeatability, their recoveries were 84.0-106.5%, coefficient of variations (CVs) were 3.4-10.6%. These results showed that IC-ELISA based on the nanobodies from the alpaca phage display antibody library were promising for high sensitive determination of multiple MCs. Copyright © 2018 Elsevier Inc. All rights reserved.

Integrated verification and testing system (IVTS) for HAL/S programs

NASA Technical Reports Server (NTRS)

Senn, E. H.; Ames, K. R.; Smith, K. A.

1983-01-01

The IVTS is a large software system designed to support user-controlled verification analysis and testing activities for programs written in the HAL/S language. The system is composed of a user interface and user command language, analysis tools and an organized data base of host system files. The analysis tools are of four major types: (1) static analysis, (2) symbolic execution, (3) dynamic analysis (testing), and (4) documentation enhancement. The IVTS requires a split HAL/S compiler, divided at the natural separation point between the parser/lexical analyzer phase and the target machine code generator phase. The IVTS uses the internal program form (HALMAT) between these two phases as primary input for the analysis tools. The dynamic analysis component requires some way to 'execute' the object HAL/S program. The execution medium may be an interpretive simulation or an actual host or target machine.

The development of a program analysis environment for Ada

NASA Technical Reports Server (NTRS)

Brown, David B.; Carlisle, Homer W.; Chang, Kai-Hsiung; Cross, James H.; Deason, William H.; Haga, Kevin D.; Huggins, John R.; Keleher, William R. A.; Starke, Benjamin B.; Weyrich, Orville R.

1989-01-01

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2.

N-linked oligosaccharides on the low density lipoprotein receptor homolog SorLA/LR11 are modified with terminal GalNAc-4-SO4 in kidney and brain.

PubMed

Fiete, Dorothy; Mi, Yiling; Oats, Edward L; Beranek, Mary C; Baenziger, Jacques U

2007-01-19

Sorting protein-related receptor (SorLA/LR11) is a highly conserved mosaic receptor that is expressed by cells in a number of different tissues including principal cells of the collecting ducts in the kidney and neurons in the central and peripheral nervous systems. SorLA/LR11 has features that indicate it serves as a sorting receptor shuttling between the plasma membrane, endosomes, and the Golgi. We have found that a fraction of SorLA/LR11 that is synthesized in the kidney and the brain bears N-linked oligosaccharides that are modified with terminal beta1,4-linked GalNAc-4-SO(4). Oligosaccharides located in the vacuolar sorting (Vps) 10p domain (Vps10p domain) are modified with beta1,4-linked GalNAc when the Vps10p domain is expressed in cells along with either of two recently cloned protein-specific beta1,4GalNAc-transferases, GalNAcTIII and GalNAcTIV. Either of two sequences with basic amino acids located within the Vps10p domain is able to mediate recognition by these beta1,4GalNAc-transferases. The highly specific modification of oligosaccharides in the Vps10p domain of SorLA/LR11 with terminal GalNAc-4-SO(4) suggests that this unusual modification may modulate the interaction of SorLA/LR11 with proteins and influence their trafficking.

Mice selected for high versus low stress reactivity: a new animal model for affective disorders.

PubMed

Touma, Chadi; Bunck, Mirjam; Glasl, Lisa; Nussbaumer, Markus; Palme, Rupert; Stein, Hendrik; Wolferstätter, Michael; Zeh, Ramona; Zimbelmann, Marina; Holsboer, Florian; Landgraf, Rainer

2008-07-01

Affective disorders such as major depression are among the most prevalent and costly diseases of the central nervous system, but the underlying mechanisms are still poorly understood. In recent years, it has become evident that alterations of the stress hormone system, in particular dysfunctions (hyper- or hypo-activity) of the hypothalamic-pituitary-adrenal (HPA) axis, play a prominent role in the development of major depressive disorders. Therefore, we aimed to generate a new animal model comprising these neuroendocrine core symptoms in order to unravel parameters underlying increased or decreased stress reactivity. Starting from a population of outbred mice (parental generation: 100 males and 100 females of the CD-1 strain), two breeding lines were established according to the outcome of a 'stress reactivity test' (SRT), consisting of a 15-min restraint period and tail blood samplings immediately before and after exposure to the stressor. Mice showing a very high or a very low secretion of corticosterone in the SRT, i.e. animals expressing a hyper- or a hypo-reactivity of the HPA axis, were selected for the 'high reactivity' (HR) and the 'low reactivity' (LR) breeding line, respectively. Additionally, a third breeding line was established consisting of animals with an 'intermediate reactivity' (IR) in the SRT. Already in the first generation, i.e. animals derived from breeding pairs selected from the parental generation, significant differences in the reactivity of the HPA axis between HR, IR, and LR mice were observed. Moreover, these differences were found across all subsequent generations and could be increased by selective breeding, which indicates a genetic basis of the respective phenotype. Repeated testing of individuals in the SRT furthermore proved that the observed differences in stress responsiveness are present already early in life and can be regarded as a robust genetic predisposition. Tests investigating the animal's emotionality including anxiety-related behavior, exploratory drive, locomotor activity, and depression-like behavior point to phenotypic similarities with behavioral changes observed in depressive patients. In general, HR males and females were 'hyperactive' in some behavioral paradigms, resembling symptoms of restlessness and agitation often seen in melancholic depression. LR mice, on the other hand, showed more passive-aggressive coping styles, corresponding to signs of retardation and retreat observed in atypical depression. Several morphometric and neuroendocrine findings further support this view. For example, monitoring the circadian rhythm of glucocorticoid secretion revealed clearly increased trough levels in HR mice, resulting in a flattened diurnal rhythm, again adding to the neuroendocrine similarities to patients suffering from melancholic depression. Taken together, our results suggest that distinct mechanisms influencing the function and regulation of the HPA axis are involved in the respective behavioral and neurobiological endophenotypes. Thus, the generated HR/IR/LR mouse lines can be a valuable model to elucidate molecular genetic, neuroendocrine, and behavioral parameters associated with altered stress reactivity, thereby improving our understanding of affective disorders, presumably including the symptomatology and pathophysiology of specific subtypes of major depression.

[Effect of different volumes of fluid resuscitation on hemorrhagic shock with pulmonary edema at high altitude in the unacclimated rat].

PubMed

Liu, Liang-ming; Hu, De-yao; Liu, Jian-cang; Li, Ping; Liu, Hou-dong; Xiao, Nan; Zhou, Xue-wu; Tian, Kun-lun; Huo, Xiao-ping; Shi, Quan-gui; He, Yan-mei; Yin, Zuo-ming

2003-05-01

To study the effects of different volumes of fluid resuscitation on hemorrhagic shock with pulmonary edema at high altitude in the unacclimated rat. One hundred and twenty-six SD rats transported to Lasa, Tibet, 3 760 meters above the sea level, were anesthetized one week later with sodium pentobarbital (30 mg/kg, intraperitoneal). Hemorrhagic shock with pulmonary edema model was induced by hemorrhage (50 mm Hg for 1 hour, 1 mmHg=0.133 kPa) plus intravenous injection of oleic acid (50 microl/kg). Experiments were then conducted in two parts. Sixty-three rats in part I were equally divided into nine groups (n=7): normal control, hemorrhagic shock control, hemorrhagic shock with pulmonary edema (HSPE) without fluid infusion, HSPE plus infusing lactated Ringer's solution (LR) with 0.5-, 1-, 1.5-, 2- or 3- fold volume shed blood, and 1 volume of LR plus mannitol (10 ml/kg). Hemodynamic parameters including mean arterial blood pressure (MAP), left intraventricular systolic pressure (LVSP) and the maximal change rate of intraventricular pressure rise or decline (+/- dp/dt max) were observed at 15, 30, 60 and 120 minutes after infusion, blood gases were measured at 30 and 120 minutes after infusion and the water content of lung and brain was determined at 120 minutes after infusion. In part II, additional 63 rats were used to observe the effect of different volumes of fluid resuscitation on survival time of HSPE rats. 0.5 volume of LR infusion significantly improved MAP, LVSP and +/- dp/dt max, prolonged the survival time of HSPE animals (all P<0.01), while it did not increase the water content of lung and brain and had no marked influence on blood gases. One volume of LR infusion slightly improved hemodynamic parameters, prolonged the survival time and increased the water content of lung. More than 1 volume of LR infusion including 1.5-, 2- and 3- fold volume LR deteriorated the hemodynamic parameters and decreased the survival time of shocked animal, meanwhile they apparently increased the water content of lung. One volume of LR plus mannitol (10 ml/kg) infusion did not improve the hemodynamic parameters and blood gases; also it did not decrease the water content of lung. The tolerance to fluid infusion for the unacclimated animal subjected to hemorrhagic shock with pulmonary edema at high altitude is significantly decreased. 0.5-1 volume of LR infusion appears to be beneficial effect on resuscitation at high altitude, while over 1 volume of LR infusion would aggravate pulmonary edema and exacerbate fluid resuscitation effect.

Microcystin-LR affects the hypothalamic-pituitary-inter-renal (HPI) axis in early life stages (embryos and larvae) of zebrafish.

PubMed

Chen, Liang; Wang, Yeke; Giesy, John P; Chen, Feng; Shi, Ting; Chen, Jun; Xie, Ping

2018-05-22

Frequencies and durations of blooms of cyanobacteria are increasing. Some cyanobacteria can produce cyanotoxins including microcystins (MCs). MCs are the most common toxic products of hazardous algal blooms (HABs), with the greatest potential for exposure and to cause toxicity. Recently, MCs have been shown to disrupt endocrine functions. In this study, for the first time, effects of MC-LR on the hypothalamic-pituitary-inter-renal (HPI) axis during early embryonic development (embryos/larvae) of zebrafish (Danio rerio), were investigated. Embryos/larvae of zebrafish were exposed to 1, 10, 100, or 300 μg MC-LR/L during the period of 4-168 h post-fertilization (hpf). Exposure to 300 μg MC-LR/L resulted in significantly greater concentrations of whole-body cortisol than those in controls. Expressions of genes along the HPI axis and mineralocorticoid receptor (MR-) and glucocorticoid receptor (GR-) centered gene networks were evaluated by use of quantitative real-time PCR. Expression of mRNA for crh was significantly down-regulated by exposure to 300 μg MC-LR/L, while expressions of crhbp, crhr1, and crhr2 were significantly up-regulated, relative to controls. MC-LR caused significantly lesser levels of mRNA for steroidogenic genes including hmgra, star, and cyp17, but expression of mRNA for hsd20b was significantly greater than that of controls. Treatment with MC-LR also altered profiles of transcription of MR- and GR-centered gene networks, which might result in multiple responses. Taken together, these results demonstrated that MC-LR affected the corticosteroid-endocrine system of larvae of zebrafish. This study provided valuable insights into molecular mechanisms behind potential toxicity and endocrine disruption of MCs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2.

PubMed

Chen, W; Kowatch, R; Lin, S; Splaingard, M; Huang, Y

2015-01-01

Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system showed to work more efficiently than the traditional manual chart review method, and it also enabled searching capabilities that were previously not possible. We report on the development and implementation of the sleep disorder i2b2 cohort identification system using natural language processing of semi-structured documents. We developed a natural language processing approach to automatically parse concepts and their values from semi-structured sleep study documents. Two parsers were developed: a regular expression parser for extracting numeric concepts and a NLP based tree parser for extracting textual concepts. Concepts were further organized into i2b2 ontologies based on document structures and in-domain knowledge. 26,550 concepts were extracted with 99% being textual concepts. 1.01 million facts were extracted from sleep study documents such as demographic information, sleep study lab results, medications, procedures, diagnoses, among others. The average accuracy of terminology parsing was over 83% when comparing against those by experts. The system is capable of capturing both standard and non-standard terminologies. The time for cohort identification has been reduced significantly from a few weeks to a few seconds. Natural language processing was shown to be powerful for quickly converting large amount of semi-structured or unstructured clinical data into discrete concepts, which in combination of intuitive domain specific ontologies, allows fast and effective interactive cohort identification through the i2b2 platform for research and clinical use.

Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2

PubMed Central

Chen, W.; Kowatch, R.; Lin, S.; Splaingard, M.

2015-01-01

Summary Nationwide Children’s Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system showed to work more efficiently than the traditional manual chart review method, and it also enabled searching capabilities that were previously not possible. Objective We report on the development and implementation of the sleep disorder i2b2 cohort identification system using natural language processing of semi-structured documents. Methods We developed a natural language processing approach to automatically parse concepts and their values from semi-structured sleep study documents. Two parsers were developed: a regular expression parser for extracting numeric concepts and a NLP based tree parser for extracting textual concepts. Concepts were further organized into i2b2 ontologies based on document structures and in-domain knowledge. Results 26,550 concepts were extracted with 99% being textual concepts. 1.01 million facts were extracted from sleep study documents such as demographic information, sleep study lab results, medications, procedures, diagnoses, among others. The average accuracy of terminology parsing was over 83% when comparing against those by experts. The system is capable of capturing both standard and non-standard terminologies. The time for cohort identification has been reduced significantly from a few weeks to a few seconds. Conclusion Natural language processing was shown to be powerful for quickly converting large amount of semi-structured or unstructured clinical data into discrete concepts, which in combination of intuitive domain specific ontologies, allows fast and effective interactive cohort identification through the i2b2 platform for research and clinical use. PMID:26171080

Habitual physical activity and plasma metabolomic patterns distinguish individuals with low vs. high weight loss during controlled energy restriction.

PubMed

Piccolo, Brian D; Keim, Nancy L; Fiehn, Oliver; Adams, Sean H; Van Loan, Marta D; Newman, John W

2015-04-01

Total weight loss induced by energy restriction is highly variable even under tightly controlled conditions. Identifying weight-loss discriminants would provide a valuable weight management tool and insights into body weight regulation. This study characterized responsiveness to energy restriction in adults from variables including the plasma metabolome, endocrine and inflammatory markers, clinical indices, body composition, diet, and physical activity. Data were derived from a controlled feeding trial investigating the effect of 3-4 dairy product servings in an energy-restricted diet (2092 kJ/d reduction) over 12 wk. Partial least squares regression was used to identify weight-loss discriminants in 67 overweight and obese adults. Linear mixed models were developed to identify discriminant variable differences in high- vs. low-weight-loss responders. Both pre- and postintervention variables (n = 127) were identified as weight-loss discriminants (root mean squared error of prediction = 1.85 kg; Q(2) = 0.43). Compared with low-responders (LR), high-responders (HR) had greater decreases in body weight (LR: 2.7 ± 1.6 kg; HR: 9.4 ± 1.8 kg, P < 0.01), BMI (in kg/m(2); LR: 1.0 ± 0.6; HR: 3.3 ± 0.5, P < 0.01), and total fat (LR: 2.2 ± 1.1 kg; HR: 8.0 ± 2.1 kg, P < 0.01). Significant group effects unaffected by the intervention were determined for the respiratory exchange ratio (LR: 0.86 ± 0.05; HR: 0.82 ± 0.03, P < 0.01), moderate physical activity (LR: 127 ± 52 min; HR: 167 ± 68 min, P = 0.02), sedentary activity (LR: 1090 ± 99 min; HR: 1017 ± 110 min, P = 0.02), and plasma stearate [LR: 102,000 ± 21,000 quantifier ion peak height (QIPH); HR: 116,000 ± 24,000 QIPH, P = 0.01]. Overweight and obese individuals highly responsive to energy restriction had accelerated reductions in adiposity, likely supported in part by higher lipid mobilization and combustion. A novel observation was that person-to-person differences in habitual physical activity and magnitude of weight loss were accompanied by unique blood metabolite signatures. This trial was registered at clinicaltrials.gov as NCT00858312. © 2015 American Society for Nutrition.

An Updated Meta-Analysis of Laparoscopic Versus Open Repair for Perforated Peptic Ulcer.

PubMed

Zhou, Chunhua; Wang, Weizhi; Wang, Jiwei; Zhang, Xiaoyu; Zhang, Qun; Li, Bowen; Xu, Zekuan

2015-09-09

Laparoscopic repair (LR) for perforated peptic ulcer (PPU) has been introduced since 1990. Although many studies comparing LR with open repair (OR) have been published, controversy remains regarding the clinical utility of laparoscopic techniques for the treatment of PPU. Thus, it is necessary for us to broaden our knowledge on this subject with the newly published articles. Twenty-four nonrandomized controlled studies (NRS) and five randomized controlled trails (RCTs) were included in our meta-analyses, which comprised 5,268 patients (1,890 in the LR group and 3,378 in the OR group). In the analysis of high quality NRS and RCTs, compared with OR, high quality evidence suggested that LR was associated with a lower incidence of overall postoperative complications; moderate evidence showed that the two procedures had the similar reoperation rate; based on the low quality evidence, LR had reduced hospital mortality and similar operative time; Moreover, LR was observed having the advantages of earlier resumption of oral intake, shorter hospital stay and less analgesic use, which were supported by very low evidence. All the evidences suggest that LR is better than OR for PPU, but more high-quality RCTs are still needed for further validation.

An Updated Meta-Analysis of Laparoscopic Versus Open Repair for Perforated Peptic Ulcer

PubMed Central

Zhou, Chunhua; Wang, Weizhi; Wang, Jiwei; Zhang, Xiaoyu; Zhang, Qun; Li, Bowen; Xu, Zekuan

2015-01-01

Laparoscopic repair (LR) for perforated peptic ulcer (PPU) has been introduced since 1990. Although many studies comparing LR with open repair (OR) have been published, controversy remains regarding the clinical utility of laparoscopic techniques for the treatment of PPU. Thus, it is necessary for us to broaden our knowledge on this subject with the newly published articles. Twenty-four nonrandomized controlled studies (NRS) and five randomized controlled trails (RCTs) were included in our meta-analyses, which comprised 5,268 patients (1,890 in the LR group and 3,378 in the OR group). In the analysis of high quality NRS and RCTs, compared with OR, high quality evidence suggested that LR was associated with a lower incidence of overall postoperative complications; moderate evidence showed that the two procedures had the similar reoperation rate; based on the low quality evidence, LR had reduced hospital mortality and similar operative time; Moreover, LR was observed having the advantages of earlier resumption of oral intake, shorter hospital stay and less analgesic use, which were supported by very low evidence. All the evidences suggest that LR is better than OR for PPU, but more high-quality RCTs are still needed for further validation. PMID:26350958

Building pathway graphs from BioPAX data in R.

PubMed

Benis, Nirupama; Schokker, Dirkjan; Kramer, Frank; Smits, Mari A; Suarez-Diez, Maria

2016-01-01

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser , which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.

Parsley: a Command-Line Parser for Astronomical Applications

NASA Astrophysics Data System (ADS)

Deich, William

Parsley is a sophisticated keyword + value parser, packaged as a library of routines that offers an easy method for providing command-line arguments to programs. It makes it easy for the user to enter values, and it makes it easy for the programmer to collect and validate the user's entries. Parsley is tuned for astronomical applications: for example, dates entered in Julian, Modified Julian, calendar, or several other formats are all recognized without special effort by the user or by the programmer; angles can be entered using decimal degrees or dd:mm:ss; time-like intervals as decimal hours, hh:mm:ss, or a variety of other units. Vectors of data are accepted as readily as scalars.

Prevalence and likelihood ratio of symptoms in patients with good therapeutic response to Lycopodium clavatum. A retrospective study.

PubMed

Eizayaga, José Enrique; Pozzi, María Isabel; Canan, María Clara; Saravia, Laura

2016-02-01

Assessment of the likelihood ratio (LR) of symptoms has been proposed as a rational means for detecting indicators to homeopathic medicines. To investigate the prevalence and LR of symptoms commonly attributed to the homeopathic medicine Lycopodium clavatum (Lyc). Secondarily, to answer the question if experienced homeopaths could intuitively infer which the main symptoms of this medicine are. The presence of 35 selected symptoms, prescribed medicines and therapeutic response were assessed retrospectively. The symptoms' prevalence in the Lyc responding population and the LR of the symptoms compared to their prevalence in the remainder of the population were calculated. Two hundred and two Lyc and 550 non Lyc cases (total 752) were included for analysis. Twenty-two symptoms were confirmed as pertaining to Lyc's semiology (prevalence %; LR): contemptuous (3.3; 6.7), urinary stones history (2.7; 5.4), egotism (5.6; 3.6), dictatorial (33.3; 3.4), haughty (8.7; 3.3), sleeps on abdomen (3.3; 3.3), intolerance to clothing in abdomen (12.0; 3.1), reproaches (4.0; 3.0), helplessness (24.0; 2.7), fear of failure (10.7; 2.6), irritability on waking in the morning (16.7; 2.5), constipation alternating with diarrhea (8.7; 2.5), intolerant to contradiction (59.3; 2.3), want of self confidence (30.0; 2.4), abdominal distension after eating (23.3; 2.1); ailments from anticipation (32.0; 1.9), irritability before menses (23.3; 1.8), conscientious (26.0; 1.6), desire of sweets (52.0; 1.6), desire of chocolate (16.7; 1.6), lack of vital heat (41.3; 1.3), and flatterer (1.3; ∞). Surveyed homeopaths' intuitive inferences correlated well with symptoms' prevalence but not with their LR. Lycopodium's main symptoms are well known by homeopaths, but their knowledge correlates well with the symptoms' prevalence and not with their LR. Retrospective assessment of prevalence and LR of symptoms in good responders might be a means for better selection of symptoms for prospective studies. Copyright © 2015 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Association of Stress Test Risk Classification With Health Status After Chronic Total Occlusion Angioplasty (from the Outcomes, Patient Health Status and Efficiency in Chronic Total Occlusion Hybrid Procedures [OPEN-CTO] Study).

PubMed

Salisbury, Adam C; Sapontis, James; Saxon, John T; Gosch, Kensey L; Lombardi, William L; Karmpaliotis, Dimitri; Moses, Jeffery W; Qintar, Mohammed; Kirtane, Ajay J; Spertus, John A; Cohen, David J; Grantham, J Aaron

2018-03-01

Stress testing is endorsed by the American College of Cardiology/American Heart Association Appropriate Use Criteria to identify appropriate candidates for Chronic Total Occlusion (CTO) Percutaneous Coronary Intervention (PCI). However, the relation between stress test risk classification and health status after CTO PCI is not known. We studied 449 patients in the 12-center OPEN CTO registry who underwent stress testing before successful CTO PCI, comparing outcomes of patients with low-risk (LR) versus intermediate to high-risk (IHR) findings. Health status was assessed using the Seattle Angina Questionnaire Angina Frequency (SAQ AF), Quality of Life (SAQ QoL), and Summary Scores (SAQ SS). Stress tests were LR in 40 (8.9%) and IHR in 409 (91.1%) patients. There were greater improvements on the SAQ AF (LR vs IHR 14.2 ± 2.7 vs 23.3 ± 1.3 points, p <0.001) and SAQ SS (LR vs IHR 20.8 ± 2.3 vs 25.4 ± 1.1 points, p = 0.03) in patients with IHR findings, but there was no difference between groups on the SAQ QoL domain (LR vs IHR 24.8 ± 3.4 vs 27.3 ± 1.6 points, p = 0.42). We observed large health status improvements after CTO PCI in both the LR and IHR groups, with the greatest reduction in angina among those with IHR stress tests. Although patients with higher risk studies may experience greater reduction in angina symptoms, on average, patients with LR stress tests also experienced large improvements in symptoms after CTO PCI, suggesting patients with refractory symptoms should be considered appropriate candidates for CTO PCI regardless of stress test findings. Copyright © 2017 Elsevier Inc. All rights reserved.

Causes and outcome of late referral of children who develop end-stage kidney disease.

PubMed

Kennedy, Sean E; Bailey, Rohan; Kainer, Gad

2012-03-01

This study aims to characterise the timing of referral to a paediatric nephrology unit of children who develop end-stage kidney disease (ESKD). This study also aims to determine whether late referral (LR) influences outcomes and to explore factors that may lead to LR. A retrospective case review of all incident patients with ESKD who received renal replacement therapy (RRT) at a single paediatric centre. Time between referral to a paediatric nephrologist and commencement of RRT, demographic and clinical data were collated. Estimated glomerular filtration rate (eGFR) at referral was calculated using height and creatinine. LR was defined as having an eGFR ≤ 30 mL/min/1.73 m(2) when first seen by a paediatric nephrologist. RRT was initiated for 74 patients < 18 years of age between 1988 and 2010. The median age at referral was 2.0 years (birth-15.9 years) and age at RRT was 10.0 years (6 days-17.4 years). Children referred before age 1 year (41%) had a more prolonged course before ESKD. Median (interquartile range) eGFR at referral of children > 1 year was 27.2 (9.0-52.0) mL/min/1.73 m(2) . Twenty-two (55%) of these children were referred late (LR) with an eGFR ≤ 30 mL/min/1.73 m(2) . LR patients were more likely to have glomerulonephritis or haemolytic uraemic syndrome and to live in a remote or outer regional area. LR patients had higher urea, lower haemoglobin and were more likely to receive haemodialysis via a vascular catheter. A significant proportion of children who develop ESKD are referred late to nephrology units with potentially preventable complications. Aetiology of renal disease and geographic isolation contribute to LR. © 2011 The Authors. Journal of Paediatrics and Child Health © 2011 Paediatrics and Child Health Division (Royal Australasian College of Physicians).

Maternal Style Selectively Shapes Amygdalar Development and Social Behavior in Rats Genetically Prone to High Anxiety.

PubMed

Cohen, Joshua L; Glover, Matthew E; Pugh, Phyllis C; Fant, Andrew D; Simmons, Rebecca K; Akil, Huda; Kerman, Ilan A; Clinton, Sarah M

2015-01-01

The early-life environment critically influences neurodevelopment and later psychological health. To elucidate neural and environmental elements that shape emotional behavior, we developed a rat model of individual differences in temperament and environmental reactivity. We selectively bred rats for high versus low behavioral response to novelty and found that high-reactive (bred high-responder, bHR) rats displayed greater risk-taking, impulsivity and aggression relative to low-reactive (bred low-responder, bLR) rats, which showed high levels of anxiety/depression-like behavior and certain stress vulnerability. The bHR/bLR traits are heritable, but prior work revealed bHR/bLR maternal style differences, with bLR dams showing more maternal attention than bHRs. The present study implemented a cross-fostering paradigm to examine the contribution of maternal behavior to the brain development and emotional behavior of bLR offspring. bLR offspring were reared by biological bLR mothers or fostered to a bLR or bHR mother and then evaluated to determine the effects on the following: (1) developmental gene expression in the hippocampus and amygdala and (2) adult anxiety/depression-like behavior. Genome-wide expression profiling showed that cross-fostering bLR rats to bHR mothers shifted developmental gene expression in the amygdala (but not hippocampus), reduced adult anxiety and enhanced social interaction. Our findings illustrate how an early-life manipulation such as cross-fostering changes the brain's developmental trajectory and ultimately impacts adult behavior. Moreover, while earlier studies highlighted hippocampal differences contributing to the bHR/bLR phenotypes, our results point to a role of the amygdala as well. Future work will pursue genetic and cellular mechanisms within the amygdala that contribute to bHR/bLR behavior either at baseline or following environmental manipulations. © 2015 S. Karger AG, Basel.

Progression of Treated versus Untreated Liver Imaging Reporting and Data System Category 4 Masses after Transcatheter Arterial Embolization Therapy.

PubMed

Ronald, James; Gupta, Rajan T; Marin, Daniele; Wang, Qi; Durocher, Nicholas S; Suhocki, Paul V; Kim, Charles Y

2018-05-01

To compare outcomes of treated vs untreated Liver Imaging Reporting and Data System category 4 (LR-4) masses after transcatheter arterial embolization. In 167 patients undergoing embolization for HCC from January 2005 to December 2012, LR-4 masses were retrospectively identified on CT and MR imaging examinations performed before embolization. In 149 patients undergoing embolization from January 2013 to December 2016, masses prospectively classified as LR-4 were identified. In total, there were 81 LR-4 masses in 62 patients (16 women; mean age 62 y; range 29-83 y). Procedures were reviewed to determine whether LR-4 masses were within or outside the liver volume that received embolization during treatment of dominant masses. Time to progression to LR-5 and by modified Response Evaluation Criteria in Solid Tumors (mRECIST) was estimated for treated vs untreated LR-4 masses using the Kaplan-Meier method and compared using the log rank test. LR-4 masses averaged 1.8 cm; 88%, 60%, 14%, and 14% demonstrated arterial phase hyperenhancement, washout, a capsule, and growth. Of LR-4 masses, 62 were within the liver volume that received embolization and considered treated, and 19 were outside and considered untreated. Response rates according to mRECIST were 37% vs 21% for treated vs untreated masses (P = .27). The 6- and 12-month rates of progression to LR-5 were 7% and 26% for treated masses vs 27% and 75% for untreated masses (P = .001). According to mRECIST, 7% and 27% of treated masses progressed vs 30% and 65% of untreated masses (P = .001). LR-4 masses that receive embolization in the setting of dominant masses elsewhere show lower rates of progression compared with untreated masses. Copyright © 2017 SIR. Published by Elsevier Inc. All rights reserved.

Reproduction impairment and endocrine disruption in female zebrafish after long-term exposure to MC-LR: A life cycle assessment.

PubMed

Hou, Jie; Li, Li; Wu, Ning; Su, Yujing; Lin, Wang; Li, Guangyu; Gu, Zemao

2016-01-01

Microcystin-LR (MC-LR) has been found to cause reproductive and developmental impairments as well as to disrupt sex hormone homeostasis of fish during acute and sub-chronic toxic experiments. However, fish in natural environments are continuously exposed to MC-LR throughout their entire life cycle as opposed to short-term exposure. Here, we tested the hypothesis that the mechanism by which MC-LR harms female fish reproduction and development within natural water bodies is through interference of the reproductive endocrine system. In the present study, zebrafish hatchlings (5 d post-fertilization) were exposed to 0, 0.3, 3 and 30 μg/L MC-LR for 90 d until reaching sexual maturity. Female zebrafish were selected, and the changes in growth and developmental indicators, ovarian ultrastructure as well as the levels of gonadal steroid hormones and vitellogenin (VTG) were examined along with the transcription of related genes in the hypothalamic-pituitary-gonadal-liver axis (HPGL-axis). The results showed for the first time, a life cycle exposure to MC-LR caused growth inhibition, decreased ovary weight and ovarian ultra-pathological lesions. Decreased ovarian testosterone levels indicated that MC-LR disrupted sex steroid hormone balance. Significantly up-regulated transcription of brain FSHβ and LHβ along with ovarian ERα, FSHR and LHR suggested positive feedback regulation in the HPGL-axis was induced as a compensatory mechanism for MC-LR damage. It was also noted that ovarian VTG content and hepatic ERα and VTG1 expression were all down-regulated, which might be responsible for reduced vitellus storage noted in our histological observations. Our findings indicate that a life cycle exposure to MC-LR impairs the development and reproduction of female zebrafish by disrupting the transcription of related HPGL-axis genes, suggesting that MC-LR has potential adverse effects on fish reproduction and thus population dynamics in MCs-contaminated aquatic environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

A comparison of faecal microbial populations of South African Windsnyer-type indigenous pigs (SAWIPs) and Large White × Landrace (LW × LR) crosses fed diets containing ensiled maize cobs.

PubMed

Kanengoni, Arnold T; Chimonyo, Michael; Tasara, Taurai; Cormican, Paul; Chapwanya, Aspinas; Ndimba, Bongani K; Dzama, Kennedy

2015-07-01

Faecal microbial communities in South African Windsnyer-type indigenous pigs (SAWIPs) and Large White × Landrace (LW × LR) crosses were investigated using high-throughput sequencing of the 16S rDNA genes. The faecal microbial communities in LW × LR crosses and SAWIPs fed control (CON) and high maize cob (HMC) diets were evaluated through parallel sequencing of 16S rDNA genes. Butrivibrio, Faecalibacterium and Desulfovibrio, although present in LW × LR pigs, were absent from the SAWIP microbial community. Bacteroides, Succiniclasticum, Peptococcus and Akkermansia were found in SAWIPs but not in LW × LR crosses. The ratios of Bacteroidia to Clostridia on the CON and HMC diets were similar (0.37 versus 0.39) in SAWIPs but different (0.24 versus 0.1) in LW × LR crosses. The faecal microbial profiles determined were different between the LW × LR and SAWIP breeds but not between pigs fed the CON and HMC diets. The composition of faecal bacterial communities in SAWIPs was determined for the first time. The differences in microbial communities detected may explain the enhanced ability of SAWIPs to digest fibrous diets compared with the LW × LR crosses. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Modular implementation of a digital hardware design automation system

NASA Astrophysics Data System (ADS)

Masud, M.

An automation system based on AHPL (A Hardware Programming Language) was developed. The project may be divided into three distinct phases: (1) Upgrading of AHPL to make it more universally applicable; (2) Implementation of a compiler for the language; and (3) illustration of how the compiler may be used to support several phases of design activities. Several new features were added to AHPL. These include: application-dependent parameters, mutliple clocks, asynchronous results, functional registers and primitive functions. The new language, called Universal AHPL, has been defined rigorously. The compiler design is modular. The parsing is done by an automatic parser generated from the SLR(1)BNF grammar of the language. The compiler produces two data bases from the AHPL description of a circuit. The first one is a tabular representation of the circuit, and the second one is a detailed interconnection linked list. The two data bases provide a means to interface the compiler to application-dependent CAD systems.

The wheat resistance gene Lr34 results in the constitutive induction of multiple defense pathways in transgenic barley.

PubMed

Chauhan, Harsh; Boni, Rainer; Bucher, Rahel; Kuhn, Benjamin; Buchmann, Gabriele; Sucher, Justine; Selter, Liselotte L; Hensel, Goetz; Kumlehn, Jochen; Bigler, Laurent; Glauser, Gaëtan; Wicker, Thomas; Krattinger, Simon G; Keller, Beat

2015-10-01

The wheat gene Lr34 encodes an ABCG-type transporter which provides durable resistance against multiple pathogens. Lr34 is functional as a transgene in barley, but its mode of action has remained largely unknown both in wheat and barley. Here we studied gene expression in uninfected barley lines transgenic for Lr34. Genes from multiple defense pathways contributing to basal and inducible disease resistance were constitutively active in seedlings and mature leaves. In addition, the hormones jasmonic acid and salicylic acid were induced to high levels, and increased levels of lignin as well as hordatines were observed. These results demonstrate a strong, constitutive re-programming of metabolism by Lr34. The resistant Lr34 allele (Lr34res) encodes a protein that differs by two amino acid polymorphisms from the susceptible Lr34sus allele. The deletion of a single phenylalanine residue in Lr34sus was sufficient to induce the characteristic Lr34-based responses. Combination of Lr34res and Lr34sus in the same plant resulted in a reduction of Lr34res expression by 8- to 20-fold when the low-expressing Lr34res line BG8 was used as a parent. Crosses with the high-expressing Lr34res line BG9 resulted in an increase of Lr34sus expression by 13- to 16-fold in progenies that inherited both alleles. These results indicate an interaction of the two Lr34 alleles on the transcriptional level. Reduction of Lr34res expression in BG8 crosses reduced the negative pleiotropic effects of Lr34res on barley growth and vigor without compromising disease resistance, suggesting that transgenic combination of Lr34res and Lr34sus can result in agronomically useful resistance. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Imaging markers for Alzheimer disease

PubMed Central

Bocchetta, Martina; Chételat, Gael; Rabinovici, Gil D.; de Leon, Mony J.; Kaye, Jeffrey; Reiman, Eric M.; Scheltens, Philip; Barkhof, Frederik; Black, Sandra E.; Brooks, David J.; Carrillo, Maria C.; Fox, Nick C.; Herholz, Karl; Nordberg, Agneta; Jack, Clifford R.; Jagust, William J.; Johnson, Keith A.; Rowe, Christopher C.; Sperling, Reisa A.; Thies, William; Wahlund, Lars-Olof; Weiner, Michael W.; Pasqualetti, Patrizio; DeCarli, Charles

2013-01-01

Revised diagnostic criteria for Alzheimer disease (AD) acknowledge a key role of imaging biomarkers for early diagnosis. Diagnostic accuracy depends on which marker (i.e., amyloid imaging, 18F-fluorodeoxyglucose [FDG]-PET, SPECT, MRI) as well as how it is measured (“metric”: visual, manual, semiautomated, or automated segmentation/computation). We evaluated diagnostic accuracy of marker vs metric in separating AD from healthy and prognostic accuracy to predict progression in mild cognitive impairment. The outcome measure was positive (negative) likelihood ratio, LR+ (LR−), defined as the ratio between the probability of positive (negative) test outcome in patients and the probability of positive (negative) test outcome in healthy controls. Diagnostic LR+ of markers was between 4.4 and 9.4 and LR− between 0.25 and 0.08, whereas prognostic LR+ and LR− were between 1.7 and 7.5, and 0.50 and 0.11, respectively. Within metrics, LRs varied up to 100-fold: LR+ from approximately 1 to 100; LR− from approximately 1.00 to 0.01. Markers accounted for 11% and 18% of diagnostic and prognostic variance of LR+ and 16% and 24% of LR−. Across all markers, metrics accounted for an equal or larger amount of variance than markers: 13% and 62% of diagnostic and prognostic variance of LR+, and 29% and 18% of LR−. Within markers, the largest proportion of diagnostic LR+ and LR− variability was within 18F-FDG-PET and MRI metrics, respectively. Diagnostic and prognostic accuracy of imaging AD biomarkers is at least as dependent on how the biomarker is measured as on the biomarker itself. Standard operating procedures are key to biomarker use in the clinical routine and drug trials. PMID:23897875

The relationships of the level of response to alcohol and additional characteristics to alcohol use disorders across adulthood: a discrete-time survival analysis.

PubMed

Trim, Ryan S; Schuckit, Marc A; Smith, Tom L

2009-09-01

A low level of response (LR) to alcohol has been shown to relate to a higher risk for alcohol use disorders (AUDs). However, no previous research has examined the association between LR and the development of AUDs in the context of additional robust risk factors for AUDs. This study evaluated whether LR and other related characteristics predicted the occurrence of AUDs across adulthood using discrete-time survival analysis (DTSA). A total of 297 probands from the San Diego Prospective Study reported on the LR to alcohol, a family history (FH) of AUDs, the typical drinking quantity, the age of drinking onset, the body mass index and the age at the baseline (T1) assessment. Alcohol use disorders (AUDs) were evaluated at the 10-year (T10), T15, T20, and T25 follow-ups. A low LR to alcohol predicted AUD occurrence over the course of adulthood even after controlling for the effects of other robust risk factors. Interaction effects revealed that the impact of FH on AUDs was only observed for subjects with high T1 drinking levels, and probands with high T1 drinking were at high risk for AUDs regardless of their age of onset. The findings illustrate that LR is a unique risk factor for AUDs across adulthood, and not simply a reflection of a broader range of risk factors. The continued investigation of how LR is related to AUD onset later in life will help inform treatment providers about this high-risk population, and future longitudinal evaluations will utilize DTSA to assess rates of AUD remission as well as the onset of drinking outcomes in adolescent samples.

The Relationships of the Level of Response to Alcohol and Additional Characteristics to Alcohol Use Disorders across Adulthood: A Discrete-Time Survival Analysis

PubMed Central

Trim, Ryan S.; Schuckit, Marc A.; Smith, Tom L.

2010-01-01

Background A low level of response (LR) to alcohol has been shown to relate to a higher risk for alcohol use disorders (AUDs). However, no previous research has examined the association between LR and the development of AUDs in the context of additional robust risk factors for AUDs. This study evaluated whether LR and other related characteristics predicted the occurrence of AUDs across adulthood using discrete-time survival analysis (DTSA). Methods 297 probands from the San Diego Prospective Study reported on the LR to alcohol, a family history (FH) of AUDs, the typical drinking quantity, the age of drinking onset, the body mass index and the age at the baseline (T1) assessment. Alcohol use disorders (AUDs) were evaluated at the 10-year (T10), T15, T20, and T25 follow-ups. Results A low LR to alcohol predicted AUD occurrence over the course of adulthood even after controlling for the effects of other robust risk factors. Interaction effects revealed that the impact of FH on AUDs was only observed for subjects with high T1 drinking levels, and probands with high T1 drinking were at high risk for AUDs regardless of their age of onset. Conclusion The findings illustrate that LR is a unique risk factor for AUDs across adulthood, and not simply a reflection of a broader range of risk factors. The continued investigation of how LR is related to AUD onset later in life will help inform treatment providers about this high-risk population, and future longitudinal evaluations will utilize DTSA to assess rates of AUD remission as well as the onset of drinking outcomes in adolescent samples. PMID:19485971

78 FR 64255 - Exelon Generation Company, LLC; Establishment of Atomic Safety and Licensing Board

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-28

.... 13- 929-02-LR-BD01] Exelon Generation Company, LLC; Establishment of Atomic Safety and Licensing... hereby given that an Atomic Safety and Licensing Board (Board) is being established to preside over the... is comprised of the following administrative judges: Paul S. Ryerson, Chairman, Atomic Safety and...

Simultaneous Microcystis Algicidal and Microcystin Degrading Capability by a Single Acinetobacter Bacterial Strain.

PubMed

Li, Hong; Ai, Hainan; Kang, Li; Sun, Xingfu; He, Qiang

2016-11-01

Measures for removal of toxic harmful algal blooms often cause lysis of algal cells and release of microcystins (MCs). In this study, Acinetobacter sp. CMDB-2 that exhibits distinct algal lysing activity and MCs degradation capability was isolated. The physiological response and morphological characteristics of toxin-producing Microcystis aeruginosa, the dynamics of intra- and extracellular MC-LR concentration were studied in an algal/bacterial cocultured system. The results demonstrated that Acinetobacter sp. CMDB-2 caused thorough decomposition of algal cells and impairment of photosynthesis within 24 h. Enhanced algal lysis and MC-LR release appeared with increasing bacterial density from 1 × 10 3 to 1 × 10 7 cells/mL; however, the MC-LR was reduced by nearly 94% within 14 h irrespective of bacterial density. Measurement of extracellular and intracellular MC-LR revealed that the toxin was decreased by 92% in bacterial cell incubated systems relative to control and bacterial cell-free filtrate systems. The results confirmed that the bacterial metabolite caused 92% lysis of Microcystis aeruginosa cells, whereas the bacterial cells were responsible for approximately 91% reduction of MC-LR. The joint efforts of the bacterium and its metabolite accomplished the sustainable removal of algae and MC-LR. This is the first report of a single bacterial strain that achieves these dual actions.

The combined effects of Dolichospermum flos-aquae, light, and temperature on microcystin production by Microcystis aeruginosa

NASA Astrophysics Data System (ADS)

Chen, Ruoqi; Li, Fangfang; Liu, Jiadong; Zheng, Hongye; Shen, Fei; Xue, Yarong; Liu, Changhong

2016-11-01

The effects of light, temperature, and coculture on the intracellular microcystin-LR (MC-LR) quota of Microcystis aeruginosa were evaluated based on coculture experiments with nontoxic Dolichospermum ( Anabaena) flos-aquae. The MC-LR quota and transcription of mcyB and mcyD genes encoding MC synthetases in M. aeruginosa were evaluated on the basis of cell counts, high-performance liquid chromatography, and reverse-transcription quantitative real-time PCR. The MC-LR quotas of M. aeruginosa in coculture with a 1/1 ratio of inoculum of the two species were significantly lower relative to monocultures 6-d after inoculation. Decreased MC-LR quotas under coculture conditions were enhanced by increasing the D. flos-aquae to M. aeruginosa ratio in the inoculum and by environmental factors, such as temperature and light intensity. Moreover, the transcriptional concentrations of mcyB and mcyD genes in M. aeruginosa were significantly inhibited by D. flos-aquae competition in coculture ( P <0.01), lowered to 20% of initial concentrations within 8 days. These data suggested that coculture eff ects by D. flos-aquae not only reduced M. aeruginosa's intracellular MC-LR quota via inhibition of genes encoding MC synthetases, but also that this eff ect was regulated by environmental factors, including temperature and light intensities.

Importance of ocean mesoscale variability for air-sea interactions in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Putrasahan, D. A.; Kamenkovich, I.; Le Hénaff, M.; Kirtman, B. P.

2017-06-01

Mesoscale variability of currents in the Gulf of Mexico (GoM) can affect oceanic heat advection and air-sea heat exchanges, which can influence climate extremes over North America. This study is aimed at understanding the influence of the oceanic mesoscale variability on the lower atmosphere and air-sea heat exchanges. The study contrasts global climate model (GCM) with 0.1° ocean resolution (high resolution; HR) with its low-resolution counterpart (1° ocean resolution with the same 0.5° atmosphere resolution; LR). The LR simulation is relevant to current generation of GCMs that are still unable to resolve the oceanic mesoscale. Similar to observations, HR exhibits positive correlation between sea surface temperature (SST) and surface turbulent heat flux anomalies, while LR has negative correlation. For HR, we decompose lateral advective heat fluxes in the upper ocean into mean (slowly varying) and mesoscale-eddy (fast fluctuations) components. We find that the eddy flux divergence/convergence dominates the lateral advection and correlates well with the SST anomalies and air-sea latent heat exchanges. This result suggests that oceanic mesoscale advection supports warm SST anomalies that in turn feed surface heat flux. We identify anticyclonic warm-core circulation patterns (associated Loop Current and rings) which have an average diameter of 350 km. These warm anomalies are sustained by eddy heat flux convergence at submonthly time scales and have an identifiable imprint on surface turbulent heat flux, atmospheric circulation, and convective precipitation in the northwest portion of an averaged anticyclone.

Prevalence, incidence and correlates of low risk HPV infection and anogenital warts in a cohort of women living with HIV in Burkina Faso and South Africa

PubMed Central

2018-01-01

Objective To report the prevalence and incidence of low-risk human papillomavirus infection (LR-HPV) and anogenital warts (AGW) among women living with HIV (WLHIV) in Burkina Faso (BF) and South Africa (SA), and to explore HIV-related factors associated with these outcomes. Methods We enrolled 1238 WLHIV (BF = 615; SA = 623) aged 25–50 years and followed them at three time points (6, 12 and 16 months) after enrolment. Presence of AGW was assessed during gynaecological examination. Cervico-vaginal swabs for enrolment and month 16 follow-up visits were tested for HPV infection by Inno-LiPA® genotyping. Logistic regression was used to assess risk factors for prevalent infection or AGW. Cox regression was used to assess risk factors for incident AGW. Results Women in SA were more likely than those in BF to have prevalent LR-HPV infection (BF: 27.1% vs. SA: 40.9%; p<0.001) and incident LR-HPV infection (BF: 25.8% vs. SA: 31.6%, p = 0.05). Prevalence of persistent LR-HPV was similar in the two countries (BF: 33.3% vs. SA: 30.4%; p = 0.54), as were prevalence and incidence of AGW (Prevalence: BF: 7.5% vs. SA: 5.7%; p = 0.21; Incidence: BF: 2.47 vs. SA: 2.33 per 100 person-years; p = 0.41). HPV6 was associated with incident AGW (BF: adjusted Hazard Ratio (aHR) = 4.88; 95%CI: 1.36–17.45; SA: aHR = 5.02; 95%CI: 1.40–17.99). Prevalent LR-HPV (BF: adjusted Odds Ratio [aOR = 1.86]; 95%CI: 1.01–3.41; SA: aOR = 1.75; 95%CI: 0.88–3.48); persistent LR-HPV (BF: aOR = 1.92; 95%CI: 0.44–8.44; SA: aOR = 2.81; 95%CI: 1.07–7.41) and prevalent AGW (BF: aOR = 1.53; 95%CI: 0.61–3.87; SA: aOR = 4.11; 95%CI: 1.20–14.10) were each associated with low CD4+ counts (i.e. <200 vs. >500 cells/μL). Duration of ART and HIV plasma viral load were not associated with any LR-HPV infection or AGW outcomes. Conclusion LR-HPV infection and AGW are common in WLHIV in sub-Saharan Africa. Type-specific HPV vaccines and effective ART with immunological reconstitution could reduce the burden of AGW in this population. PMID:29715305

Life-cycle exposure to microcystin-LR interferes with the reproductive endocrine system of male zebrafish.

PubMed

Su, Yujing; Li, Li; Hou, Jie; Wu, Ning; Lin, Wang; Li, Guangyu

2016-06-01

Recently, MC-LR reproductive toxicity drew great attention. Limited information was available on endocrine-disrupting effects of MC-LR on the reproduction system in fish. In the present study, zebrafish hatchlings (5 d post-fertilization) were exposed to 0, 0.3, 3 and 30μg/L MC-LR for 90 d until they reached sexual maturity. Male zebrafish were selected, and changes in growth and developmental parameters, testicular histological structure as well as the levels of gonadal steroid hormones were studied along with the related-gene transcriptional responses in the hypothalamic-pituitary-gonadal axis (HPG-axis). The results, for the first time, show a life cycle exposure to MC-LR causes growth inhibition, testicular damage and delayed sperm maturation. A significant decrease in T/E2 ratio indicated that MC-LR disrupted sex steroid hormones balance. The changes in transcriptional responses of HPG-axis related genes revealed that MC-LR promoted the conversion of T to E2 in circulating blood. It was also noted that vtg1 mRNA expression in the liver was up-regulated, which implied that MC-LR could induce estrogenic-like effects at environmentally relevant concentrations and long-term exposure. Our findings indicated that a life cycle exposure to MC-LR causes endocrine disruption with organic and functional damage of the testis, which might compromise the quality of life for the survivors and pose a potent threat on fish reproduction and thus population dynamics in MCs-contaminated aquatic environments. Copyright © 2016 Elsevier B.V. All rights reserved.

Automatic Lung-RADS™ classification with a natural language processing system.

PubMed

Beyer, Sebastian E; McKee, Brady J; Regis, Shawn M; McKee, Andrea B; Flacke, Sebastian; El Saadawi, Gilan; Wald, Christoph

2017-09-01

Our aim was to train a natural language processing (NLP) algorithm to capture imaging characteristics of lung nodules reported in a structured CT report and suggest the applicable Lung-RADS™ (LR) category. Our study included structured, clinical reports of consecutive CT lung screening (CTLS) exams performed from 08/2014 to 08/2015 at an ACR accredited Lung Cancer Screening Center. All patients screened were at high-risk for lung cancer according to the NCCN Guidelines ® . All exams were interpreted by one of three radiologists credentialed to read CTLS exams using LR using a standard reporting template. Training and test sets consisted of consecutive exams. Lung screening exams were divided into two groups: three training sets (500, 120, and 383 reports each) and one final evaluation set (498 reports). NLP algorithm results were compared with the gold standard of LR category assigned by the radiologist. The sensitivity/specificity of the NLP algorithm to correctly assign LR categories for suspicious nodules (LR 4) and positive nodules (LR 3/4) were 74.1%/98.6% and 75.0%/98.8% respectively. The majority of mismatches occurred in cases where pulmonary findings were present not currently addressed by LR. Misclassifications also resulted from the failure to identify exams as follow-up and the failure to completely characterize part-solid nodules. In a sub-group analysis among structured reports with standardized language, the sensitivity and specificity to detect LR 4 nodules were 87.0% and 99.5%, respectively. An NLP system can accurately suggest the appropriate LR category from CTLS exam findings when standardized reporting is used.

Automatic Lung-RADS™ classification with a natural language processing system

PubMed Central

Beyer, Sebastian E.; Regis, Shawn M.; McKee, Andrea B.; Flacke, Sebastian; El Saadawi, Gilan; Wald, Christoph

2017-01-01

Background Our aim was to train a natural language processing (NLP) algorithm to capture imaging characteristics of lung nodules reported in a structured CT report and suggest the applicable Lung-RADS™ (LR) category. Methods Our study included structured, clinical reports of consecutive CT lung screening (CTLS) exams performed from 08/2014 to 08/2015 at an ACR accredited Lung Cancer Screening Center. All patients screened were at high-risk for lung cancer according to the NCCN Guidelines®. All exams were interpreted by one of three radiologists credentialed to read CTLS exams using LR using a standard reporting template. Training and test sets consisted of consecutive exams. Lung screening exams were divided into two groups: three training sets (500, 120, and 383 reports each) and one final evaluation set (498 reports). NLP algorithm results were compared with the gold standard of LR category assigned by the radiologist. Results The sensitivity/specificity of the NLP algorithm to correctly assign LR categories for suspicious nodules (LR 4) and positive nodules (LR 3/4) were 74.1%/98.6% and 75.0%/98.8% respectively. The majority of mismatches occurred in cases where pulmonary findings were present not currently addressed by LR. Misclassifications also resulted from the failure to identify exams as follow-up and the failure to completely characterize part-solid nodules. In a sub-group analysis among structured reports with standardized language, the sensitivity and specificity to detect LR 4 nodules were 87.0% and 99.5%, respectively. Conclusions An NLP system can accurately suggest the appropriate LR category from CTLS exam findings when standardized reporting is used. PMID:29221286

Effect of cyanotoxins on the hypothalamic-pituitary-gonadal axis in male adult mouse.

PubMed

Xiong, Xiaolu; Zhong, Anyuan; Xu, Huajun

2014-01-01

Microcystins LR (MC-LR) are hepatotoxic cyanotoxins that have been shown to induce reproductive toxicity, and Hypothalamic-Pituitary-Gonadal Axis (HPG) is responsible for the control of reproductive functions. However, few studies have been performed to evaluate the effects of MC-LR on HPG axis. This study aimed to investigate the MC-LR-induced toxicity in the reproductive system of mouse and focus on the HPG axis. Adult male C57BL/6 mice were exposed to various concentrations of MC-LR (0, 3.75, 7.50, 15.00 and 30.00 µg/kg body weight per day) for 1 to 14 days, and it was found that exposure to different concentrations of MC-LR significantly disturbed sperm production in the mice testes in a dose- and time-dependent manner. To elucidate the associated possible mechanisms, the serum levels of testosterone, follicle-stimulating hormone (FSH) and luteinizing hormone (LH) were assessed. Meanwhile, PCR assays were employed to detect alterations in a series of genes involved in HPG axis, such as FSH, LH, gonadotropin-releasing hormone (GnRH) and their complement receptors. Furthermore, the effect of MC-LR on the viability and testosterone production of Leydig cells were tested in vitro. MC-LR significantly impaired the spermatogenesis of mice possibly through the direct or indirect inhibition of GnRH synthesis at the hypothalamic level, which resulted in reduction of serum levels of LH that lead to suppression of testosterone production in the testis of mice. MC-LR may be a GnRH toxin that would disrupt the reproductive system of mice.

U.S. EPA, Pesticide Product Label, SCOTTS "ALL-OUT" SPOT WEEDER, 03/15/1968

EPA Pesticide Factsheets

2011-04-14

... drift lH" ill'l'lic;,'i.'11 to I'l';lr1>)" t'.an:<'11 [>1<'11 •..• , fJfl\\·:vrs lll' ~hnd.:. COlltl'llt~; l'Il,I,)' pr"".:urc, !)o !lot 1I,;l' 1I"'lr firl' (II' U\\,l'll fLil'l', S(1)',· in ...

Nitric oxide generated by nitrate reductase increases nitrogen uptake capacity by inducing lateral root formation and inorganic nitrogen uptake under partial nitrate nutrition in rice

PubMed Central

Sun, Huwei; Li, Jiao; Song, Wenjing; Tao, Jinyuan; Huang, Shuangjie; Chen, Si; Hou, Mengmeng; Xu, Guohua; Zhang, Yali

2015-01-01

Increasing evidence shows that partial nitrate nutrition (PNN) can be attributed to improved plant growth and nitrogen-use efficiency (NUE) in rice. Nitric oxide (NO) is a signalling molecule involved in many physiological processes during plant development and nitrogen (N) assimilation. It remains unclear whether molecular NO improves NUE through PNN. Two rice cultivars (cvs Nanguang and Elio), with high and low NUE, respectively, were used in the analysis of NO production, nitrate reductase (NR) activity, lateral root (LR) density, and 15N uptake under PNN, with or without NO production donor and inhibitors. PNN increased NO accumulation in cv. Nanguang possibly through the NIA2-dependent NR pathway. PNN-mediated NO increases contributed to LR initiation, 15NH4 +/15NO3 – influx into the root, and levels of ammonium and nitrate transporters in cv. Nanguang but not cv. Elio. Further results revealed marked and specific induction of LR initiation and 15NH4 +/15NO3 – influx into the roots of plants supplied with NH4 ++sodium nitroprusside (SNP) relative to those supplied with NH4 + alone, and considerable inhibition upon the application of cPTIO or tungstate (NR inhibitor) in addition to PNN, which is in agreement with the change in NO fluorescence in the two rice cultivars. The findings suggest that NO generated by the NR pathway plays a pivotal role in improving the N acquisition capacity by increasing LR initiation and the inorganic N uptake rate, which may represent a strategy for rice plants to adapt to a fluctuating nitrate supply and increase NUE. PMID:25784715

Multi-Virulence-Locus Sequence Typing of Staphylococcus lugdunensis Generates Results Consistent with a Clonal Population Structure and Is Reliable for Epidemiological Typing

PubMed Central

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis

2014-01-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. PMID:25078912

Local recurrence of prostate cancer after radical prostatectomy is at risk to be missed in 68Ga-PSMA-11-PET of PET/CT and PET/MRI: comparison with mpMRI integrated in simultaneous PET/MRI.

PubMed

Freitag, Martin T; Radtke, Jan P; Afshar-Oromieh, Ali; Roethke, Matthias C; Hadaschik, Boris A; Gleave, Martin; Bonekamp, David; Kopka, Klaus; Eder, Matthias; Heusser, Thorsten; Kachelriess, Marc; Wieczorek, Kathrin; Sachpekidis, Christos; Flechsig, Paul; Giesel, Frederik; Hohenfellner, Markus; Haberkorn, Uwe; Schlemmer, Heinz-Peter; Dimitrakopoulou-Strauss, A

2017-05-01

The positron emission tomography (PET) tracer 68 Ga-PSMA-11, targeting the prostate-specific membrane antigen (PSMA), is rapidly excreted into the urinary tract. This leads to significant radioactivity in the bladder, which may limit the PET-detection of local recurrence (LR) of prostate cancer (PC) after radical prostatectomy (RP), developing in close proximity to the bladder. Here, we analyze if there is additional value of multi-parametric magnetic resonance imaging (mpMRI) compared to the 68 Ga-PSMA-11-PET-component of PET/CT or PET/MRI to detect LR. One hundred and nineteen patients with biochemical recurrence after prior RP underwent both hybrid 68 Ga-PSMA-11-PET/CT low-dose (1 h p.i.) and -PET/MRI (2-3 h p.i.) including a mpMRI protocol of the prostatic bed. The comparison of both methods was restricted to the abdomen with focus on LR (McNemar). Bladder-LR distance and recurrence size were measured in axial T2w-TSE. A logistic regression was performed to determine the influence of these variables on detectability in 68 Ga-PSMA-11-PET. Standardized-uptake-value (SUV mean ) quantification of LR was performed. There were 93/119 patients that had at least one pathologic finding. In addition, 18/119 Patients (15.1%) were diagnosed with a LR in mpMRI of PET/MRI but only nine were PET-positive in PET/CT and PET/MRI. This mismatch was statistically significant (p = 0.004). Detection of LR using the PET-component was significantly influenced by proximity to the bladder (p = 0.028). The PET-pattern of LR-uptake was classified into three types (1): separated from bladder; (2): fuses with bladder, and (3): obliterated by bladder). The size of LRs did not affect PET-detectability (p = 0.84), mean size was 1.7 ± 0.69 cm long axis, 1.2 ± 0.46 cm short-axis. SUV mean in nine men was 8.7 ± 3.7 (PET/CT) and 7.0 ± 4.2 (PET/MRI) but could not be quantified in the remaining nine cases (obliterated by bladder). The present study demonstrates additional value of hybrid 68 Ga-PSMA-11-PET/MRI by gaining complementary diagnostic information compared to the 68 Ga-PSMA-11-PET/CT low-dose for patients with LR of PC.

Xyce parallel electronic simulator reference guide, version 6.1

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

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

2014-03-01

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .

Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress

DOE PAGES

Dash, Madhumita; Yordanov, Yordan S.; Georgieva, Tatyana; ...

2017-02-10

Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here in this study, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) genemore » with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.« less

Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress

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

Dash, Madhumita; Yordanov, Yordan S.; Georgieva, Tatyana

Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here in this study, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) genemore » with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.« less

Determination of microcystin-LR in drinking water using UPLC tandem mass spectrometry-matrix effects and measurement.

PubMed

Li, Wei; Duan, Jinming; Niu, Chaoying; Qiang, Naichen; Mulcahy, Dennis

2011-10-01

A simple detection method using ultra-performance liquid chromatography electrospray ionisation tandem mass spectrometry (UPLC-ESI-MS-MS) coupled with the sample dilution method for determining trace microcystin-LR (MC-LR) in drinking water is presented. The limit of detection (LOD) was 0.04 µg/L and the limit of quantitation (LOQ) was 0.1 µg/L. Water matrix effects of ionic strength, dissolved organic carbon (DOC) and pH were examined. The results indicate that signal detection intensity for MC-LR was significantly suppressed as the ionic strength increased from ultrapure water condition, whereas it increased slightly with solution pH and DOC at low concentrations. However, addition of methanol (MeOH) into the sample was able to counter the signal suppression effects. In this study, dilution of the tap water sample by adding 4% MeOH (v/v) was observed to be adequate to compensate for the signal suppression. The recoveries of the samples fortified with MC-LR (0.2, 1, and 10 µg/L) for three different tap water samples ranged from 84.4% to 112.9%.

Diagnosing clinically significant dehydration in children with acute gastroenteritis using noninvasive methods: a meta-analysis.

PubMed

Freedman, Stephen B; Vandermeer, Ben; Milne, Andrea; Hartling, Lisa

2015-04-01

To determine the most accurate, noninvasive method of assessing dehydration. The following data sources were searched: electronic databases, gray literature, scientific meetings, reference lists, and authors of unpublished studies. Eligible studies were comparative outpatient evaluations that used an accepted reference standard and were conducted in developed countries in children aged <18 years with gastroenteritis. Data extraction was completed independently by multiple reviewers before a consensus was made. Nine studies that included 1039 participants were identified. The 4-item Clinical Dehydration Scale (CDS), the "Gorelick" score, and unstructured physician assessment were evaluated in 3, 2, and 5 studies, respectively. Bedside ultrasound, capillary digital videography, and urinary measurements were each evaluated in one study. The CDS had a positive likelihood ratio (LR) range of 1.87-11.79 and a negative LR range of 0.30-0.71 to predict 6% dehydration. When combined with the 4-item Gorelick Score, the positive LR was 1.93 (95% CI 1.07-3.49) and negative LR was of 0.40 (95% CI 0.24-0.68). Unstructured dehydration assessment had a pooled positive LR of 2.13 (95% CI 1.33-3.44) and negative LR of 0.48 (95% CI 0.28-0.82) to detect ≥ 5% dehydration. Overall, the clinical scales evaluated provide some improved diagnostic accuracy. However, test characteristics indicate that their ability to identify children both with and without dehydration is suboptimal. Current evidence does not support the routine use of ultrasound or urinalysis to determine dehydration severity. Copyright © 2015 Elsevier Inc. All rights reserved.

Xyce parallel electronic simulator reference guide, version 6.0.

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

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

2013-08-01

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .

Nodal Stage of Surgically Resected Non-Small Cell Lung Cancer and Its Effect on Recurrence Patterns and Overall Survival

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

Varlotto, John M., E-mail: john.varlotto@umassmemorial.org; Yao, Aaron N.; DeCamp, Malcolm M.

Purpose: Current National Comprehensive Cancer Network guidelines recommend postoperative radiation therapy (PORT) for patients with resected non-small cell lung cancer (NSCLC) with N2 involvement. We investigated the relationship between nodal stage and local-regional recurrence (LR), distant recurrence (DR) and overall survival (OS) for patients having an R0 resection. Methods and Materials: A multi-institutional database of consecutive patients undergoing R0 resection for stage I-IIIA NSCLC from 1995 to 2008 was used. Patients receiving any radiation therapy before relapse were excluded. A total of 1241, 202, and 125 patients were identified with N0, N1, and N2 involvement, respectively; 161 patients received chemotherapy.more » Cumulative incidence rates were calculated for LR and DR as first sites of failure, and Kaplan-Meier estimates were made for OS. Competing risk analysis and proportional hazards models were used to examine LR, DR, and OS. Independent variables included age, sex, surgical procedure, extent of lymph node sampling, histology, lymphatic or vascular invasion, tumor size, tumor grade, chemotherapy, nodal stage, and visceral pleural invasion. Results: The median follow-up time was 28.7 months. Patients with N1 or N2 nodal stage had rates of LR similar to those of patients with N0 disease, but were at significantly increased risk for both DR (N1, hazard ratio [HR] = 1.84, 95% confidence interval [CI]: 1.30-2.59; P=.001; N2, HR = 2.32, 95% CI: 1.55-3.48; P<.001) and death (N1, HR = 1.46, 95% CI: 1.18-1.81; P<.001; N2, HR = 2.33, 95% CI: 1.78-3.04; P<.001). LR was associated with squamous histology, visceral pleural involvement, tumor size, age, wedge resection, and segmentectomy. The most frequent site of LR was the mediastinum. Conclusions: Our investigation demonstrated that nodal stage is directly associated with DR and OS but not with LR. Thus, even some patients with, N0-N1 disease are at relatively high risk of local recurrence. Prospective identification of risk factors for local recurrence may aid in selecting an appropriate population for further study of postoperative radiation therapy.« less

Comparison of the HEART and TIMI Risk Scores for Suspected Acute Coronary Syndrome in the Emergency Department.

PubMed

Sun, Benjamin C; Laurie, Amber; Fu, Rongwei; Ferencik, Maros; Shapiro, Michael; Lindsell, Christopher J; Diercks, Deborah; Hoekstra, James W; Hollander, Judd E; Kirk, J Douglas; Peacock, W Frank; Anantharaman, Venkataraman; Pollack, Charles V

2016-03-01

The emergency department evaluation for suspected acute coronary syndrome (ACS) is common, costly, and challenging. Risk scores may help standardize clinical care and screening for research studies. The Thrombolysis in Myocardial Infarction (TIMI) and HEART are two commonly cited risk scores. We tested the null hypothesis that the TIMI and HEART risk scores have equivalent test characteristics. We analyzed data from the Internet Tracking Registry of Acute Coronary Syndromes (i*trACS) from 9 EDs on patients with suspected ACS, 1999-2001. We excluded patients with an emergency department diagnosis consistent with ACS, or without sufficient data to calculate TIMI and HEART scores. The primary outcome was 30-day major adverse cardiovascular events, including all-cause death, acute myocardial infarction, and urgent revascularization. We describe test characteristics of the TIMI and HEART risk scores. The study cohort included 8255 patients with 508 (6.2%) 30-day major adverse cardiovascular events. Receiver operating curve and reclassification analyses favored HEART [c statistic: 0.753, 95% confidence interval (CI): 0.733-0.773; continuous net reclassification improvement: 0.608, 95% CI: 0.527-0.689] over TIMI (c statistic: 0.678, 95% CI: 0.655-0.702). A HEART score 0-3 [negative predictive value (NPV) 0.982, 95% CI: 0.978-0.986; positive predictive value (PPV) 0.103, 95% CI: 0.094-0.113; likelihood ratio (LR) positive 1.76; LR negative 0.28] demonstrates similar or superior NPV/PPV/LR compared with TIMI = 0 (NPV 0.978, 95% CI: 0.971-0.983; PPV 0.077, 95% CI: 0.071-0.084; LR positive 1.28; LR negative 0.35) and TIMI = 0-1 (NPV 0.963, 95% CI: 0.958-0.968; PPV 0.102, 95% CI: 0.092-0.113; LR positive 1.73; LR negative 0.58). The HEART score has better discrimination than TIMI and outperforms TIMI within previously published "low-risk" categories.

Comparative study of cyanotoxins affecting cytoskeletal and chromatin structures in CHO-K1 cells.

PubMed

Gácsi, Mariann; Antal, Otilia; Vasas, Gábor; Máthé, Csaba; Borbély, György; Saker, Martin L; Gyori, János; Farkas, Anna; Vehovszky, Agnes; Bánfalvi, Gáspár

2009-06-01

In this study we compared the effects of the two frequently occuring and most dangerous cyanobacterial toxins on the cellular organization of microfilaments, microtubules and on the chromatin structure in Chinese hamster ovary (CHO-K1) cells. These compounds are the widely known microcystin-LR (MC-LR) and cylindrospermopsin (CYN) classified as the highest-priority cyanotoxin. Toxic effects were tested in a concentration and time dependent manner. The hepatotoxic MC-LR did not cause significant cytotoxicity on CHO-K1 cells under 20 microM, but caused apoptotic changes at higher concentrations. Apoptotic shrinkage was associated with the shortening and loss of actin filaments and with a concentration dependent depolymerization of microtubules. No necrosis was observed over the concentration range (1-50 microM MC-LR) tested. Cylindrospermopsin did cause apoptosis at low concentrations (1-2 microM) and over short exposure periods (12h). Necrosis was observed at higher concentrations (5-10 microM) and following longer exposure periods (24 or 48h). Cyanotoxins also affected the chromatin structure. The condensation process was inhibited by MC-LR at a later stage and manifested as broken elongated prechromosomes. CYN inhibited chromatin condensation at the early fibrillary stage leading to blurred fluorescent images of apoptotic bodies and preventing the formation of metaphase chromosomes. Cylindrospermopsin exhibited a more pronounced toxic effect causing cytoskeletal and nuclear changes as well as apoptotic and necrotic alterations.

Clinical usefulness of the faecal calprotectin test in suspected paediatric inflammatory bowel disease.

PubMed

Akobeng, Anthony K

2018-04-29

The faecal calprotectin (FC) test is increasingly being used in clinical practice to help select children with gastrointestinal symptoms who might have inflammatory bowel disease (IBD) and benefit from endoscopies. We provide an overview of the advantages and limitations of the FC test. PubMed was searched for meta-analyses that had investigated the diagnostic accuracy of the FC test and the pooled sensitivity and specificity for distinguishing IBD from non-IBD patients were used to calculate likelihood ratios (LR). These were applied to practical examples to explain how easily clinicians can use the results to modify pre-test probabilities of IBD and generate post-test probabilities for IBD. The positive LR and negative LR of the FC test were 2.8 and 0.015, respectively. The usefulness of the FC test depended on the pre-test probability of IBD. When the pre-test probability of IBD was low, a positive FC test did not necessarily indicate IBD. However, because of the very small negative LR, a negative FC result virtually ruled out IBD in most cases. The FC test should not be used indiscriminately in children with gastrointestinal symptoms but should be targeted at those who are likely to have IBD. ©2018 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Bead-based competitive fluorescence immunoassay for sensitive and rapid diagnosis of cyanotoxin risk in drinking water.

PubMed

Yu, Hye-Weon; Jang, Am; Kim, Lan Hee; Kim, Sung-Jo; Kim, In S

2011-09-15

Due to the increased occurrence of cyanobacterial blooms and their toxins in drinking water sources, effective management based on a sensitive and rapid analytical method is in high demand for security of safe water sources and environmental human health. Here, a competitive fluorescence immunoassay of microcystin-LR (MCYST-LR) is developed in an attempt to improve the sensitivity, analysis time, and ease-of-manipulation of analysis. To serve this aim, a bead-based suspension assay was introduced based on two major sensing elements: an antibody-conjugated quantum dot (QD) detection probe and an antigen-immobilized magnetic bead (MB) competitor. The assay was composed of three steps: the competitive immunological reaction of QD detection probes against analytes and MB competitors, magnetic separation and washing, and the optical signal generation of QDs. The fluorescence intensity was found to be inversely proportional to the MCYST-LR concentration. Under optimized conditions, the proposed assay performed well for the identification and quantitative analysis of MCYST-LR (within 30 min in the range of 0.42-25 μg/L, with a limit of detection of 0.03 μg/L). It is thus expected that this enhanced assay can contribute both to the sensitive and rapid diagnosis of cyanotoxin risk in drinking water and effective management procedures.

Left-right asymmetry is formed in individual cells by intrinsic cell chirality.

PubMed

Hatori, Ryo; Ando, Tadashi; Sasamura, Takeshi; Nakazawa, Naotaka; Nakamura, Mitsutoshi; Taniguchi, Kiichiro; Hozumi, Shunya; Kikuta, Junichi; Ishii, Masaru; Matsuno, Kenji

2014-08-01

Many animals show left-right (LR) asymmetric morphology. The mechanisms of LR asymmetric development are evolutionarily divergent, and they remain elusive in invertebrates. Various organs in Drosophila melanogaster show stereotypic LR asymmetry, including the embryonic gut. The Drosophila embryonic hindgut twists 90° left-handedly, thereby generating directional LR asymmetry. We recently revealed that the hindgut epithelial cell is chiral in shape and other properties; this is termed planar cell chirality (PCC). We previously showed by computer modeling that PCC is sufficient to induce the hindgut rotation. In addition, both the PCC and the direction of hindgut twisting are reversed in Myosin31DF (Myo31DF) mutants. Myo31DF encodes Drosophila MyosinID, an actin-based motor protein, whose molecular functions in LR asymmetric development are largely unknown. Here, to understand how PCC directs the asymmetric cell-shape, we analyzed PCC in genetic mosaics composed of cells homozygous for mutant Myo31DF, some of which also overexpressed wild-type Myo31DF. Wild-type cell-shape chirality only formed in the Myo31DF-overexpressing cells, suggesting that cell-shape chirality was established in each cell and reflects intrinsic PCC. A computer model recapitulating the development of this genetic mosaic suggested that mechanical interactions between cells are required for the cell-shape behavior seen in vivo. Our mosaic analysis also suggested that during hindgut rotation in vivo, wild-type Myo31DF suppresses the elongation of cell boundaries, supporting the idea that cell-shape chirality is an intrinsic property determined in each cell. However, the amount and distribution of F-actin and Myosin II, which are known to help generate the contraction force on cell boundaries, did not show differences between Myo31DF mutant cells and wild-type cells, suggesting that the static amount and distribution of these proteins are not involved in the suppression of cell-boundary elongation. Taken together, our results suggest that cell-shape chirality is intrinsically formed in each cell, and that mechanical force from intercellular interactions contributes to its formation and/or maintenance. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Stochastic Downscaling of Digital Elevation Models

NASA Astrophysics Data System (ADS)

Rasera, Luiz Gustavo; Mariethoz, Gregoire; Lane, Stuart N.

2016-04-01

High-resolution digital elevation models (HR-DEMs) are extremely important for the understanding of small-scale geomorphic processes in Alpine environments. In the last decade, remote sensing techniques have experienced a major technological evolution, enabling fast and precise acquisition of HR-DEMs. However, sensors designed to measure elevation data still feature different spatial resolution and coverage capabilities. Terrestrial altimetry allows the acquisition of HR-DEMs with centimeter to millimeter-level precision, but only within small spatial extents and often with dead ground problems. Conversely, satellite radiometric sensors are able to gather elevation measurements over large areas but with limited spatial resolution. In the present study, we propose an algorithm to downscale low-resolution satellite-based DEMs using topographic patterns extracted from HR-DEMs derived for example from ground-based and airborne altimetry. The method consists of a multiple-point geostatistical simulation technique able to generate high-resolution elevation data from low-resolution digital elevation models (LR-DEMs). Initially, two collocated DEMs with different spatial resolutions serve as an input to construct a database of topographic patterns, which is also used to infer the statistical relationships between the two scales. High-resolution elevation patterns are then retrieved from the database to downscale a LR-DEM through a stochastic simulation process. The output of the simulations are multiple equally probable DEMs with higher spatial resolution that also depict the large-scale geomorphic structures present in the original LR-DEM. As these multiple models reflect the uncertainty related to the downscaling, they can be employed to quantify the uncertainty of phenomena that are dependent on fine topography, such as catchment hydrological processes. The proposed methodology is illustrated for a case study in the Swiss Alps. A swissALTI3D HR-DEM (with 5 m resolution) and a SRTM-derived LR-DEM from the Western Alps are used to downscale a SRTM-based LR-DEM from the eastern part of the Alps. The results show that the method is capable of generating multiple high-resolution synthetic DEMs that reproduce the spatial structure and statistics of the original DEM.

Comparison of Astigmatism Induced by Combined Inferior Oblique Anterior Transposition Procedure and Lateral Rectus Recession Alone

PubMed Central

Eum, Sun Jung

2016-01-01

Purpose The purpose of this study is to compare the magnitude and axis of astigmatism induced by a combined inferior oblique (IO) anterior transposition procedure with lateral rectus (LR) recession versus LR recession alone. Methods Forty-six patients were retrospectively analyzed. The subjects were divided into two groups: those having concurrent inferior oblique muscle overaction (IOOA) and intermittent exotropia (group 1, 20 patients) and those having only intermittent exotropia as a control (group 2, 26 patients). Group 1 underwent combined anterior transposition of IO with LR recession and group 2 underwent LR recession alone. Induced astigmatism was defined as the difference between preoperative and postoperative astigmatism using double-angle vector analysis. Cylinder power, axis of induced astigmatism, and spherical equivalent were analyzed at 1 week, 1 month, and 3 months after surgery. Results Larger changes in the axis of induced astigmatism were observed in group 1, with 4.5° incyclotorsion, than in group 2 at 1 week after surgery (axis, 84.5° vs. 91°; p < 0.001). However, there was no statistically significant inter-group difference thereafter. Relaxation and rapid regression in the incyclotorsion of induced astigmatism were observed over-time. Spherical equivalent significantly decreased postoperatively at 1 month in both groups, indicating a myopic shift (p = 0.011 for group 1 and p = 0.019 for group 2) but did not show significant differences at 3 months after surgery (p = 0.107 for group 1 and p = 0.760 for group 2). Conclusions Combined IO anterior transposition procedures caused an increased change in the axis of induced astigmatism, including temporary incyclotorsion, during the first week after surgery. However, this significant difference was not maintained thereafter. Thus, combined IO surgery with LR recession does not seem to produce a sustained astigmatic change, which can be a potential risk factor of postoperative amblyopia or diplopia compared with LR recession alone. PMID:27980365

Comparison of Astigmatism Induced by Combined Inferior Oblique Anterior Transposition Procedure and Lateral Rectus Recession Alone.

PubMed

Eum, Sun Jung; Chun, Bo Young

2016-12-01

The purpose of this study is to compare the magnitude and axis of astigmatism induced by a combined inferior oblique (IO) anterior transposition procedure with lateral rectus (LR) recession versus LR recession alone. Forty-six patients were retrospectively analyzed. The subjects were divided into two groups: those having concurrent inferior oblique muscle overaction (IOOA) and intermittent exotropia (group 1, 20 patients) and those having only intermittent exotropia as a control (group 2, 26 patients). Group 1 underwent combined anterior transposition of IO with LR recession and group 2 underwent LR recession alone. Induced astigmatism was defined as the difference between preoperative and postoperative astigmatism using double-angle vector analysis. Cylinder power, axis of induced astigmatism, and spherical equivalent were analyzed at 1 week, 1 month, and 3 months after surgery. Larger changes in the axis of induced astigmatism were observed in group 1, with 4.5° incyclotorsion, than in group 2 at 1 week after surgery (axis, 84.5° vs. 91°; p < 0.001). However, there was no statistically significant inter-group difference thereafter. Relaxation and rapid regression in the incyclotorsion of induced astigmatism were observed over-time. Spherical equivalent significantly decreased postoperatively at 1 month in both groups, indicating a myopic shift ( p = 0.011 for group 1 and p = 0.019 for group 2) but did not show significant differences at 3 months after surgery ( p = 0.107 for group 1 and p = 0.760 for group 2). Combined IO anterior transposition procedures caused an increased change in the axis of induced astigmatism, including temporary incyclotorsion, during the first week after surgery. However, this significant difference was not maintained thereafter. Thus, combined IO surgery with LR recession does not seem to produce a sustained astigmatic change, which can be a potential risk factor of postoperative amblyopia or diplopia compared with LR recession alone.

High novelty-seeking rats are resilient to negative physiological effects of the early life stress.

PubMed

Clinton, Sarah M; Watson, Stanley J; Akil, Huda

2014-01-01

Exposure to early life stress dramatically impacts adult behavior, physiology, and neuroendocrine function. Using rats bred for novelty-seeking differences and known to display divergent anxiety, depression, and stress vulnerability, we examined the interaction between early life adversity and genetic predisposition for high- versus low-emotional reactivity. Thus, bred Low Novelty Responder (bLR) rats, which naturally exhibit high anxiety- and depression-like behavior, and bred High Novelty Responder (bHR) rats, which show low anxiety/depression together with elevated aggression, impulsivity, and addictive behavior, were subjected to daily 3 h maternal separation (MS) stress postnatal days 1-14. We hypothesized that MS stress would differentially impact adult bHR/bLR behavior, physiology (stress-induced defecation), and neuroendocrine reactivity. While MS stress did not impact bHR and bLR anxiety-like behavior in the open field test and elevated plus maze, it exacerbated bLRs' already high physiological response to stress - stress-induced defecation. In both tests, MS bLR adult offspring showed exaggerated stress-induced defecation compared to bLR controls while bHR offspring were unaffected. MS also selectively impacted bLRs' (but not bHRs') neuroendocrine stress reactivity, producing an exaggerated corticosterone acute stress response in MS bLR versus control bLR rats. These findings highlight how genetic predisposition shapes individuals' response to early life stress. Future work will explore neural mechanisms underlying the distinct behavioral and neuroendocrine consequences of MS in bHR/bLR animals.

An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity.

PubMed

Qiao, Qin; Le Manach, Séverine; Huet, Hélène; Duvernois-Berthet, Evelyne; Chaouch, Soraya; Duval, Charlotte; Sotton, Benoit; Ponger, Loïc; Marie, Arul; Mathéron, Lucrèce; Lennon, Sarah; Bolbach, Gérard; Djediat, Chakib; Bernard, Cécile; Edery, Marc; Marie, Benjamin

2016-12-01

Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L -1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L -1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L -1  MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a wider range of biological pathways, compared with pure MC-LR, and even 1 μg L -1  MC-LR potentially induces a health risk for aquatic organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Combining evidence using likelihood ratios in writer verification

NASA Astrophysics Data System (ADS)

Srihari, Sargur; Kovalenko, Dimitry; Tang, Yi; Ball, Gregory

2013-01-01

Forensic identification is the task of determining whether or not observed evidence arose from a known source. It involves determining a likelihood ratio (LR) - the ratio of the joint probability of the evidence and source under the identification hypothesis (that the evidence came from the source) and under the exclusion hypothesis (that the evidence did not arise from the source). In LR- based decision methods, particularly handwriting comparison, a variable number of input evidences is used. A decision based on many pieces of evidence can result in nearly the same LR as one based on few pieces of evidence. We consider methods for distinguishing between such situations. One of these is to provide confidence intervals together with the decisions and another is to combine the inputs using weights. We propose a new method that generalizes the Bayesian approach and uses an explicitly defined discount function. Empirical evaluation with several data sets including synthetically generated ones and handwriting comparison shows greater flexibility of the proposed method.

Effects of a new advanced glycation inhibitor, LR-90, on mitigating arterial stiffening and improving arterial elasticity and compliance in a diabetic rat model: aortic impedance analysis.

PubMed

Satheesan, S; Figarola, J L; Dabbs, T; Rahbar, S; Ermel, R

2014-06-01

We determined the effects of treatment with LR-90, an inhibitor of advanced glycation end products, on the mechanical properties of the arterial system in streptozotocin (STZ)-induced diabetic Sprague Dawley rats, using aortic impedance analysis, and further investigated the effects of LR-90 on the progression of aortic pathology. STZ-induced diabetic rats were treated with or without LR-90 (50 mg L(-1) in drinking water) for 8 weeks and compared with control groups. Arterial BP measurements, various metabolic parameters, aortic histopathology, collagen cross-linking, AGE accumulation, and RAGE protein expression in aortic tissue were determined. Pulsatile parameters were evaluated using a standard Fourier series expansion technique and impulse response function of the filtered aortic input impedance spectra. LR-90 reduced glycated haemoglobin and triglycerides levels, although it had no effect on the glycaemic status. LR-90 did not affect arterial BP, but prevented the diabetes-induced increase in peripheral resistance and variations in aortic distensibility, as it reduced aortic characteristic impedance by 21%. LR-90 also prevented the elevation in wave reflection factor, as indicated by a 22.5% reduction and an associated increase of 23.5% in wave transit time, suggesting it prevents the augmentation of the systolic load of the left ventricle. Moreover, LR-90 inhibited collagen cross-linking and the accumulation of AGE and RAGE in the vasculature of diabetic rats. Treatment with LR-90 may impart significant protection against diabetes-induced aortic stiffening and cardiac hypertrophy and provides an additional therapeutic option for treatment of AGE associated diabetic complications. © 2014 The British Pharmacological Society.

The utility of serum tryptase in the diagnosis of food-induced anaphylaxis.

PubMed

Wongkaewpothong, Patcharaporn; Pacharn, Punchama; Sripramong, Chaweewan; Boonchoo, Siribangon; Piboonpocanun, Surapon; Visitsunthorn, Nualanong; Vichyanond, Pakit; Jirapongsananuruk, Orathai

2014-07-01

This study investigates the utility of serum tryptase for the confirmation of shrimp-induced anaphylaxis. Patients with a history of shrimp allergy and positive skin prick tests (SPT) to commercial shrimp extract were recruited for shrimp challenges. Serum total tryptase was obtained at baseline and 60 min (peak) after the onset of symptoms. Thirty-nine patients were challenged. There were 12 patients with anaphylaxis, 20 with mild reactions and 7 without symptoms (control group). Characteristic features and baseline tryptase were not different among the 3 groups. The peak tryptase levels were higher than the baseline in anaphylaxis and mild reaction groups (P<0.05). The delta-tryptase (peak minus baseline) and the tryptase ratio (peak divided by baseline) in the anaphylaxis group were higher than the mild reaction and control groups (P<0.01). The optimum cut-off for peak tryptase to confirm anaphylaxis was 2.99 µg/L with 50% sensitivity, 85% specificity, 3.33 positive likelihood ratio (LR) and 0.59 negative LR. The manufacturer's cut-off for peak tryptase was >11.4 µg/L with 17% sensitivity, 100% specificity, infinity positive LR and 0.83 negative LR. The best cut-off for delta-tryptase was ≥0.8 µg/L with 83% sensitivity, 93% specificity, 11.86 positive LR and 0.18 negative LR. The best cut-off for tryptase ratio was ≥1.5 with 92% sensitivity, 96% specificity, 23 positive LR and 0.08 negative LR. The peak tryptase level should be compared with the baseline value to confirm anaphylaxis. The tryptase ratio provide the best sensitivity, specificity, positive and negative LR than a single peak serum tryptase for the confirmation of shrimp-induced anaphylaxis.

Genetic predisposition to high anxiety- and depression-like behavior coincides with diminished DNA methylation in the adult rat amygdala

PubMed Central

McCoy, Chelsea R.; Jackson, Nateka L.; Day, Jeremy; Clinton, Sarah M.

2016-01-01

Understanding biological mechanisms that shape vulnerability to emotional dysfunction is critical for elucidating the neurobiology of psychiatric illnesses like anxiety and depression. To elucidate molecular and epigenetic alterations in the brain that contribute to individual differences in emotionality, our laboratory utilized a rodent model of temperamental differences. Rats bred for low response to novelty (Low Responders, LRs) are inhibited in novel situations and display high anxiety, helplessness, and diminished sociability compared to High Novelty Responder (HR) rats. Our current transcriptome profiling experiment identified widespread gene expression differences in the amygdala of adult HR/LR rats; we hypothesize that HR/LR gene expression and downstream behavioral differences stem from distinct epigenetic (specifically DNA methylation) patterning in the HR/LR brain. Although we found similar levels of DNA methyltransferase proteins in the adult HR/LR amygdala, next-generation sequencing analysis of the methylome revealed 793 differentially methylated genomic sites between the groups. Most of the differentially methylated sites were hypermethylated in HR versus LR, so we next tested the hypothesis that enhancing DNA methylation in LRs would improve their anxiety/depression-like phenotype. We found that increasing DNA methylation in LRs (via increased dietary methyl donor content) improved their anxiety-like behavior and decreased their typically high levels of Forced Swim Test (FST) immobility; however, dietary methyl donor depletion exacerbated LRs’ high FST immobility. These data are generally consistent with findings in depressed patients showing that treatment with DNA methylation-promoting agents improves depressive symptoms, and highlight epigenetic mechanisms that may contribute to individual differences in risk for emotional dysfunction. PMID:27965039

Accumulation of free and covalently bound microcystins in tissues of Lymnaea stagnalis (Gastropoda) following toxic cyanobacteria or dissolved microcystin-LR exposure.

PubMed

Lance, Emilie; Neffling, Milla-Riina; Gérard, Claudia; Meriluoto, Jussi; Bormans, Myriam

2010-03-01

Accumulation of free microcystins (MCs) in freshwater gastropods has been demonstrated but accumulation of MCs covalently bound to tissues has never been considered so far. Here, we follow the accumulation of total (free and bound) MCs in Lymnaea stagnalis exposed to i) dissolved MC-LR (33 and 100 microg L(-1)) and ii) Planktothrix agardhii suspensions producing 5 and 33 microg MC-LR equivalents L(-1) over a 5-week period, and after a 3-week depuration period. Snails exposed to dissolved MC-LR accumulated up to 0.26 microg total MCs g(-1) dry weight (DW), with no detection of bound MCs. Snails exposed to MCs producing P. agardhii accumulated up to 69.9 microg total MCs g(-1) DW, of which from 17.7 to 66.7% were bound. After depuration, up to 15.3 microg g(-1) DW of bound MCs were detected in snails previously exposed to toxic cyanobacteria, representing a potential source of MCs transfer through the food web. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

Identifying common donors in DNA mixtures, with applications to database searches.

PubMed

Slooten, K

2017-01-01

Several methods exist to compute the likelihood ratio LR(M, g) evaluating the possible contribution of a person of interest with genotype g to a mixed trace M. In this paper we generalize this LR to a likelihood ratio LR(M 1 , M 2 ) involving two possibly mixed traces M 1 and M 2 , where the question is whether there is a donor in common to both traces. In case one of the traces is in fact a single genotype, then this likelihood ratio reduces to the usual LR(M, g). We explain how our method conceptually is a logical consequence of the fact that LR calculations of the form LR(M, g) can be equivalently regarded as a probabilistic deconvolution of the mixture. Based on simulated data, and using a semi-continuous mixture evaluation model, we derive ROC curves of our method applied to various types of mixtures. From these data we conclude that searches for a common donor are often feasible in the sense that a very small false positive rate can be combined with a high probability to detect a common donor if there is one. We also show how database searches comparing all traces to each other can be carried out efficiently, as illustrated by the application of the method to the mixed traces in the Dutch DNA database. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Linking Semantic and Knowledge Representations in a Multi-Domain Dialogue System

DTIC Science & Technology

2007-06-01

accuracy evaluation presented in the next section shows that the generic version of the grammar performs similarly well on two evaluation domains...of extra insertions; for example, discourse adverbials such as now were inserted if present in the lattice. In addition, different tense and pronoun...automatic lexicon specialization technique improves parser speed and accuracy. 1 Introduction This paper presents an architecture of a language

An efficient representation of spatial information for expert reasoning in robotic vehicles

NASA Technical Reports Server (NTRS)

Scott, Steven; Interrante, Mark

1987-01-01

The previous generation of robotic vehicles and drones was designed for a specific task, with limited flexibility in executing their mission. This limited flexibility arises because the robotic vehicles do not possess the intelligence and knowledge upon which to make significant tactical decisions. Current development of robotic vehicles is toward increased intelligence and capabilities, adapting to a changing environment and altering mission objectives. The latest techniques in artificial intelligence (AI) are being employed to increase the robotic vehicle's intelligent decision-making capabilities. This document describes the design of the SARA spatial database tool, which is composed of request parser, reasoning, computations, and database modules that collectively manage and derive information useful for robotic vehicles.

Lateral Root Initiation in Arabidopsis: Developmental Window, Spatial Patterning, Density and Predictability

PubMed Central

DUBROVSKY, J. G.; GAMBETTA, G. A.; HERNÁNDEZ-BARRERA, A.; SHISHKOVA, S.; GONZÁLEZ, I.

2006-01-01

• Background and Aims The basic regulatory mechanisms that control lateral root (LR) initiation are still poorly understood. An attempt is made to characterize the pattern and timing of LR initiation, to define a developmental window in which LR initiation takes place and to address the question of whether LR initiation is predictable. • Methods The spatial patterning of LRs and LR primordia (LRPs) on cleared root preparations were characterized. New measures of LR and LRP densities (number of LRs and/or LRPs divided by the length of the root portions where they are present) were introduced and illustrate the shortcomings of the more customarily used measure through a comparative analysis of the mutant aux1-7. The enhancer trap line J0121 was used to monitor LR initiation in time-lapse experiments and a plasmolysis-based method was developed to determine the number of pericycle cells between successive LRPs. • Key Results LRP initiation occurred strictly acropetally and no de novo initiation events were found between already developed LRs or LRPs. However, LRPs did not become LRs in a similar pattern. The longitudinal spacing of lateral organs was variable and the distance between lateral organs was proportional to the number of cells and the time between initiations of successive LRPs. There was a strong tendency towards alternation in LR initiation between the two pericycle cell files adjacent to the protoxylem poles. LR density increased with time due to the emergence of slowly developing LRPs and appears to be unique for individual Arabidopsis accessions. • Conclusions. In Arabidopsis there is a narrow developmental window for LR initiation, and no specific cell-count or distance-measuring mechanisms have been found that determine the site of successive initiation events. Nevertheless, the branching density and lateral organ density (density of LRs and LRPs) are accession-specific, and based on the latter density the average distance between successive LRs can be predicted. PMID:16390845

Bedside clinical signs associated with impending death in patients with advanced cancer: preliminary findings of a prospective, longitudinal cohort study.

PubMed

Hui, David; Dos Santos, Renata; Chisholm, Gary; Bansal, Swati; Souza Crovador, Camila; Bruera, Eduardo

2015-03-15

Five highly specific physical signs associated with death within 3 days among cancer patients were recently reported that may aid in the diagnosis of impending death. In this study, the frequency and onset of another 52 bedside physical signs and their diagnostic performance for impending death were examined. Three hundred fifty-seven consecutive patients with advanced cancer who had been admitted to acute palliative care units at 2 tertiary care cancer centers were enrolled. Fifty-two physical signs were systematically documented every 12 hours from admission to death or discharge. The frequency and median time of onset of each sign from death backwards were examined, and the likelihood ratios (LRs) associated with death within 3 days were calculated. Two hundred three of the 357 patients (57%) died at the end of the admission. Eight physical signs that were highly diagnostic of impending death were identified. These signs occurred in 5% to 78% of the patients within the last 3 days of life, had a late onset, and had a high specificity (>95%) and a high positive LR for death within 3 days. They included nonreactive pupils (positive LR, 16.7; 95% confidence interval [CI], 14.9-18.6), a decreased response to verbal stimuli (positive LR, 8.3; 95% CI, 7.7-9), a decreased response to visual stimuli (positive LR, 6.7; 95% CI, 6.3-7.1), an inability to close eyelids (positive LR, 13.6; 95% CI, 11.7-15.5), drooping of the nasolabial fold (positive LR, 8.3; 95% CI, 7.7-8.9), hyperextension of the neck (positive LR, 7.3; 95% CI, 6.7-8), grunting of vocal cords (positive LR, 11.8; 95% CI, 10.3-13.4), and upper gastrointestinal bleeding (positive LR, 10.3; 95% CI, 9.5-11.1). Eight highly specific physical signs associated with death within 3 days among cancer patients were identified. These signs may inform the diagnosis of impending death. © 2015 American Cancer Society.

Comparison of conventional versus three-dimensional ultrasound in fetal renal pelvis measurement and their potential prediction of neonatal uropathies.

PubMed

Duin, L K; Nijhuis, J G; Scherjon, S A; Vossen, M; Willekes, C

2016-01-01

To establish a threshold value for fetal renal pelvis dilatation measured by automatic volume calculation (SonoAVC) in the third trimester of pregnancy to predict neonatal uropathies, and to compare these results with conventional antero-posterior (AP) measurement, fetal kidney 3D volume and renal parenchymal thickness. In a prospective cohort study, 125 fetuses with renal pelvis AP diameter of ≥5 mm both at 20 weeks of gestation and in the third trimester, underwent an additional 3D volume measurement of the fetal kidney in the third trimester. Receiver operating characteristic (ROC) curves for establishing threshold values for fetal renal pelvis volume, AP measurement, fetal kidney volume and renal parenchymal thickness to predict neonatal uropathies were analyzed. Also, sensitivity, specificity, area under the curve (AUC) and likelihood ratios were calculated. A cut-off point of 1.58 cm³ was identified in the third trimester of pregnancy (AUC 0.865 (95% CI 0.789-0.940), sensitivity 76.3%, specificity 87.4%, LR+ 6.06, LR- 0.27) for measurements with SonoAVC. A cut-off value of 11.5 mm was established in the third trimester of pregnancy (AUC 0.828 (95% CI 0.737-0.918), sensitivity 71.1%, specificity 85.1%, LR+ 4.77, LR- 0.34) for the conventional AP measurement. A cut-off point for fetal kidney volume was calculated at 13.29 cm³ (AUC 0.769 (95% CI 0.657-0.881), sensitivity 71%, specificity 66%, LR+ 2.09, LR- 0.44). For renal parenchymal thickness, a cut-off point of 8.4 mm was established (AUC 0.216 (95% CI 0.117-0.315), sensitivity 31.6%, specificity 32.6%, LR+ 0.47, LR- 2.10). This study demonstrates that 3D fetal renal pelvis volume measurements and AP measurements both have a good and comparable diagnostic performance, fetal renal volume a fair accuracy and renal parenchymal thickness a poor accuracy in predicting postnatal renal outcome.

Revisiting the Ceara Rise, equatorial Atlantic Ocean: isotope stratigraphy of ODP Leg 154

NASA Astrophysics Data System (ADS)

Wilkens, Roy; Drury, Anna Joy; Westerhold, Thomas; Lyle, Mitchell; Gorgas, Thomas; Tian, Jun

2017-04-01

Isotope stratigraphy has become the method of choice for investigating both past ocean temperatures and global ice volume. Lisiecki and Raymo (2005) published a stacked record of 57 globally distributed benthic δ18O records versus age (LR04 stack). In this study LR04 is compared to high resolution records collected at all of the sites drilled during Ocean Drilling Program (ODP) Leg 154 on the Ceara Rise, in the western equatorial Atlantic Ocean. Newly developed software - the Code for Ocean Drilling Data (CODD) - is used to check data splices of the Ceara sites and better align out-of-splice data with in-splice data. CODD allows to depth and age scaled core images recovered from core table photos enormously facilitating data analysis. The entire splices of ODP Sites 925, 926, 927, 928 and 929 were reviewed. Most changes were minor although several large enough to affect age models based on orbital tuning. We revised the astronomically tuned age model for the Ceara Rise by tuning darker, more clay rich layers to Northern Hemisphere insolation minima. Then we assembled a regional composite benthic stable isotope record from published data. This new Ceara Rise stack provides a new regional reference section for the equatorial Atlantic covering the last 5 million years with an independent age model compared to the non-linear ice volume models of the LR04 stack. Comparison shows that the benthic δ18O composite is consistent with the LR04 stack from 0 - 4 Ma despite a short interval between 1.80 and 1.90 Ma, where LR04 exhibits 2 maxima but where Ceara Rise contains only 1. The interval between 4.0 and 4.5 Ma in the Ceara Rise compilation is decidedly different from LR04, reflecting both the low amplitude of the signal over this interval and the limited amount of data available for the LR04 stack. Our results also point out that precession cycles have been misinterpreted as obliquity in the LR04 stack as suggested by the Ceara Rise composite at 4.2 Ma.

Open Radio Communications Architecture Core Framework V1.1.0 Volume 1 Software Users Manual

DTIC Science & Technology

2005-02-01

on a PC utilizing the KDE desktop that comes with Red Hat Linux . The default desktop for most Red Hat Linux installations is the GNOME desktop. The...SCA) v2.2. The software was designed for a desktop computer running the Linux operating system (OS). It was developed in C++, uses ACE/TAO for CORBA...middleware, Xerces for the XML parser, and Red Hat Linux for the Operating System. The software is referred to as, Open Radio Communication

Diagnostic Performance of Peripapillary Retinal Nerve Fiber Layer Thickness for Detection of Glaucoma in an Elderly Population: The ALIENOR Study.

PubMed

Schweitzer, Cedric; Korobelnik, Jean-Francois; Le Goff, Melanie; Rahimian, Olivier; Malet, Florence; Rougier, Marie-Benedicte; Delyfer, Marie-Noelle; Dartigues, Jean-Francois; Delcourt, Cecile

2016-11-01

To assess diagnostic accuracy of spectral-domain optical coherence tomography (SD-OCT) to discriminate glaucoma and control subjects in an elderly population. The antioxidants, essential lipids, nutrition and ocular maladies study (ALIENOR: "Antioxydants, Lipides Essentiels, Nutrition et Maladies Oculaires") is a population-based study. From 2009 to 2010, a total of 624 subjects, aged 74 years or older underwent a complete eye examination, including optic disc color photography and SD-OCT examination of the macula and the optic nerve head. Glaucoma diagnosis was made using retinophotography of the optic nerve head and International Society for Epidemiologic and Geographical Ophthalmology criteria. Average and sectorial peripapillary retinal nerve fiber layer thicknesses (RNFLT) were compared between glaucoma and control subjects using area under the receiver operating characteristic curves (AUC), positive and negative likelihood ratios (LR+/LR-), and diagnostic odds ratios (DOR). A total of 532 subjects had complete data, 492 were classified as controls and 40 were classified as glaucoma. Mean age was 82.1 ± 4.2 years and average RNFLT was significantly different between both groups (controls: 88.7 ± 12.2 μm, glaucoma: 65.4 ± 14.4 μm, P < 0.001). Highest AUC values were observed for average (0.895), temporal-inferior (0.874), and temporal-superior (0.868) RNFLT. Temporal-superior RNFLT had the highest DOR (25.31; LR+, 4.65; LR-, 0.18), followed by average RNFLT (DOR: 24.80; LR+, 6.36; LR-, 0.26). When using the normative database provided by the machine, DOR increased to 31.03 (LR+, 1.75; LR-, 0.06) if at least one parameter was considered abnormal (at P < 0.05). Parameters of SD-OCT RNFL may provide valuable information in a screening strategy to improve glaucoma detection in a general population of elderly people.

Effects of Restoration of Blood Flow on the Development of Aortic Atherosclerosis in ApoE-/- Mice With Unilateral Renal Artery Stenosis.

PubMed

Pathak, Alokkumar S; Huang, Jianhua; Rojas, Mauricio; Bazemore, Taylor C; Zhou, Ruihai; Stouffer, George A

2016-04-03

Chronic unilateral renal artery stenosis (RAS) causes accelerated atherosclerosis in apolipoprotein E-deficient (ApoE(-/-)) mice, but effects of restoration of renal blood flow on aortic atherosclerosis are unknown. Male ApoE(-/-) mice underwent sham surgery (n=16) or had partial ligation of the right renal artery (n=41) with the ligature being removed 4 days later (D4LR; n=6), 8 days later (D8LR; n=11), or left in place for 90 days (chronic RAS; n=24). Ligature removal at 4 or 8 days resulted in improved renal blood flow, decreased plasma angiotensin II levels, a return of systolic blood pressure to baseline, and increased plasma levels of neutrophil gelatinase associated lipocalin. Chronic RAS resulted in increased lipid staining in the aortic arch (33.2% [24.4, 47.5] vs 11.6% [6.1, 14.2]; P<0.05) and descending thoracic aorta (10.2% [6.4, 25.9] vs 4.9% [2.8, 7.8]; P<0.05), compared to sham surgery. There was an increased amount of aortic arch lipid staining in the D8LR group (22.7% [22.1, 32.7]), compared to sham-surgery, but less than observed with chronic RAS. Lipid staining in the aortic arch was not increased in the D4LR group, and lipid staining in the descending aorta was not increased in either the D8LR or D4LR groups. There was less macrophage expression in infrarenal aortic atheroma in the D4LR and D8LR groups compared to the chronic RAS group. Restoration of renal blood flow at either 4 or 8 days after unilateral RAS had a beneficial effect on systolic blood pressure, aortic lipid deposition, and atheroma inflammation. © 2016 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

High Nuclear Hypoxia-Inducible Factor 1 Alpha Expression Is a Predictor of Distant Recurrence in Patients With Resected Pancreatic Adenocarcinoma

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

Colbert, Lauren E.; Winship Cancer Institute, Emory University, Atlanta, Georgia; Memorial Sloan-Kettering Cancer Center, New York, New York

Purpose: To evaluate nuclear hypoxia-inducible factor 1α (HIF-1α) expression as a prognostic factor for distant recurrence (DR) and local recurrence (LR) after pancreatic adenocarcinoma resection. Methods and Materials: Tissue specimens were collected from 98 patients with pancreatic adenocarcinoma who underwent resection without neoadjuvant therapy between January 2000 and December 2011. Local recurrence was defined as radiographic or pathologic evidence of progressive disease in the pancreas, pancreatic bed, or associated nodal regions. Distant recurrence was defined as radiographically or pathologically confirmed recurrent disease in other sites. Immunohistochemical staining was performed and scored by an independent pathologist blinded to patient outcomes. Highmore » HIF-1α overall expression score was defined as high percentage and intensity staining and thus score >1.33. Univariate analysis was performed for HIF-1α score with LR alone and with DR. Multivariate logistic regression was used to determine predictors of LR and DR. Results: Median follow-up time for all patients was 16.3 months. Eight patients (8%) demonstrated isolated LR, 26 patients (26.5%) had isolated DR, and 13 patients had both LR and DR. Fifty-three patients (54%) had high HIF-1α expression, and 45 patients (46%) had low HIF-1α expression. High HIF-1α expression was significantly associated with DR (P=.03), and low HIF-1α expression was significantly associated with isolated LR (P=.03). On multivariate logistic regression analysis, high HIF-1α was the only significant predictor of DR (odds ratio 2.46 [95% confidence interval 1.06-5.72]; P=.03). In patients with a known recurrence, an HIF-1α score ≥2.5 demonstrated a specificity of 100% for DR. Conclusions: High HIF-1α expression is a significant predictor of distant failure versus isolated local failure in patients undergoing resection of pancreatic adenocarcinoma. Expression of HIF-1α may have utility in determining candidates for adjuvant local radiation therapy and systemic chemotherapy.« less

LHC signals for singlet neutrinos from a natural warped seesaw mechanism. I

NASA Astrophysics Data System (ADS)

Agashe, Kaustubh; Du, Peizhi; Hong, Sungwoo

2018-04-01

Recently, it was shown in K. Agashe et al. [Phys. Rev. D 94, 013001 (2016), 10.1103/PhysRevD.94.013001] that a straightforward implementation of the type I seesaw mechanism in a warped extra dimensional framework is in reality a natural realization of "inverse" seesaw; i.e., the Standard Model (SM) neutrino mass is dominantly generated by exchange of pseudo-Dirac TeV-mass SM singlet neutrinos. By the AdS /CFT correspondence, this scenario is dual to these singlet particles being composites of some new strong dynamics, along with the SM Higgs boson (and possibly the top quark), with the rest of the SM particles being mostly elementary. We study signals from production of these heavy neutrinos at the Large Hadron Collider (LHC). We focus on the scenario where the strong sector has a global S U (2 )L×S U (2 )R×U (1 )X symmetry; such a left-right (LR) structure being motivated by consistency with the electroweak (EW) precision tests. The singlet neutrinos are charged under S U (2 )R×U (1 )X symmetry, thus can be produced from WR± exchange, as in four-dimensional LR symmetric models. However, the direct coupling of light quarks to WR± is negligible, due to WR± also being composite (cf. four-dimensional LR models); nonetheless, a sizable coupling can be induced by mixings among the various types of W± bosons. Furthermore, WR± decays dominantly into the singlet and composite partner of charged lepton (cf. SM lepton itself in four-dimensional LR model). This heavy charged lepton, in turn, decays into SM lepton, plus Z /Higgs , thus the latter can be used for extra identification of the signal. For a benchmark scenario with WR± of mass 2 TeV and singlet neutrino of mass 750 GeV, we find that, in both the dilepton +dijet +Higgs and trilepton +Higgs channels, significant evidence can be seen at the 14 TeV LHC for an integrated luminosity of 300 fb-1 and that even discovery is possible with slightly more luminosity.

Independent Predictors of Prognosis Based on Oral Cavity Squamous Cell Carcinoma Surgical Margins.

PubMed

Buchakjian, Marisa R; Ginader, Timothy; Tasche, Kendall K; Pagedar, Nitin A; Smith, Brian J; Sperry, Steven M

2018-05-01

Objective To conduct a multivariate analysis of a large cohort of oral cavity squamous cell carcinoma (OCSCC) cases for independent predictors of local recurrence (LR) and overall survival (OS), with emphasis on the relationship between (1) prognosis and (2) main specimen permanent margins and intraoperative tumor bed frozen margins. Study Design Retrospective cohort study. Setting Tertiary academic head and neck cancer program. Subjects and Methods This study included 426 patients treated with OCSCC resection between 2005 and 2014 at University of Iowa Hospitals and Clinics. Patients underwent excision of OCSCC with intraoperative tumor bed frozen margin sampling and main specimen permanent margin assessment. Multivariate analysis of the data set to predict LR and OS was performed. Results Independent predictors of LR included nodal involvement, histologic grade, and main specimen permanent margin status. Specifically, the presence of a positive margin (odds ratio, 6.21; 95% CI, 3.3-11.9) or <1-mm/carcinoma in situ margin (odds ratio, 2.41; 95% CI, 1.19-4.87) on the main specimen was an independent predictor of LR, whereas intraoperative tumor bed margins were not predictive of LR on multivariate analysis. Similarly, independent predictors of OS on multivariate analysis included nodal involvement, extracapsular extension, and a positive main specimen margin. Tumor bed margins did not independently predict OS. Conclusion The main specimen margin is a strong independent predictor of LR and OS on multivariate analysis. Intraoperative tumor bed frozen margins do not independently predict prognosis. We conclude that emphasis should be placed on evaluating the main specimen margins when estimating prognosis after OCSCC resection.

MRI of the sacroiliac joints in spondyloarthritis: the added value of intra-articular signal changes for a 'positive MRI'.

PubMed

Laloo, Frederiek; Herregods, N; Jaremko, J L; Verstraete, K; Jans, L

2018-05-01

To determine if intra-articular signal changes at the sacroiliac joint space on MRI have added diagnostic value for spondyloarthritis, when compared to bone marrow edema (BME). A retrospective study was performed on the MRIs of sacroiliac joints of 363 patients, aged 16-45 years, clinically suspected of sacroiliitis. BME of the sacroiliac joints was correlated to intra-articular sacroiliac joint MR signal changes: high T1 signal, fluid signal, ankylosis and vacuum phenomenon (VP). These MRI findings were correlated with final clinical diagnosis. Sensitivity (SN), specificity (SP), likelihood ratios (LR), predictive values and post-test probabilities were calculated. BME had SN of 68.9%, SP of 74.0% and LR+ of 2.6 for diagnosis of spondyloarthritis. BME in absence of intra-articular signal changes had a lower SN and LR+ for spondyloarthritis (SN = 20.5%, LR+ 1.4). Concomitant BME and high T1 signal (SP = 97.2%, LR + = 10.5), BME and fluid signal (SP = 98.6%, LR + = 10.3) or BME and ankylosis (SP = 100%) had higher SP and LR+ for spondyloarthritis. Concomitant BME and VP had low LR+ for spondyloarthritis (SP = 91%, LR + =0.9). When BME was absent, intra-articular signal changes were less prevalent, but remained highly specific for spondyloarthritis. Our results suggest that both periarticular and intra-articular MR signal of the sacroiliac joint should be examined to determine whether an MRI is 'positive' or 'not positive' for sacroiliitis associated with spondyloarthritis.

Different uptake of 123I-MIBG in the two main liver lobes: A persistant unsolved mistery.

PubMed

Bonacina, M; Albano, D; Steimberg, N; Bosio, G; Camoni, L; Bertagna, F; Giubbini, R; Mazzoleni, G

2018-05-10

After radiopharmaceutical injection, a heightened 123 I-MIBG concentration is frequently observed in the left hepatic lobe compared to the right one, but the reason of this finding remains unknown. Our aim was to retrospectively analyze the different 123 I-MIBG uptake pattern between the two hepatic lobes and correlate our results with some epidemiological/clinical features. Ninety-four 123 I-MIBG scintigraphies from 71 patients were selected. Regions of interest were drawn in the right and left lobes using transverse tomographic sections and left to right activity ratios (L/R ratio) were calculated at 6 and 24h after radiotracer administration. Twenty-seven examinations were positive for hypermetabolic lesions while the remaining 67 were negative. In all cases mean early and delayed L/R ratios were greater than 1.00; average early L/R ratio was 1.37 and delayed L/R ratio 1.52. The delayed L/R ratio was significantly higher than the early one. There was no difference in the L/R ratios with regard to age, gender, primary disease and result of scintigraphy. 123 I-MIBG uptake was higher in left hepatic lobe compared to right and this ratio did not correlate with any epidemiological or clinical feature. The reason of this metabolic is not yet explained and some biomolecular hypotheses could be tested in 3D dynamic in vitro models. Copyright © 2018 Sociedad Española de Medicina Nuclear e Imagen Molecular. Publicado por Elsevier España, S.L.U. All rights reserved.

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

Canavan, Joycelin, E-mail: canavanjoycelin@gmail.com; Truong, Pauline T.; Smith, Sally L.

Purpose: To evaluate whether local recurrence (LR) risk has changed over time among women with stage I breast cancer treated with breast-conserving therapy. Methods and Materials: Subjects were 5974 women aged ≥50 years diagnosis with pT1N0 breast cancer from 1989 to 2006, treated with breast-conserving surgery and radiation therapy. Clinicopathologic characteristics, treatment, and LR outcomes were compared among 4 cohorts stratified by year of diagnosis: 1989 to 1993 (n=1077), 1994 to 1998 (n=1633), 1999 to 2002 (n=1622), and 2003 to 2006 (n=1642). Multivariable analysis was performed, with year of diagnosis as a continuous variable. Results: Median follow-up time was 8.6more » years. Among patients diagnosed in 1989 to 1993, 1994 to 1998, 1999 to 2002, and 2003 to 2006, the proportions of grade 1 tumors increased (16% vs 29% vs 40% vs 39%, respectively, P<.001). Surgical margin clearance rates increased from 82% to 93% to 95% and 88%, respectively (P<.001). Over time, the proportions of unknown estrogen receptor (ER) status decreased (29% vs 10% vs 1.2% vs 0.5%, respectively, P<.001), whereas ER-positive tumors increased (56% vs 77% vs 86% vs 86%, respectively, P<.001). Hormone therapy use increased (23% vs 23% vs 62% vs 73%, respectively, P<.001), and chemotherapy use increased (2% vs 5% vs 10% vs 13%, respectively, P<.001). The 5-year cumulative incidence rates of LR over the 4 time periods were 2.8% vs 1.7% vs 0.9% vs 0.8%, respectively (Gray's test, P<.001). On competing risk multivariable analysis, year of diagnosis was significantly associated with decreased LR (hazard ratio, 0.92 per year, P=.0003). Relative to grade 1 histology, grades 2, 3, and unknown were associated with increased LR. Hormone therapy use was associated with reduced LR. Conclusion: Significant changes in the multimodality management of stage I breast cancer have occurred over the past 2 decades. More favorable-risk tumors were diagnosed, and margin clearance and systemic therapy use increased. These changes contributed to the observed declining LR rates among patients treated with breast-conserving therapy.« less

Impact of P2Y12 inhibition by clopidogrel on cardiovascular mortality in unselected patients treated by percutaneous coronary angioplasty: a prospective registry.

PubMed

El Ghannudi, Soraya; Ohlmann, Patrick; Meyer, Nicolas; Wiesel, Marie-Louise; Radulescu, Bogdan; Chauvin, Michel; Bareiss, Pierre; Gachet, Christian; Morel, Olivier

2010-06-01

The aim of this study was to determine whether low platelet response to the P2Y(12) receptor antagonist clopidogrel as assessed by Vasodilator-stimulated phosphoprotein flow cytometry test (VASP- FCT) predicts cardiovascular events in a high-risk population undergoing percutaneous coronary intervention (PCI). Impaired platelet responsiveness to clopidogrel is thought to be a determinant of cardiovascular events after PCI. The platelet VASP-FCT is a new assay specific to the P2Y(12) adenosine diphosphate receptor-pathway. In this test, platelet activation is expressed as platelet reactivity index (PRI). Four-hundred sixty-one unselected patients undergoing urgent (n = 346) or planned (n = 115) PCI were prospectively enrolled. Patients were classified as low-response (LR) and response (R) to clopidogrel, depending on their PRI. Optimal PRI cutoff was determined by receiver-operator characteristic curve analysis to 61% (LR: PRI > or =61% and R: PRI <61%). Follow-up was obtained at a mean of 9 +/- 2 months in 453 patients (98.3%). At follow-up, total cardiac mortality rates and possible and total stent thrombosis were higher in LR patients. Multivariate analysis identified creatinine clearance (hazard ratio [HR]: 0.95; 95% confidence interval [CI]: 0.93 to 0.98, p < 0.001), drug-eluting stent (HR: 5.73; 95% CI: 1.40 to 23.43, p = 0.015), C-reactive protein (HR: 1.01; 95% CI: 1.001 to 1.019, p = 0.024), and LR to clopidogrel (HR: 4.00; 95% CI: 1.08 to 14.80, p = 0.037) as independent predictors of cardiac death. The deleterious impact of LR to clopidogrel on cardiovascular death was significantly higher in patients implanted with drug-eluting stent. In patients undergoing PCI, LR to clopidogrel assessed by VASP-FCT is an independent predictor of cardiovascular death at the PRI cutoff value of > or =61%. The LR clinical impact seems to be dependent on the type of stent implanted. Copyright 2010 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Orbital magnetic resonance imaging is useful in age-related distance esotropia.

PubMed

Gómez de Liaño Sanchez, Pilar; Olavarri González, Gloria; Merino Sanz, Pilar; Escribano Villafruela, Jose C

To describe findings for orbital magnetic resonance imaging (MRI) in patients with age-related distance esotropia (ARDE). We compared 31 orbital MRI from patients with ARDE (77±7 SD years) with 2 control groups: 32 orbits from individuals aged 18-50 years (33±8 SD years) and 16 orbits from individuals aged >60 years (77±7 SD years). MRI scans were acquired using 3D fast field echo in T1 sequence without fat saturation. Exclusion criteria for all groups were neurological or thyroid disease and a relevant ophthalmological history (e.g., high myopia, diplopia from another etiology, complicated cataract surgery, etc.). Muscle displacement and characteristics of the lateral rectus-superior rectus (LR-SR) intermuscular band were analyzed. The analysis of the muscles and angles revealed a series of statistically significant differences (p<0.07) between the groups. Subjects with ARDE had LR pulley positions 1.32±0.19mm lower than in younger controls, and the medial rectus (MR) pulley positions were 0.68±0.19mm lower than in younger. Older controls had LR and MR pulley positions 0.85±0.20mm and 0.49±0.23mm lower than in younger. ARDE subjects had LR pulley positions 0.46±0.26mm lower than in older control group. The LR-SR band was absent in 35.5% of ARDE patients and in 12.5% of older control group (p=0.168). MRI showed that displacements of LR and LR-SR band degeneration could facilitate the diagnosis of patients with ARDE. Copyright © 2017 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

A population-based validation study of the DCIS Score predicting recurrence risk in individuals treated by breast-conserving surgery alone.

PubMed

Rakovitch, Eileen; Nofech-Mozes, Sharon; Hanna, Wedad; Baehner, Frederick L; Saskin, Refik; Butler, Steven M; Tuck, Alan; Sengupta, Sandip; Elavathil, Leela; Jani, Prashant A; Bonin, Michel; Chang, Martin C; Robertson, Susan J; Slodkowska, Elzbieta; Fong, Cindy; Anderson, Joseph M; Jamshidian, Farid; Miller, Dave P; Cherbavaz, Diana B; Shak, Steven; Paszat, Lawrence

2015-07-01

Validated biomarkers are needed to improve risk assessment and treatment decision-making for women with ductal carcinoma in situ (DCIS) of the breast. The Oncotype DX DCIS Score (DS) was shown to predict the risk of local recurrence (LR) in individuals with low-risk DCIS treated by breast-conserving surgery (BCS) alone. Our objective was to confirm these results in a larger population-based cohort of individuals. We used an established population-based cohort of individuals diagnosed with DCIS treated with BCS alone from 1994 to 2003 with validation of treatment and outcomes. Central pathology assessment excluded cases with invasive cancer, DCIS < 2 mm or positive margins. Cox model was used to determine the relationship between independent covariates, the DS (hazard ratio (HR)/50 Cp units (U)) and LR. Tumor blocks were collected for 828 patients. Final evaluable population includes 718 cases, of whom 571 had negative margins. Median follow-up was 9.6 years. 100 cases developed LR following BCS alone (DCIS, N = 44; invasive, N = 57). In the primary pre-specified analysis, the DS was associated with any LR (DCIS or invasive) in ER+ patients (HR 2.26; P < 0.001) and in all patients regardless of ER status (HR 2.15; P < 0.001). DCIS Score provided independent information on LR risk beyond clinical and pathologic variables including size, age, grade, necrosis, multifocality, and subtype (adjusted HR 1.68; P = 0.02). DCIS was associated with invasive LR (HR 1.78; P = 0.04) and DCIS LR (HR 2.43; P = 0.005). The DCIS Score independently predicts and quantifies individualized recurrence risk in a population of patients with pure DCIS treated by BCS alone.

Revisiting the Ceara Rise, equatorial Atlantic Ocean: isotope stratigraphy of ODP Leg 154 from 0 to 5 Ma

NASA Astrophysics Data System (ADS)

Wilkens, Roy H.; Westerhold, Thomas; Drury, Anna J.; Lyle, Mitchell; Gorgas, Thomas; Tian, Jun

2017-07-01

Isotope stratigraphy has become the method of choice for investigating both past ocean temperatures and global ice volume. Lisiecki and Raymo (2005) published a stacked record of 57 globally distributed benthic δ18O records versus age (LR04 stack). In this study LR04 is compared to high-resolution records collected at all of the sites drilled during ODP Leg 154 on the Ceara Rise, in the western equatorial Atlantic Ocean. Newly developed software is used to check data splices of the Ceara Rise sites and better align out-of-splice data with in-splice data. Core images recovered from core table photos are depth and age scaled and greatly assist in the data analysis. The entire splices of ODP sites 925, 926, 927, 928 and 929 were reviewed. Most changes were minor although several were large enough to affect age models based on orbital tuning. A Ceara Rise composite record of benthic δ18O is out of sync with LR04 between 1.80 and 1.90 Ma, where LR04 exhibits two maxima but Ceara Rise data contain only one. The interval between 4.0 and 4.5 Ma in the Ceara Rise compilation is decidedly different from LR04, reflecting both the low amplitude of the signal over this interval and the limited amount of data available for the LR04 stack. A regional difference in benthic δ18O of 0.2 ‰ relative to LR04 was found. Independent tuning of Site 926 images and physical property data to the Laskar et al. (2004) orbital solution and integration of available benthic stable isotope data from the Ceara Rise provides a new regional reference section for the equatorial Atlantic covering the last 5 million years.

Interferon-alpha/beta deficiency greatly exacerbates arthritogenic disease in mice infected with wild-type chikungunya virus but not with the cell culture-adapted live-attenuated 181/25 vaccine candidate

PubMed Central

Gardner, Christina L.; Burke, Crystal W.; Higgs, Stephen T.; Klimstra, William B.; Ryman, Kate D.

2012-01-01

In humans, chikungunya virus (CHIKV) infection causes fever, rash, and acute and persisting polyarthalgia/arthritis associated with joint swelling. We report a new CHIKV disease model in adult mice that distinguishes the wild-type CHIKV-LR strain from the live-attenuated vaccine strain (CHIKV-181/25). Although eight-week old normal mice inoculated in the hind footpad developed no hind limb swelling with either virus, CHIKV-LR replicated in musculoskeletal tissues and caused detectable inflammation. In mice deficient in STAT1-dependent interferon (IFN) responses, CHIKV-LR caused significant swelling of the inoculated and contralateral limbs and dramatic inflammatory lesions, while CHIKV-181/25 vaccine and another arthritogenic alphavirus, Sindbis, failed to induce swelling. IFN responses suppressed CHIKV-LR and CHIKV-181/25 replication equally in dendritic cells in vitro whereas macrophages were refractory to infection independently of STAT1-mediated IFN responses. Glycosaminoglycan (GAG) binding may be a CHIKV vaccine attenuation mechanism as CHIKV-LR infectivity was not dependent upon GAG, while CHIKV-181/25 was highly dependent. PMID:22305131

A pM leveled photoelectrochemical sensor for microcystin-LR based on surface molecularly imprinted TiO2@CNTs nanostructure.

PubMed

Liu, Meichuan; Ding, Xue; Yang, Qiwei; Wang, Yu; Zhao, Guohua; Yang, Nianjun

2017-06-05

A simple and highly sensitive photoelectrochemical (PEC) sensor towards Microcystin-LR (MC-LR), a kind of typical cyanobacterial toxin in water samples, was developed on a surface molecular imprinted TiO 2 coated multiwalled carbon nanotubes (MI-TiO 2 @CNTs) hybrid nanostructure. It was synthesized using a feasible two-step sol-gel method combining with in situ surface molecular imprinting technique (MIT). With a controllable core-shell tube casing structure, the resultant MI-TiO 2 @CNTs are enhanced greatly in visible-light driven response capacity. In comparison with the traditional TiO 2 (P25) and non-imprinted (NI-)TiO 2 @CNTs, the MI-TiO 2 @CNTs based PEC sensor showed a much higher photoelectric oxidation capacity towards MC-LR. Using this sensor, the determination of MC-LR was doable in a wide linear range from 1.0pM to 3.0nM with a high photocurrent response sensitivity. An outstanding selectivity towards MC-LR was further achieved with this sensor, proven by simultaneously monitoring 100-fold potential co-existing interferences. The superiority of the obtained MC-LR sensor in sensitivity and selectivity is mainly attributed to the high specific surface area and excellent photoelectric activity of TiO 2 @CNTs heterojunction structure, as well as the abundant active recognition sites on its functionalized molecular imprinting surface. A promising PEC analysis platform with high sensitivity and selectivity for MC-LR has thus been provided. Copyright © 2017 Elsevier B.V. All rights reserved.

Successful introduction and audit of a step-down oral antibiotic strategy for low risk paediatric febrile neutropaenia in a UK, multicentre, shared care setting.

PubMed

Dommett, R; Geary, J; Freeman, S; Hartley, J; Sharland, M; Davidson, A; Tulloh, R; Taj, M; Stoneham, S; Chisholm, J C

2009-11-01

Patients with febrile neutropaenia (FN) can be stratified according to their risk of significant complications, allowing reduced intensity therapy for low risk (LR) episodes. Serious events are very rare in low risk episodes making randomised trials difficult. Introduction of new evidence-based guidelines followed by re-auditing of the outcome is an alternative strategy. New guidelines for the management of LR FN were implemented in 4 specialist paediatric oncology centres (POCs) and in their associated shared care units (POSCUs). All patients commenced empirical intravenous antibiotic therapy and after 48h those with blood culture negative episodes designated LR were eligible for discharge on oral co-amoxiclav. Prospective data collection on FN episodes in all treatment centres was undertaken over a 1-year period. Seven hundred and sixty two eligible episodes of FN were recorded in 368 patients; 213 episodes were initiated in POCs and 549 episodes were initiated in POSCUs. In 40% of episodes no clinical or microbiological focus of infection was found. At 48h, 212 (27%) episodes were classified as LR and 143 of these (19%) were managed on the LR protocol. There was a low hospital readmission rate (8/143 episodes; 5.6%), no intensive care admissions and no deaths in LR episodes. Almost all LR episodes (209/212) occurred in the shared care setting. Rapid step-down to oral antibiotics was a feasible and safe management strategy for LR FN in the shared care setting in England.

Nitric oxide mediates strigolactone signaling in auxin and ethylene-sensitive lateral root formation in sunflower seedlings

PubMed Central

Bharti, Niharika; Bhatla, Satish C

2015-01-01

Strigolactones (SLs) play significant role in shaping root architecture whereby auxin-SL crosstalk has been observed in SL-mediated responses of primary root elongation, lateral root formation and adventitious root (AR) initiation. Whereas GR24 (a synthetic strigolactone) inhibits LR and AR formation, the effect of SL biosynthesis inhibitor (fluridone) is just the opposite (root proliferation). Naphthylphthalamic acid (NPA) leads to LR proliferation but completely inhibits AR development. The diffusive distribution of PIN1 in the provascular cells in the differentiating zone of the roots in response to GR24, fluridone or NPA treatments further indicates the involvement of localized auxin accumulation in LR development responses. Inhibition of LR formation by GR24 treatment coincides with inhibition of ACC synthase activity. Profuse LR development by fluridone and NPA treatments correlates with enhanced [Ca2+]cyt in the apical region and differentiating zones of LR, indicating a critical role of [Ca2+] in LR development in response to the coordinated action of auxins, ethylene and SLs. Significant enhancement of carotenoid cleavage dioxygenase (CCD) activity (enzyme responsible for SL biosynthesis) in tissue homogenates in presence of cPTIO (NO scavenger) indicates the role of endogenous NO as a negative modulator of CCD activity. Differences in the spatial distribution of NO in the primary and lateral roots further highlight the involvement of NO in SL-modulated root morphogenesis in sunflower seedlings. Present work provides new report on the negative modulation of SL biosynthesis through modulation of CCD activity by endogenous nitric oxide during SL-modulated LR development. PMID:26076049

Nitric oxide mediates strigolactone signaling in auxin and ethylene-sensitive lateral root formation in sunflower seedlings.

PubMed

Bharti, Niharika; Bhatla, Satish C

2015-01-01

Strigolactones (SLs) play significant role in shaping root architecture whereby auxin-SL crosstalk has been observed in SL-mediated responses of primary root elongation, lateral root formation and adventitious root (AR) initiation. Whereas GR24 (a synthetic strigolactone) inhibits LR and AR formation, the effect of SL biosynthesis inhibitor (fluridone) is just the opposite (root proliferation). Naphthylphthalamic acid (NPA) leads to LR proliferation but completely inhibits AR development. The diffusive distribution of PIN1 in the provascular cells in the differentiating zone of the roots in response to GR24, fluridone or NPA treatments further indicates the involvement of localized auxin accumulation in LR development responses. Inhibition of LR formation by GR24 treatment coincides with inhibition of ACC synthase activity. Profuse LR development by fluridone and NPA treatments correlates with enhanced [Ca(2+)]cyt in the apical region and differentiating zones of LR, indicating a critical role of [Ca(2+)] in LR development in response to the coordinated action of auxins, ethylene and SLs. Significant enhancement of carotenoid cleavage dioxygenase (CCD) activity (enzyme responsible for SL biosynthesis) in tissue homogenates in presence of cPTIO (NO scavenger) indicates the role of endogenous NO as a negative modulator of CCD activity. Differences in the spatial distribution of NO in the primary and lateral roots further highlight the involvement of NO in SL-modulated root morphogenesis in sunflower seedlings. Present work provides new report on the negative modulation of SL biosynthesis through modulation of CCD activity by endogenous nitric oxide during SL-modulated LR development.

DICOM index tracker enterprise: advanced system for enterprise-wide quality assurance and patient safety monitoring

NASA Astrophysics Data System (ADS)

Zhang, Min; Pavlicek, William; Panda, Anshuman; Langer, Steve G.; Morin, Richard; Fetterly, Kenneth A.; Paden, Robert; Hanson, James; Wu, Lin-Wei; Wu, Teresa

2015-03-01

DICOM Index Tracker (DIT) is an integrated platform to harvest rich information available from Digital Imaging and Communications in Medicine (DICOM) to improve quality assurance in radiology practices. It is designed to capture and maintain longitudinal patient-specific exam indices of interests for all diagnostic and procedural uses of imaging modalities. Thus, it effectively serves as a quality assurance and patient safety monitoring tool. The foundation of DIT is an intelligent database system which stores the information accepted and parsed via a DICOM receiver and parser. The database system enables the basic dosimetry analysis. The success of DIT implementation at Mayo Clinic Arizona calls for the DIT deployment at the enterprise level which requires significant improvements. First, for geographically distributed multi-site implementation, the first bottleneck is the communication (network) delay; the second is the scalability of the DICOM parser to handle the large volume of exams from different sites. To address this issue, DICOM receiver and parser are separated and decentralized by site. To facilitate the enterprise wide Quality Assurance (QA), a notable challenge is the great diversities of manufacturers, modalities and software versions, as the solution DIT Enterprise provides the standardization tool for device naming, protocol naming, physician naming across sites. Thirdly, advanced analytic engines are implemented online which support the proactive QA in DIT Enterprise.

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

Peulen, Heike; Mantel, Frederick; Department of Radiation Oncology, University Hospital Zurich, Zurich

Purpose: Fibrotic changes after stereotactic body radiation therapy (SBRT) for stage I non-small cell lung cancer (NSCLC) are difficult to distinguish from local recurrences (LR), hampering proper patient selection for salvage therapy. This study validates previously reported high-risk computed tomography (CT) features (HRFs) for detection of LR in an independent patient cohort. Methods and Materials: From a multicenter database, 13 patients with biopsy-proven LR were matched 1:2 to 26 non-LR control patients based on dose, planning target volume (PTV), follow-up time, and lung lobe. Tested HRFs were enlarging opacity, sequential enlarging opacity, enlarging opacity after 12 months, bulging margin, linear marginmore » disappearance, loss of air bronchogram, and craniocaudal growth. Additionally, 2 new features were analyzed: the occurrence of new unilateral pleural effusion, and growth based on relative volume, assessed by manual delineation. Results: All HRFs were significantly associated with LR except for loss of air bronchogram. The best performing HRFs were bulging margin, linear margin disappearance, and craniocaudal growth. Receiver operating characteristic analysis of the number of HRFs to detect LR had an area under the curve (AUC) of 0.97 (95% confidence interval [CI] 0.9-1.0), which was identical to the performance described in the original report. The best compromise (closest to 100% sensitivity and specificity) was found at ≥4 HRFs, with a sensitivity of 92% and a specificity of 85%. A model consisting of only 2 HRFs, bulging margin and craniocaudal growth, resulted in a sensitivity of 85% and a specificity of 100%, with an AUC of 0.96 (95% CI 0.9-1.0) (HRFs ≥2). Pleural effusion and relative growth did not significantly improve the model. Conclusion: We successfully validated CT-based HRFs for detection of LR after SBRT for early-stage NSCLC. As an alternative to number of HRFs, we propose a simplified model with the combination of the 2 best HRFs: bulging margin and craniocaudal growth, although validation is warranted.« less

The Role of Cerl2 in the Establishment of Left-Right Asymmetries during Axis Formation and Heart Development

PubMed Central

2017-01-01

The formation of the asymmetric left-right (LR) body axis is one of the fundamental aspects of vertebrate embryonic development, and one still raising passionate discussions among scientists. Although the conserved role of nodal is unquestionable in this process, several of the details around this signaling cascade are still unanswered. To further understand this mechanism, we have been studying Cerberus-like 2 (Cerl2), an inhibitor of Nodal, and its role in the generation of asymmetries in the early vertebrate embryo. The absence of Cerl2 results in a wide spectrum of malformations commonly known as heterotaxia, which comprises defects in either global organ position (e.g., situs inversus totalis), reversed orientation of at least one organ (e.g., situs ambiguus), and mirror images of usually asymmetric paired organs (e.g., left or right isomerisms of the lungs). Moreover, these laterality defects are frequently associated with congenital heart diseases (e.g., transposition of the great arteries, or atrioventricular septal defects). Here, reviewing the knowledge on the establishment of LR asymmetry in mouse embryos, the emerging conclusion is that as necessary as is the activation of the Nodal signaling cascade, the tight control that Cerl2-mediates on Nodal signaling is equally important, and that generates a further regionalized LR genetic program in the proper time and space. PMID:29367552

An iterated Laplacian based semi-supervised dimensionality reduction for classification of breast cancer on ultrasound images.

PubMed

Liu, Xiao; Shi, Jun; Zhou, Shichong; Lu, Minhua

2014-01-01

The dimensionality reduction is an important step in ultrasound image based computer-aided diagnosis (CAD) for breast cancer. A newly proposed l2,1 regularized correntropy algorithm for robust feature selection (CRFS) has achieved good performance for noise corrupted data. Therefore, it has the potential to reduce the dimensions of ultrasound image features. However, in clinical practice, the collection of labeled instances is usually expensive and time costing, while it is relatively easy to acquire the unlabeled or undetermined instances. Therefore, the semi-supervised learning is very suitable for clinical CAD. The iterated Laplacian regularization (Iter-LR) is a new regularization method, which has been proved to outperform the traditional graph Laplacian regularization in semi-supervised classification and ranking. In this study, to augment the classification accuracy of the breast ultrasound CAD based on texture feature, we propose an Iter-LR-based semi-supervised CRFS (Iter-LR-CRFS) algorithm, and then apply it to reduce the feature dimensions of ultrasound images for breast CAD. We compared the Iter-LR-CRFS with LR-CRFS, original supervised CRFS, and principal component analysis. The experimental results indicate that the proposed Iter-LR-CRFS significantly outperforms all other algorithms.

SOL - SIZING AND OPTIMIZATION LANGUAGE COMPILER

NASA Technical Reports Server (NTRS)

Scotti, S. J.

1994-01-01

SOL is a computer language which is geared to solving design problems. SOL includes the mathematical modeling and logical capabilities of a computer language like FORTRAN but also includes the additional power of non-linear mathematical programming methods (i.e. numerical optimization) at the language level (as opposed to the subroutine level). The language-level use of optimization has several advantages over the traditional, subroutine-calling method of using an optimizer: first, the optimization problem is described in a concise and clear manner which closely parallels the mathematical description of optimization; second, a seamless interface is automatically established between the optimizer subroutines and the mathematical model of the system being optimized; third, the results of an optimization (objective, design variables, constraints, termination criteria, and some or all of the optimization history) are output in a form directly related to the optimization description; and finally, automatic error checking and recovery from an ill-defined system model or optimization description is facilitated by the language-level specification of the optimization problem. Thus, SOL enables rapid generation of models and solutions for optimum design problems with greater confidence that the problem is posed correctly. The SOL compiler takes SOL-language statements and generates the equivalent FORTRAN code and system calls. Because of this approach, the modeling capabilities of SOL are extended by the ability to incorporate existing FORTRAN code into a SOL program. In addition, SOL has a powerful MACRO capability. The MACRO capability of the SOL compiler effectively gives the user the ability to extend the SOL language and can be used to develop easy-to-use shorthand methods of generating complex models and solution strategies. The SOL compiler provides syntactic and semantic error-checking, error recovery, and detailed reports containing cross-references to show where each variable was used. The listings summarize all optimizations, listing the objective functions, design variables, and constraints. The compiler offers error-checking specific to optimization problems, so that simple mistakes will not cost hours of debugging time. The optimization engine used by and included with the SOL compiler is a version of Vanderplatt's ADS system (Version 1.1) modified specifically to work with the SOL compiler. SOL allows the use of the over 100 ADS optimization choices such as Sequential Quadratic Programming, Modified Feasible Directions, interior and exterior penalty function and variable metric methods. Default choices of the many control parameters of ADS are made for the user, however, the user can override any of the ADS control parameters desired for each individual optimization. The SOL language and compiler were developed with an advanced compiler-generation system to ensure correctness and simplify program maintenance. Thus, SOL's syntax was defined precisely by a LALR(1) grammar and the SOL compiler's parser was generated automatically from the LALR(1) grammar with a parser-generator. Hence unlike ad hoc, manually coded interfaces, the SOL compiler's lexical analysis insures that the SOL compiler recognizes all legal SOL programs, can recover from and correct for many errors and report the location of errors to the user. This version of the SOL compiler has been implemented on VAX/VMS computer systems and requires 204 KB of virtual memory to execute. Since the SOL compiler produces FORTRAN code, it requires the VAX FORTRAN compiler to produce an executable program. The SOL compiler consists of 13,000 lines of Pascal code. It was developed in 1986 and last updated in 1988. The ADS and other utility subroutines amount to 14,000 lines of FORTRAN code and were also updated in 1988.

Potential role for a B-catenin coactivator (high mobility group AT-hook 1 protein) during the latency-reactivation cycle of bovine herpesverus 1

USDA-ARS?s Scientific Manuscript database

The latency-related (LR)-RNA encoded by bovine herpes virus 1 (BoHV-1) is abundantly expressed in latently infected sensory neurons. Although the LR gene encodes several products, ORF2 appears to play a dominant role during the latency-reactivation cycle because a mutant virus containing stop codons...

ß-catenin, a transcription factor activated by canonical Wnt signaling, is expressed in sensory neurons of calves latently infected with bovine herpesvirus 1

USDA-ARS?s Scientific Manuscript database

Like many a-herpesvirinae subfamily members, bovine herpes virus 1 (BoHV-1) expresses an abundant transcript in latently infected sensory neurons: the latency-related (LR) RNA. LR-RNA encodes a protein (ORF2) that inhibits apoptosis, interacts with Notch family members, interferes with Notch mediate...

Does this adult patient with suspected bacteremia require blood cultures?

PubMed

Coburn, Bryan; Morris, Andrew M; Tomlinson, George; Detsky, Allan S

2012-08-01

Clinicians order blood cultures liberally among patients in whom bacteremia is suspected, though a small proportion of blood cultures yield true-positive results. Ordering blood cultures inappropriately may be both wasteful and harmful. To review the accuracy of easily obtained clinical and laboratory findings to inform the decision to obtain blood cultures in suspected bacteremia. A MEDLINE and EMBASE search (inception to April 2012) yielded 35 studies that met inclusion criteria for evaluating the accuracy of clinical variables for bacteremia in adult immunocompetent patients, representing 4566 bacteremia and 25,946 negative blood culture episodes. Data were extracted to determine the prevalence and likelihood ratios (LRs) of findings for bacteremia. The pretest probability of bacteremia varies depending on the clinical context, from low (eg, cellulitis: 2%) to high (eg, septic shock: 69%). Elevated temperatures alone do not accurately predict bacteremia (for ≥38°C [>100.3°F], LR, 1.9 [95% CI, 1.4-2.4]; for ≥38.5°C [>101.2°F], LR, 1.4 [95% CI, 1.1-2.0]), nor does isolated leukocytosis (LR, <1.7). The severity of chills graded on an ordinal scale (shaking chills, LR, 4.7; 95% CI, 3.0-7.2) may be more useful. Both the systemic inflammatory response syndrome (SIRS) and a multivariable decision rule with major and minor criteria are sensitive (but not specific) predictors of bacteremia (SIRS, negative LR, 0.09 [95% CI, 0.03-0.26]; decision rule, negative LR, 0.08 [95% CI, 0.04-0.17]). Blood cultures should not be ordered for adult patients with isolated fever or leukocytosis without considering the pretest probability. SIRS and the decision rule may be helpful in identifying patients who do not need blood cultures. These conclusions do not apply to immunocompromised patients or when endocarditis is suspected.

Screening for urinary tract infection in women with hyperemesis gravidarum.

PubMed

Tan, Peng Chiong; King, Anthonia Siaw Jia; Omar, Siti Zawiah

2012-01-01

The aim of this study was to evaluate urine microscopy, dipstick analysis and urinary symptoms in screening for urinary tract infection (UTI) in hyperemesis gravidarum (HG).   A prospective cross-sectional study was performed on women at first hospitalization for HG. A clean-catch mid-stream urine sample from each recruit was sent for microscopy (for bacteria, leucocytes and erythrocytes), dipstick analysis (for leukocyte esterase, nitrites, protein and hemoglobin) and microbiological culture. The presence of current urinary symptoms was elicited by questionnaire. UTI is defined as at least 10(5) colony-forming units/mL of a single uropathogen on culture. Screening test parameters were analyzed against UTI. UTI was diagnosed in 15/292 subjects (5.1%). Receiver-operator characteristic curve analysis of microscopic urine leucocytes revealed area under the curve=0.64, 95% confidence interval (CI) 0.5-0.79, P=0.063 and erythrocytes area under the curve=0.53, 95%CI 0.39-0.67, P=0.67 for UTI indicating the limited screening utility of these parameters. Microscopic bacteriuria (likelihood ratio [LR] 1.1, 95%CI 0.7-1.5) and urine dipstick leukocyte esterase (LR 1.4, 95%CI 1.1-1.8), nitrites (LR 2.3, 95%CI 0.3-17.2), protein (LR 1.0, 95%CI 0.7-1.6) and hemoglobin (LR 0.8, 95%CI 0.4-1.5) were not useful screening tests for UTI in HG. Elicited symptoms were also not predictive of UTI. Urine microscopy, dipstick analysis and urinary symptoms were not useful in screening for UTI in HG. UTI should be established by urine culture in HG before starting antibiotic treatment. © 2011 The Authors. Journal of Obstetrics and Gynaecology Research © 2011 Japan Society of Obstetrics and Gynecology.

SIZ1 Regulation of Phosphate Starvation-Induced Root Architecture Remodeling Involves the Control of Auxin Accumulation1[C][W][OA

PubMed Central

Miura, Kenji; Lee, Jiyoung; Gong, Qingqiu; Ma, Shisong; Jin, Jing Bo; Yoo, Chan Yul; Miura, Tomoko; Sato, Aiko; Bohnert, Hans J.; Hasegawa, Paul M.

2011-01-01

Phosphate (Pi) limitation causes plants to modulate the architecture of their root systems to facilitate the acquisition of Pi. Previously, we reported that the Arabidopsis (Arabidopsis thaliana) SUMO E3 ligase SIZ1 regulates root architecture remodeling in response to Pi limitation; namely, the siz1 mutations cause the inhibition of primary root (PR) elongation and the promotion of lateral root (LR) formation. Here, we present evidence that SIZ1 is involved in the negative regulation of auxin patterning to modulate root system architecture in response to Pi starvation. The siz1 mutations caused greater PR growth inhibition and LR development of seedlings in response to Pi limitation. Similar root phenotypes occurred if Pi-deficient wild-type seedlings were supplemented with auxin. N-1-Naphthylphthalamic acid, an inhibitor of auxin efflux activity, reduced the Pi starvation-induced LR root formation of siz1 seedlings to a level equivalent to that seen in the wild type. Monitoring of the auxin-responsive reporter DR5::uidA indicated that auxin accumulates in PR tips at early stages of the Pi starvation response. Subsequently, DR5::uidA expression was observed in the LR primordia, which was associated with LR elongation. The time-sequential patterning of DR5::uidA expression occurred earlier in the roots of siz1 as compared with the wild type. In addition, microarray analysis revealed that several other auxin-responsive genes, including genes involved in cell wall loosening and biosynthesis, were up-regulated in siz1 relative to wild-type seedlings in response to Pi starvation. Together, these results suggest that SIZ1 negatively regulates Pi starvation-induced root architecture remodeling through the control of auxin patterning. PMID:21156857

Locating Anomalies in Complex Data Sets Using Visualization and Simulation

NASA Technical Reports Server (NTRS)

Panetta, Karen

2001-01-01

The research goals are to create a simulation framework that can accept any combination of models written at the gate or behavioral level. The framework provides the ability to fault simulate and create scenarios of experiments using concurrent simulation. In order to meet these goals we have had to fulfill the following requirements. The ability to accept models written in VHDL, Verilog or the C languages. The ability to propagate faults through any model type. The ability to create experiment scenarios efficiently without generating every possible combination of variables. The ability to accept adversity of fault models beyond the single stuck-at model. Major development has been done to develop a parser that can accept models written in various languages. This work has generated considerable attention from other universities and industry for its flexibility and usefulness. The parser uses LEXX and YACC to parse Verilog and C. We have also utilized our industrial partnership with Alternative System's Inc. to import vhdl into our simulator. For multilevel simulation, we needed to modify the simulator architecture to accept models that contained multiple outputs. This enabled us to accept behavioral components. The next major accomplishment was the addition of "functional fault models". Functional fault models change the behavior of a gate or model. For example, a bridging fault can make an OR gate behave like an AND gate. This has applications beyond fault simulation. This modeling flexibility will make the simulator more useful for doing verification and model comparison. For instance, two or more versions of an ALU can be comparatively simulated in a single execution. The results will show where and how the models differed so that the performance and correctness of the models may be evaluated. A considerable amount of time has been dedicated to validating the simulator performance on larger models provided by industry and other universities.

When the Viking Missions Discovered Life on the Red Planet

NASA Astrophysics Data System (ADS)

Bianciardi, G.; Miller, J. D.; Straat, P. A.; Levin, G. V.

2012-09-01

The first (and only) dedicated life detection experiments on another planet were performed by the Viking Landers of 1976. In the Viking Labeled Release (LR) experiment of Levin and Straat, injections of organic compounds into Martian soil samples caused radioactive gas to evolve approaching plateaus of 10,000 - 15,000 cpm over several sols (Martian days). These "actives" were run at lander sites 1 and 2 with similar results. In contrast, the LR response to the 160o C control sample soils was very low. In conjunction with the active experiment results this negative result from the controls satisfied the pre-mission criteria for life. However, a controversy immediately arose concerning a biologic interpretation of the data. In an attempt to resolve this issue in the current work, we have employed complexity analysis of the Viking LR data for the initial six sols, and of terrestrial LR pilot studies using bacteria-laden, active soil (Biol 5) and sterilized soil (Biol 6). . Measures of mathematical complexity permitted a deep analysis of signal structure. Martian LR active response data were strongly superimposable upon the terrestrial biological time series, forming a welldefined cluster; and the heat-treated control samples, terrestrial and Martian, also clustered together, but distant from the active group, suggesting that the LR had, indeed, detected biological activity on Mars. The results presente herein are a key subset of the details published earlier by the same authors (IJASS, 13 (1), 14-26, 2012).

Clinical Diagnosis of Bordetella Pertussis Infection: A Systematic Review.

PubMed

Ebell, Mark H; Marchello, Christian; Callahan, Maria

2017-01-01

Bordetella pertussis (BP) is a common cause of prolonged cough. Our objective was to perform an updated systematic review of the clinical diagnosis of BP without restriction by patient age. We identified prospective cohort studies of patients with cough or suspected pertussis and assessed study quality using QUADAS-2. We performed bivariate meta-analysis to calculate summary estimates of accuracy and created summary receiver operating characteristic curves to explore heterogeneity by vaccination status and age. Of 381 studies initially identified, 22 met our inclusion criteria, of which 14 had a low risk of bias. The overall clinical impression was the most accurate predictor of BP (positive likelihood ratio [LR+], 3.3; negative likelihood ratio [LR-], 0.63). The presence of whooping cough (LR+, 2.1) and posttussive vomiting (LR+, 1.7) somewhat increased the likelihood of BP, whereas the absence of paroxysmal cough (LR-, 0.58) and the absence of sputum (LR-, 0.63) decreased it. Whooping cough and posttussive vomiting have lower sensitivity in adults. Clinical criteria defined by the Centers for Disease Control and Prevention were sensitive (0.90) but nonspecific. Typical signs and symptoms of BP may be more sensitive but less specific in vaccinated patients. The clinician's overall impression was the most accurate way to determine the likelihood of BP infection when a patient initially presented. Clinical decision rules that combine signs, symptoms, and point-of-care tests have not yet been developed or validated. © Copyright 2017 by the American Board of Family Medicine.

Autotaxin/Lpar3 signaling regulates Kupffer's vesicle formation and left-right asymmetry in zebrafish.

PubMed

Lai, Shih-Lei; Yao, Wan-Ling; Tsao, Ku-Chi; Houben, Anna J S; Albers, Harald M H G; Ovaa, Huib; Moolenaar, Wouter H; Lee, Shyh-Jye

2012-12-01

Left-right (L-R) patterning is essential for proper organ morphogenesis and function. Calcium fluxes in dorsal forerunner cells (DFCs) are known to regulate the formation of Kupffer's vesicle (KV), a central organ for establishing L-R asymmetry in zebrafish. Here, we identify the lipid mediator lysophosphatidic acid (LPA) as a regulator of L-R asymmetry in zebrafish embryos. LPA is produced by Autotaxin (Atx), a secreted lysophospholipase D, and triggers various cellular responses through activation of specific G protein-coupled receptors (Lpar1-6). Knockdown of Atx or LPA receptor 3 (Lpar3) by morpholino oligonucleotides perturbed asymmetric gene expression in lateral plate mesoderm and disrupted organ L-R asymmetries, whereas overexpression of lpar3 partially rescued those defects in both atx and lpar3 morphants. Similar defects were observed in embryos treated with the Atx inhibitor HA130 and the Lpar1-3 inhibitor Ki16425. Knockdown of either Atx or Lpar3 impaired calcium fluxes in DFCs during mid-epiboly stage and compromised DFC cohesive migration, KV formation and ciliogenesis. Application of LPA to DFCs rescued the calcium signal and laterality defects in atx morphants. This LPA-dependent L-R asymmetry is mediated via Wnt signaling, as shown by the accumulation of β-catenin in nuclei at the dorsal side of both atx and lpar3 morphants. Our results suggest a major role for the Atx/Lpar3 signaling axis in regulating KV formation, ciliogenesis and L-R asymmetry via a Wnt-dependent pathway.

La Description des langues naturelles en vue d'applications linguistiques: Actes du colloque (The Description of Natural Languages with a View to Linguistic Applications: Conference Papers). Publication K-10.

ERIC Educational Resources Information Center

Ouellon, Conrad, Comp.

Presentations from a colloquium on applications of research on natural languages to computer science address the following topics: (1) analysis of complex adverbs; (2) parser use in computerized text analysis; (3) French language utilities; (4) lexicographic mapping of official language notices; (5) phonographic codification of Spanish; (6)…

The power and limits of a rule-based morpho-semantic parser.

PubMed Central

Baud, R. H.; Rassinoux, A. M.; Ruch, P.; Lovis, C.; Scherrer, J. R.

1999-01-01

The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors. PMID:10566313

The power and limits of a rule-based morpho-semantic parser.

PubMed

Baud, R H; Rassinoux, A M; Ruch, P; Lovis, C; Scherrer, J R

1999-01-01

The venue of Electronic Patient Record (EPR) implies an increasing amount of medical texts readily available for processing, as soon as convenient tools are made available. The chief application is text analysis, from which one can drive other disciplines like indexing for retrieval, knowledge representation, translation and inferencing for medical intelligent systems. Prerequisites for a convenient analyzer of medical texts are: building the lexicon, developing semantic representation of the domain, having a large corpus of texts available for statistical analysis, and finally mastering robust and powerful parsing techniques in order to satisfy the constraints of the medical domain. This article aims at presenting an easy-to-use parser ready to be adapted in different settings. It describes its power together with its practical limitations as experienced by the authors.

Acute-onset floaters and flashes: is this patient at risk for retinal detachment?

PubMed

Hollands, Hussein; Johnson, Davin; Brox, Anya C; Almeida, David; Simel, David L; Sharma, Sanjay

2009-11-25

Acute onset of monocular floaters and/or flashes represents a common presentation to primary care physicians, and the most likely diagnosis is posterior vitreous detachment (PVD). A significant proportion of patients with acute PVD develop an associated retinal tear that can lead to retinal detachment and permanent vision loss if left untreated. To quantify the association between relevant clinical variables and risk of retinal tear in patients presenting with acute-onset floaters and/or flashes and PVD. Structured MEDLINE (January 1950-September 2009) and EMBASE (January 1980-September 2009) searches and a hand search of references and citations of retrieved articles yielded 17 relevant studies. Studies of high-level methods that related elements of the history or physical examination in patients presenting with floaters and/or flashes and PVD to the likelihood of retinal tear. For patients with acute onset of floaters and/or flashes who are self-referred or referred to an ophthalmologist, the prevalence of retinal tear is 14% (95% confidence interval [CI], 12%-16%). Subjective visual reduction is the most important symptom associated with retinal tear (likelihood ratio [LR], 5.0; 95% CI, 3.1-8.1). Vitreous hemorrhage on slitlamp biomicroscopy is the best-studied finding with the narrowest positive LR for retinal tear (summary LR, 10; 95% CI, 5.1-20). Absence of vitreous pigment during this examination is the best-studied finding with the narrowest negative LR (summary LR, 0.23; 95% CI, 0.12-0.43). Patients initially diagnosed as having uncomplicated PVD have a 3.4% chance of a retinal tear within 6 weeks. The risk increases with new onset of at least 10 floaters (summary LR, 8.1-36) or subjective visual reduction (summary LR, 2.3-17) during this period. Primary care physicians should evaluate patients with acute-onset floaters and/or flashes due to suspected PVD, or patients with known PVD and a change in symptoms, for high-risk features of retinal tear and detachment. Physicians should always assess these patients' visual acuity. Patients at increased risk should be triaged for urgent ophthalmologic assessment.

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

Bahig, Houda; Simard, Dany; Létourneau, Laurent

Purpose: To determine the incidence of pseudoprogression (PP) after spine stereotactic body radiation therapy based on a detailed and quantitative assessment of magnetic resonance imaging (MRI) morphologic tumor alterations, and to identify predictive factors distinguishing PP from local recurrence (LR). Methods and Materials: A retrospective analysis of 35 patients with 49 spinal segments treated with spine stereotactic body radiation therapy, from 2009 to 2014, was conducted. The median number of follow-up MRI studies was 4 (range, 2-7). The gross tumor volumes (GTVs) within each of the 49 spinal segments were contoured on the pretreatment and each subsequent follow-up T1- andmore » T2-weighted MRI sagittal sequence. T2 signal intensity was reported as the mean intensity of voxels constituting each volume. LR was defined as persistent GTV enlargement on ≥2 serial MRI studies for ≥6 months or on pathologic confirmation. PP was defined as a GTV enlargement followed by stability or regression on subsequent imaging within 6 months. Kaplan-Meier analysis was used for estimation of actuarial local control, disease-free survival, and overall survival. Results: The median follow-up was 23 months (range, 1-39 months). PP was identified in 18% of treated segments (9 of 49) and LR in 29% (14 of 49). Earlier volume enlargement (5 months for PP vs 15 months for LR, P=.005), greater GTV to reference nonirradiated vertebral body T2 intensity ratio (+30% for PP vs −10% for LR, P=.005), and growth confined to 80% of the prescription isodose line (80% IDL) (8 of 9 PP cases vs 1 of 14 LR cases, P=.002) were associated with PP on univariate analysis. Multivariate analysis confirmed an earlier time to volume enlargement and growth within the 80% IDL as significant predictors of PP. LR involved the epidural space in all but 1 lesion, whereas PP was confined to the vertebral body in 7 of 9 cases. Conclusions: PP was observed in 18% of treated spinal segments. Tumor growth confined to the 80% IDL and earlier time to tumor enlargement were predictive for PP.« less

An improved survivability prognosis of breast cancer by using sampling and feature selection technique to solve imbalanced patient classification data.

PubMed

Wang, Kung-Jeng; Makond, Bunjira; Wang, Kung-Min

2013-11-09

Breast cancer is one of the most critical cancers and is a major cause of cancer death among women. It is essential to know the survivability of the patients in order to ease the decision making process regarding medical treatment and financial preparation. Recently, the breast cancer data sets have been imbalanced (i.e., the number of survival patients outnumbers the number of non-survival patients) whereas the standard classifiers are not applicable for the imbalanced data sets. The methods to improve survivability prognosis of breast cancer need for study. Two well-known five-year prognosis models/classifiers [i.e., logistic regression (LR) and decision tree (DT)] are constructed by combining synthetic minority over-sampling technique (SMOTE), cost-sensitive classifier technique (CSC), under-sampling, bagging, and boosting. The feature selection method is used to select relevant variables, while the pruning technique is applied to obtain low information-burden models. These methods are applied on data obtained from the Surveillance, Epidemiology, and End Results database. The improvements of survivability prognosis of breast cancer are investigated based on the experimental results. Experimental results confirm that the DT and LR models combined with SMOTE, CSC, and under-sampling generate higher predictive performance consecutively than the original ones. Most of the time, DT and LR models combined with SMOTE and CSC use less informative burden/features when a feature selection method and a pruning technique are applied. LR is found to have better statistical power than DT in predicting five-year survivability. CSC is superior to SMOTE, under-sampling, bagging, and boosting to improve the prognostic performance of DT and LR.

An improved survivability prognosis of breast cancer by using sampling and feature selection technique to solve imbalanced patient classification data

PubMed Central

2013-01-01

Background Breast cancer is one of the most critical cancers and is a major cause of cancer death among women. It is essential to know the survivability of the patients in order to ease the decision making process regarding medical treatment and financial preparation. Recently, the breast cancer data sets have been imbalanced (i.e., the number of survival patients outnumbers the number of non-survival patients) whereas the standard classifiers are not applicable for the imbalanced data sets. The methods to improve survivability prognosis of breast cancer need for study. Methods Two well-known five-year prognosis models/classifiers [i.e., logistic regression (LR) and decision tree (DT)] are constructed by combining synthetic minority over-sampling technique (SMOTE) ,cost-sensitive classifier technique (CSC), under-sampling, bagging, and boosting. The feature selection method is used to select relevant variables, while the pruning technique is applied to obtain low information-burden models. These methods are applied on data obtained from the Surveillance, Epidemiology, and End Results database. The improvements of survivability prognosis of breast cancer are investigated based on the experimental results. Results Experimental results confirm that the DT and LR models combined with SMOTE, CSC, and under-sampling generate higher predictive performance consecutively than the original ones. Most of the time, DT and LR models combined with SMOTE and CSC use less informative burden/features when a feature selection method and a pruning technique are applied. Conclusions LR is found to have better statistical power than DT in predicting five-year survivability. CSC is superior to SMOTE, under-sampling, bagging, and boosting to improve the prognostic performance of DT and LR. PMID:24207108

Validation of an enzyme-linked immunosorbent assay for the quantification of human IgG directed against the repeat region of the circumsporozoite protein of the parasite Plasmodium falciparum

PubMed Central

2012-01-01

Background Several pre-erythrocytic malaria vaccines based on the circumsporozoite protein (CSP) antigen of Plasmodium falciparum are in clinical development. Vaccine immunogenicity is commonly evaluated by the determination of anti-CSP antibody levels using IgG-based assays, but no standard assay is available to allow comparison of the different vaccines. Methods The validation of an anti-CSP repeat region enzyme-linked immunosorbent assay (ELISA) is described. This assay is based on the binding of serum antibodies to R32LR, a recombinant protein composed of the repeat region of P. falciparum CSP. In addition to the original recombinant R32LR, an easy to purify recombinant His-tagged R32LR protein has been constructed to be used as solid phase antigen in the assay. Also, hybridoma cell lines have been generated producing human anti-R32LR monoclonal antibodies to be used as a potential inexhaustible source of anti-CSP repeats standard, instead of a reference serum. Results The anti-CSP repeats ELISA was shown to be robust, specific and linear within the analytical range, and adequately fulfilled all validation criteria as defined in the ICH guidelines. Furthermore, the coefficient of variation for repeatability and intermediate precision did not exceed 23%. Non-interference was demonstrated for R32LR-binding sera, and the assay was shown to be stable over time. Conclusions This ELISA, specific for antibodies directed against the CSP repeat region, can be used as a standard assay for the determination of humoral immunogenicity in the development of any CSP-based P. falciparum malaria vaccine. PMID:23173602

LrABCF1, a GCN-type ATP-binding cassette transporter from lilium regale, is involved in defense responses against viral and fungal pathogens

USDA-ARS?s Scientific Manuscript database

ATP-binding cassette (ABC) transporters are essential for membrane translocation in diverse biological processes, such as plant development and defense response. Here, a general control non-derepressible (GCN)-type ABC transporter gene, designated LrABCF1, was identified from Cucumber mosaic virus (...

Constraints on flavor-dependent long range forces from solar neutrinos and KamLAND

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Abhijit; Dighe, Amol; Joshipura, Anjan S.

2007-05-01

Flavor-dependent long range (LR) leptonic forces, like those mediated by the Le-Lμ or Le-Lτ gauge bosons, constitute a minimal extension of the standard model that preserves its renormalizability. We study the impact of such interactions on the solar neutrino oscillations when the interaction range RLR is much larger than the Earth-Sun distance. The LR potential can dominate over the standard charged current potential inside the Sun in spite of strong constraints on the coupling α of the LR force coming from the atmospheric neutrino data and laboratory search for new forces. We demonstrate that the solar and atmospheric neutrino mass scales do not get trivially decoupled even if θ13 is vanishingly small. In addition, for α≳10-52 and normal hierarchy, resonant enhancement of θ13 results in nontrivial energy dependent effects on the νe survival probability. We perform a complete three generation analysis, and obtain constraints on α through a global fit to the solar neutrino and KamLAND data. We get the 3σ limits αeμ<3.4×10-53 and αeτ<2.5×10-53 when RLR is much smaller than our distance from the galactic center. With larger RLR, the collective LR potential due to all the electrons in the galaxy becomes significant and the constraints on α become stronger by up to two orders of magnitude.

Resolution enhancement of tri-stereo remote sensing images by super resolution methods

NASA Astrophysics Data System (ADS)

Tuna, Caglayan; Akoguz, Alper; Unal, Gozde; Sertel, Elif

2016-10-01

Super resolution (SR) refers to generation of a High Resolution (HR) image from a decimated, blurred, low-resolution (LR) image set, which can be either a single frame or multi-frame that contains a collection of several images acquired from slightly different views of the same observation area. In this study, we propose a novel application of tri-stereo Remote Sensing (RS) satellite images to the super resolution problem. Since the tri-stereo RS images of the same observation area are acquired from three different viewing angles along the flight path of the satellite, these RS images are properly suited to a SR application. We first estimate registration between the chosen reference LR image and other LR images to calculate the sub pixel shifts among the LR images. Then, the warping, blurring and down sampling matrix operators are created as sparse matrices to avoid high memory and computational requirements, which would otherwise make the RS-SR solution impractical. Finally, the overall system matrix, which is constructed based on the obtained operator matrices is used to obtain the estimate HR image in one step in each iteration of the SR algorithm. Both the Laplacian and total variation regularizers are incorporated separately into our algorithm and the results are presented to demonstrate an improved quantitative performance against the standard interpolation method as well as improved qualitative results due expert evaluations.

Does This Patient Have Infectious Mononucleosis?: The Rational Clinical Examination Systematic Review.

PubMed

Ebell, Mark H; Call, Marlene; Shinholser, JoAnna; Gardner, Jack

2016-04-12

Early, accurate diagnosis of infectious mononucleosis can help clinicians target treatment, avoid antibiotics, and provide an accurate prognosis. To systematically review the literature regarding the value of the clinical examination and white blood cell count for the diagnosis of mononucleosis. The databases of PubMed (from 1966-2016) and EMBASE (from 1947-2015) were searched and a total of 670 articles and abstracts were reviewed for eligibility. Eleven studies were included that reported data sufficient to calculate sensitivity, specificity, or both for clinical examination findings and white blood cell count parameters compared with a valid reference standard. Data were abstracted from each article by at least 2 reviewers, with discrepancies reconciled by consensus. Clinical findings evaluated in only 1 study are reported with sensitivity, specificity, likelihood ratio (LR), and 95% confidence interval, which were calculated from the available data. Findings evaluated in only 2 studies were summarized with their range, findings evaluated in 3 studies were summarized with a univariate random-effects summary, and findings evaluated in 4 or more studies were summarized with a bivariate random-effects meta-analysis. Sensitivity, specificity, and LRs for the diagnosis of mononucleosis. Mononucleosis is most commonly present among patients aged 5 to 25 years (especially those aged 16-20 years, among whom approximately 1 in 13 patients presenting with sore throat has mononucleosis). The likelihood of mononucleosis is reduced with the absence of any lymphadenopathy (summary sensitivity, 0.91; positive LR range, 0.23-0.44), whereas the likelihood increases with the presence of posterior cervical adenopathy (summary specificity, 0.87; positive LR, 3.1 [95% CI, 1.6-5.9]), inguinal or axillary adenopathy (specificity range, 0.82-0.91; positive LR range, 3.0-3.1), palatine petechiae (specificity, 0.95; positive LR, 5.3 [95% CI, 2.1-13]), and splenomegaly (specificity range, 0.71-0.99; positive LR range, 1.9-6.6). Symptoms are of limited value for the diagnosis of mononucleosis; sore throat and fatigue are sensitive (range, 0.81-0.83) but nonspecific. The presence of atypical lymphocytosis significantly increases the likelihood of mononucleosis (summary LR, 11.4 [95% CI, 2.7-35] for atypical lymphocytes ≥10%, 26 [95% CI, 9.6-68] for those with 20%, and 50 [95% CI, 38-64] for those with 40%). The combination of a patient having greater than 50% lymphocytes and greater than 10% atypical lymphocytes also is useful (specificity, 0.99; positive LR, 54 [95% CI, 8.4-189]). In adolescent and adult patients presenting with sore throat, the presence of posterior cervical, inguinal or axillary adenopathy, palatine petechiae, splenomegaly, or atypical lymphocytosis is associated with an increased likelihood of mononucleosis.

Sequencing of five left-right cerebral asymmetry genes in a cohort of schizophrenia and schizotypal disorder patients from Russia.

PubMed

Levchenko, Anastasia; Davtian, Stepan; Petrova, Natalia; Malashichev, Yegor

2014-04-01

Schizophrenia is a severe psychiatric disorder, affecting ∼1% of the human population. The genetic contribution to schizophrenia is significant, but the genetics are complex and many aspects of brain functioning, from neural development to synapse structure, seem to be involved in the pathogenesis. A novel way to study the molecular causes of schizophrenia is to study the genetics of left-right (LR) brain asymmetry, the disease feature often observed in schizophrenic patients. In this study, we analyzed by sequencing five candidate LR cerebral asymmetry genes in a cohort of 95 schizophrenia and schizotypal disorder patients from Saint Petersburg, Russia. The gene list included LMO4, LRRTM1, FOXP2, the PCDH11X/Y gene pair, and SRY. We found 17 previously unreported variants in the genes LRRTM1, FOXP2, LMO4, and PCDH11X in the 3'-UTR and 5'-UTR. The variants might contribute toward an altered mRNA processing, which could lead to altered mRNA amounts in developing neurons of the brain and establishment of an incorrect LR asymmetry profile. This is the first study in which multiple candidate genes for cerebral LR asymmetry and schizophrenia have been analyzed by sequencing. The approach to study the genetics of schizophrenia from the perspective of an LR cerebral asymmetry disturbance deserves more attention.

Novel method to leukoreduce murine blood for transfusion: how to reduce animal usage.

PubMed

Fischer, Dania; Büssow, Julian; Meybohm, Patrick; Zacharowski, Kai; Jennewein, Carla

2016-01-01

Basic research on the pathomechanisms of transfusion-related adverse events depends on murine transfusion models, in which leukoreduction (LR) is a prevalent standard. The commonly used neonatal LR filter (LRF) is associated with considerable animal numbers. A more efficient method would help support the guiding principles of "replacement, reduction, refinement" (3Rs). Blood from C57BL/6 and C57BL/6-Tg(UBC-GFP)30Scha/J mice was leukoreduced using (1) a neonatal LRF, (2) a syringe LRF, or (3) CD45 microbeads. Product quality was assessed according to US Food and Drug Administration (FDA) standards. White blood cell numbers were analyzed by flow cytometry; hemoglobin concentrations and hematocrit were measured and in vivo posttransfusion recoveries were determined after 2 weeks of storage. Using the neonatal filter, a LR of 99.56% was achieved with wastage of 12.4 mL in comparison to 99.68% and 1-mL hold-up volume with the syringe filter and 99.11 ± 0.24% LR and 0.1-mL wastage using microbeads. All techniques achieved FDA quality standards, apart from posttransfusion recovery rate, which was only reached by the microbeads-based technique. LR with CD45 microbeads not only reduces animal usage but also provides a more efficacious method regarding posttransfusion red blood cell recovery and, hence, provides a promising alternative to commonly used methods. © 2015 AABB.

Clinical signs of impending death in cancer patients.

PubMed

Hui, David; dos Santos, Renata; Chisholm, Gary; Bansal, Swati; Silva, Thiago Buosi; Kilgore, Kelly; Crovador, Camila Souza; Yu, Xiaoying; Swartz, Michael D; Perez-Cruz, Pedro Emilio; Leite, Raphael de Almeida; Nascimento, Maria Salete de Angelis; Reddy, Suresh; Seriaco, Fabiola; Yennu, Sriram; Paiva, Carlos Eduardo; Dev, Rony; Hall, Stacy; Fajardo, Julieta; Bruera, Eduardo

2014-06-01

The physical signs of impending death have not been well characterized in cancer patients. A better understanding of these signs may improve the ability of clinicians to diagnose impending death. We examined the frequency and onset of 10 bedside physical signs and their diagnostic performance for impending death. We systematically documented 10 physical signs every 12 hours from admission to death or discharge in 357 consecutive patients with advanced cancer admitted to two acute palliative care units. We examined the frequency and median onset of each sign from death backward and calculated their likelihood ratios (LRs) associated with death within 3 days. In total, 203 of 357 patients (52 of 151 in the U.S., 151 of 206 in Brazil) died. Decreased level of consciousness, Palliative Performance Scale ≤20%, and dysphagia of liquids appeared at high frequency and >3 days before death and had low specificity (<90%) and positive LR (<5) for impending death. In contrast, apnea periods, Cheyne-Stokes breathing, death rattle, peripheral cyanosis, pulselessness of radial artery, respiration with mandibular movement, and decreased urine output occurred mostly in the last 3 days of life and at lower frequency. Five of these signs had high specificity (>95%) and positive LRs for death within 3 days, including pulselessness of radial artery (positive LR: 15.6; 95% confidence interval [CI]: 13.7-17.4), respiration with mandibular movement (positive LR: 10; 95% CI: 9.1-10.9), decreased urine output (positive LR: 15.2; 95% CI: 13.4-17.1), Cheyne-Stokes breathing (positive LR: 12.4; 95% CI: 10.8-13.9), and death rattle (positive LR: 9; 95% CI: 8.1-9.8). We identified highly specific physical signs associated with death within 3 days among cancer patients. ©AlphaMed Press.

The prevalence of tarsal tunnel syndrome in patients with lumbosacral radiculopathy.

PubMed

Zheng, Chaojun; Zhu, Yu; Jiang, Jianyuan; Ma, Xiaosheng; Lu, Feizhou; Jin, Xiang; Weber, Robert

2016-03-01

Tarsal tunnel syndrome (TTS) is a painful foot condition. Lumbosacral radiculopathy (LR) may also present with symptoms occurring in TTS. However, no studies have been reported to determine the possible coexistence of these two conditions. The aim of our study was to identify the prevalence of TTS in patients with confirmed LR and to analyze the clinical and electrodiagnostic features of patients with both TTS and LR. Medial and lateral plantar nerve mixed studies, peroneal motor studies and deep peroneal sensory studies were performed in 81 normal subjects and 561 patients with LR. The Tinel's test and other provocative tests were performed in the LR patient group, and the clinical symptoms of TTS were also analyzed. The frequency of TTS was investigated in all radiculopathy group patients with different nerve root lesions. Concomitant TTS was found in 27 (4.8%) patients with LR. Abnormal results of sensory/mixed conduction tests were observed in 25/27 (92.6%) patients, and 11/27 (40.7%) patients had abnormal results of motor conduction tests. Positivity for the Tinel's test and special provocative tests was found in 15/27 (55.6%) and 17/27 (63.0%) patients, respectively. Overall, 9/27 (33.3%) patients had typical symptoms, and suspicious clinical symptoms were found in the other 14/27 (51.9%) patients. The frequency of coexisting TTS was not statistically different among the single-level L4, L5 or S1 radiculopathy, or between the single-level and multi-level radiculopathies (P > 0.05). The findings suggest that the prevalence of TTS is significant in patients with LR. Thus, more caution should be paid when diagnosing and managing patients with LR due to the possible existence of TTS, as their management strategies are quite different.

Allelopathic effects of microcystin-LR on the germination, growth and metabolism of five charophyte species and a submerged angiosperm.

PubMed

Rojo, Carmen; Segura, Matilde; Cortés, Francisco; Rodrigo, María A

2013-11-15

Microcystins (MCs) are produced by cyanobacteria in aquatic environments and adversely affect macrophytes at very high concentrations. However, the effects of MC on macrophytes at concentrations of environmental relevance are largely unknown. The main objective of this study was to analyze the allelopathic effects of MC-LR at natural concentrations (1, 8 and 16 μg MC-LR/L) on five charophyte species (Chara aspera, C. baltica, C. hispida, C. vulgaris and Nitella hyalina) and the angiosperm Myriophyllum spicatum. Macrophyte specimens were obtained from a restored area located in Albufera de València Natural Park, a protected coastal Mediterranean wetland. Two different experiments were conducted involving (i) the addition of MC-LR to natural sediment to evaluate its effects on seed germination and (ii) the addition of MC-LR to water cultures of macrophytes to evaluate its effects on growth and metabolic functions. In water, the MC-LR concentration decreased by 84% in two weeks; the loss was not significant in sediment. The first seedlings (all C. hispida) emerged from the wetland sediment following a delay of a few days in the presence of MC-LR. The germination rates in 8 and 16 μg MC-LR/L treatments were 44% and 11% of that occurring in the absence of MC, but these differences disappeared over time. The final density was 6-7 germlings/dm(3). Final germling length was unaffected by MC-LR. Rotifers (Lecane spp.) emerging from the natural sediment during the experiment were favored by MC-LR; the opposite pattern was observed in the cladoceran Daphnia magna. The growth rates of C. vulgaris, C. baltica and N. hyalina were unaffected by MC exposure, whereas those of C. hispida and C. aspera were reduced in the MC treatments relative to the control treatment. The concentration of chlorophyll-a and the in vivo net photosynthetic rate were lower in the presence of MC-LR, even at the lowest concentration, for all of the characeans tested. M. spicatum was sensitive to the presence of MC-LR in the culture medium; the growth and chlorophyll-a concentrations were reduced. Therefore, environmentally relevant concentrations of MC might induce important changes in macrophyte meadows and the structure of the associated plankton community. Synchrony or delay in the processes evaluated here in response to environmentally relevant concentrations of cyanobacteria MC exudates can enhance understanding of the turning point to alternative states and the point of no return in eutrophicated shallow lakes. Copyright © 2013 Elsevier B.V. All rights reserved.

Does the patient with chest pain have a coronary heart disease? Diagnostic value of single symptoms and signs--a meta-analysis.

PubMed

Haasenritter, Jorg; Stanze, Damaris; Widera, Grit; Wilimzig, Christian; Abu Hani, Maren; Sonnichsen, Andreas C; Bosner, Stefan; Rochon, Justine; Donner-Banzhoff, Norbert

2012-10-01

To determine the diagnostic value of single symptoms and signs for coronary heart disease (CHD) in patients with chest pain. Searches of two electronic databases (EMBASE 1980 to March 2008, PubMed 1966 to May 2009) and hand searching in seven journals were conducted. Eligible studies recruited patients presenting with acute or chronic chest pain. The target disease was CHD, with no restrictions regarding case definitions, eg, stable CHD, acute coronary syndrome (ACS), acute myocardial infarction (MI), or major cardiac event (MCE). Diagnostic tests of interest were items of medical history and physical examination. Bivariate random effects model was used to derive summary estimates of positive (pLR) and negative likelihood ratios (nLR). We included 172 studies providing data on the diagnostic value of 42 symptoms and signs. With respect to case definition of CHD, diagnostically most useful tests were history of CHD (pLR=3.59), known MI (pLR=3.21), typical angina (pLR=2.35), history of diabetes mellitus (pLR=2.16), exertional pain (pLR=2.13), history of angina pectoris (nLR=0.42), and male sex (nLR=0.49) for diagnosing stable CHD; pain radiation to right arm/shoulder (pLR=4.43) and palpitation (pLR=0.47) for diagnosing MI; visceral pain (pLR=2.05) for diagnosing ACS; and typical angina (pLR=2.60) and pain reproducible by palpation (pLR=0.13) for predicting MCE. We comprehensively reported the accuracy of a broad spectrum of single symptoms and signs for diagnosing myocardial ischemia. Our results suggested that the accuracy of several symptoms and signs varied in the published studies according to the case definition of CHD.

The Auxin Biosynthetic TRYPTOPHAN AMINOTRANSFERASE RELATED TaTAR2.1-3A Increases Grain Yield of Wheat.

PubMed

Shao, An; Ma, Wenying; Zhao, Xueqiang; Hu, Mengyun; He, Xue; Teng, Wan; Li, Hui; Tong, Yiping

2017-08-01

Controlling the major auxin biosynthetic pathway to manipulate auxin content could be a target for genetic engineering of crops with desired traits, but little progress had been made because low or high auxin contents often cause developmental inhibition. Here, we performed a genome-wide analysis of bread wheat ( Triticum aestivum ) to identify the Tryptophan Aminotransferase of Arabidopsis1/Tryptophan Aminotransferase-Related (TAA1/TAR) genes that function in the tryptophan-dependent pathway of auxin biosynthesis. Sequence mining together with gene cloning identified 15 TaTAR genes, among which 12 and three genes were phylogenetically close to Arabidopsis ( Arabidopsis thaliana ) AtTAR2 and AtTAR3, respectively. TaTAR2.1 had the most abundant transcripts in the TaTAR2 genes and was expressed mainly in roots and up-regulated by low nitrogen (N) availability. Knockdown of TaTAR2.1 caused vegetative and reproductive deficiencies and impaired lateral root (LR) growth under both high- and low-N conditions. Overexpressing TaTAR2.1-3A in wheat enhanced LR branching, plant height, spike number, grain yield, and aerial N accumulation under different N supply levels. In addition, overexpressing TaTAR2.1-3A in Arabidopsis elevated auxin accumulation in the primary root tip, LR tip, LR primordia, and cotyledon and hypocotyl and increased primary root length, visible LR number, and shoot fresh weight under high- and low-N conditions. Our results indicate that TaTAR2.1 is critical for wheat growth and also shows potential for genetic engineering to reach the aim of improving the grain yield of wheat. © 2017 American Society of Plant Biologists. All Rights Reserved.

Rapid embedding methods into epoxy and LR White resins for morphological and immunological analysis of cryofixed biological specimens.

PubMed

McDonald, Kent L

2014-02-01

A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.

Accurately estimating PSF with straight lines detected by Hough transform

NASA Astrophysics Data System (ADS)

Wang, Ruichen; Xu, Liangpeng; Fan, Chunxiao; Li, Yong

2018-04-01

This paper presents an approach to estimating point spread function (PSF) from low resolution (LR) images. Existing techniques usually rely on accurate detection of ending points of the profile normal to edges. In practice however, it is often a great challenge to accurately localize profiles of edges from a LR image, which hence leads to a poor PSF estimation of the lens taking the LR image. For precisely estimating the PSF, this paper proposes firstly estimating a 1-D PSF kernel with straight lines, and then robustly obtaining the 2-D PSF from the 1-D kernel by least squares techniques and random sample consensus. Canny operator is applied to the LR image for obtaining edges and then Hough transform is utilized to extract straight lines of all orientations. Estimating 1-D PSF kernel with straight lines effectively alleviates the influence of the inaccurate edge detection on PSF estimation. The proposed method is investigated on both natural and synthetic images for estimating PSF. Experimental results show that the proposed method outperforms the state-ofthe- art and does not rely on accurate edge detection.

Occurrence of Toxic Cyanobacterial Blooms in Rio de la Plata Estuary, Argentina: Field Study and Data Analysis

PubMed Central

Giannuzzi, L.; Carvajal, G.; Corradini, M. G.; Araujo Andrade, C.; Echenique, R.; Andrinolo, D.

2012-01-01

Water samples were collected during 3 years (2004–2007) at three sampling sites in the Rio de la Plata estuary. Thirteen biological, physical, and chemical parameters were determined on the water samples. The presence of microcystin-LR in the reservoir samples, and also in domestic water samples, was confirmed and quantified. Microcystin-LR concentration ranged between 0.02 and 8.6 μg.L−1. Principal components analysis was used to identify the factors promoting cyanobacteria growth. The proliferation of cyanobacteria was accompanied by the presence of high total and fecal coliforms bacteria (>1500 MNP/100 mL), temperature ≥25°C, and total phosphorus content ≥1.24 mg·L−1. The observed fluctuating patterns of Microcystis aeruginosa, total coliforms, and Microcystin-LR were also described by probabilistic models based on the log-normal and extreme value distributions. The sampling sites were compared in terms of the distribution parameters and the probability of observing high concentrations for Microcystis aeruginosa, total coliforms, and microcystin-LR concentration. PMID:22523486

Functional analysis of a pathogenesis-related thaumatin-like protein gene TaLr35PR5 from wheat induced by leaf rust fungus.

PubMed

Zhang, Jiarui; Wang, Fei; Liang, Fang; Zhang, Yanjun; Ma, Lisong; Wang, Haiyan; Liu, Daqun

2018-05-04

Plants have evolved multifaceted defence mechanisms to resist pathogen infection. Production of the pathogenesis-related (PR) proteins in response to pathogen attack has been implicated in plant disease resistance specialized in systemic-acquired resistance (SAR). Our earlier studies have reported that a full length TaLr35PR5 gene, encoding a protein exhibiting amino acid and structural similarity to a sweet protein thaumatin, was isolated from wheat near-isogenic line TcLr35. The present study aims to understand the function of TaLr35PR5 gene in Lr35-mediated adult resistance to Puccinia triticina. We determined that the TaLr35PR5 protein contained a functional secretion peptide by utilizing the yeast signal sequence trap system. Using a heterologous expression assay on onion epidermal cells we found that TaLr35PR5 protein was secreted into the apoplast of onion cell. Expression of TaLr35PR5 was significantly reduced in BSMV-induced gene silenced wheat plants, and pathology test on these silenced plants revealed that Lr35-mediated resistance phenotype was obviously altered, indicating that Lr35-mediated resistance was compromised. All these findings strongly suggest that TaLr35PR5 is involved in Lr35-mediated adult wheat defense in response to leaf rust attack.

Phytophthora parasitica Effector PpRxLR2 Suppresses Nicotiana benthamiana Immunity.

PubMed

Dalio, R J D; Maximo, H J; Oliveira, T S; Dias, R O; Breton, M C; Felizatti, H; Machado, M

2018-04-01

Phytophthora species secrete several classes of effector proteins during interaction with their hosts. These proteins can have multiple functions including modulation of host physiology and immunity. The RxLR effectors have the ability to enter plant cells using the plant machinery. Some of these effectors have been characterized as immunity suppressors; however, very little is known about their functions in the interaction between Phytophthora parasitica and its hosts. Using a bioinformatics pipeline, we have identified 172 candidate RxLR effectors (CREs) in the isolate IAC 01_95 of P. parasitica. Of these 172 CREs, 93 were found to be also present in eight other genomes of P. parasitica, isolated from different hosts and continents. After transcriptomics and gene expression analysis, we have found five CREs to be up-regulated in in-vitro and in-planta samples. Subsequently, we selected three CREs for functional characterization in the model plant Nicotiana benthamiana. We show that PpRxLR2 is able to completely suppress INF-1-induced cell death, whereas PpRxLR3 and PpRxLR5 moderately suppressed N. benthamiana immunity in a less-extensive manner. Moreover, we confirmed the effector-triggered susceptibility activity of these proteins after transient transformation and infection of N. benthamiana plants. All three CREs enhanced virulence of P. parasitica during the interaction with N. benthamiana. These effectors, in particular PpRxLR2, can be targeted for the development of biotechnology-based control strategies of P. parasitica diseases.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English.

PubMed

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory-which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in-constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English

PubMed Central

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L.

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory—which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in—constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues. PMID:27303315

Responses of the antioxidative and biotransformation enzymes in the aquatic fungus Mucor hiemalis exposed to cyanotoxins.

PubMed

Balsano, Evelyn; Esterhuizen-Londt, Maranda; Hoque, Enamul; Lima, Stephan Pflugmacher

2017-08-01

To investigate antioxidative and biotransformation enzyme responses in Mucor hiemalis towards cyanotoxins considering its use in mycoremediation applications. Catalase (CAT), glutathione reductase (GR), and glutathione peroxidase (GPx) in M. hiemalis maintained their activities at all tested microcystin-LR (MC-LR) exposure concentrations. Cytosolic glutathione S-transferase (GST) activity decreased with exposure to 100 µg MC-LR l -1 while microsomal GST remained constant. Cylindrospermopsin (CYN) at 100 µg l -1 led to an increase in CAT activity and inhibition of GR, as well as to a concentration-dependent GPx inhibition. Microsomal GST was inhibited at all concentrations tested. β-N-methylamino-L-alanine (BMAA) inhibited GR activity in a concentration-dependent manner, however, CAT, GPx, and GST remained unaffected. M. hiemalis showed enhanced oxidative stress tolerance and intact biotransformation enzyme activity towards MC-LR and BMAA in comparison to CYN, confirming its applicability in bioreactor technology in terms of viability and survival in their presence.

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods

PubMed Central

de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C. W.; Petersen, Esben T.; De Vis, Jill B.

2018-01-01

Objective In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Materials and methods Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). Results The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson’s correlation coefficients >0.83, R2 .67–.97). The results from the downsampled data and the high-resolution data were similar. Conclusion Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed. PMID:29672584

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

PubMed

van der Kleij, Lisa A; de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C W; Petersen, Esben T; De Vis, Jill B

2018-01-01

In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson's correlation coefficients >0.83, R2 .67-.97). The results from the downsampled data and the high-resolution data were similar. Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed.

A fresh frozen plasma to red blood cell transfusion ratio of 1:1 mitigates lung injury in a rat model of damage control resuscitation for hemorrhagic shock.

PubMed

Zhao, Jingxiang; Pan, Guocheng; Wang, Bo; Zhang, Yuhua; You, Guoxing; Wang, Ying; Gao, Dawei; Zhou, Hong; Zhao, Lian

2015-06-01

We aimed to evaluate the effects of resuscitation with different ratios of fresh frozen plasma (FFP) to red blood cells (RBCs) on pulmonary inflammatory injury and to illuminate the beneficial effects of FFP on lung protection compared with lactated ringers (LR) using a rat model of hemorrhagic shock. Rats underwent pressure-controlled hemorrhage for 60 minutes and were then transfused with LR for initial resuscitation. Thereafter, the rats were transfused with varying ratios of FFP:RBC (1:4, 1:2, 1:1, and 2:1) or LR:RBC (1:1) to hold their mean arterial pressure (MAP) at 100 ± 3 mm Hg for 30 minutes. After 4 hours of observation, lung tissue was harvested to determine the wet/dry weight, myeloperoxidase levels, tumor necrosis factor α levels, macrophage inflammatory protein 2 (MIP-2) levels, inducible nitric oxide synthase activity, and the nuclear factor κB p65 DNA-binding activity. With an increase in the FFP:RBC ratio, the volume of required RBC to maintain the target MAP decreased. The MAP value in each group was not significantly different during the whole experiment period. The values of the wet/dry weights and MIP-2 were significantly lower in the FFP:RBC = 1:1 group than the other groups (P < .05). All parameters detected above were predominantly lower in the FFP:RBC = 1:1 group than the FFP:RBC = 1:2 group and the LR:RBC = 1:1 group (P < .05). In addition, all parameter values were lower in the FFP:RBC = 1:1 group than in the FFP:RBC = 2:1 group, but only the wet/dry weight, myeloperoxidase, and MIP-2 values were significantly different (P < .05). Resuscitation with a 1:1 ratio of FFP to RBC results in decreased lung inflammation. Compared with LR, FFP could further mitigate lung inflammatory injury. Copyright © 2015. Published by Elsevier Inc.

Photocatalytic Removal of Microcystin-LR by Advanced WO3-Based Nanoparticles under Simulated Solar Light

PubMed Central

Zhao, Chao; Li, Dawei; Feng, Chuanping; Zhang, Zhenya; Sugiura, Norio; Yang, Yingnan

2015-01-01

A series of advanced WO3-based photocatalysts including CuO/WO3, Pd/WO3, and Pt/WO3 were synthesized for the photocatalytic removal of microcystin-LR (MC-LR) under simulated solar light. In the present study, Pt/WO3 exhibited the best performance for the photocatalytic degradation of MC-LR. The MC-LR degradation can be described by pseudo-first-order kinetic model. Chloride ion (Cl−) with proper concentration could enhance the MC-LR degradation. The presence of metal cations (Cu2+ and Fe3+) improved the photocatalytic degradation of MC-LR. This study suggests that Pt/WO3 photocatalytic oxidation under solar light is a promising option for the purification of water containing MC-LR. PMID:25884038

Radiation-Driven Formation of Reactive Oxygen Species in Oxychlorine-Containing Mars Surface Analogues

NASA Astrophysics Data System (ADS)

Georgiou, Christos D.; Zisimopoulos, Dimitrios; Kalaitzopoulou, Electra; Quinn, Richard C.

2017-04-01

The present study demonstrates that γ-radiolyzed perchlorate-containing Mars soil salt analogues (in a CO2 atmosphere) generate upon H2O wetting the reactive oxygen species (ROS) superoxide radical (O2•-), hydrogen peroxide (H2O2), and hydroxyl radicals (•OH). This study also validates that analogue radiolysis forms oxychlorine species that, in turn, can UV-photolyze to •OH upon UV photolysis. This investigation was made possible by the development of a new assay for inorganic-origin O2•- and H2O2 determination and by the modification of a previous assay for soil •OH. Results show that radiolyzed Mg(ClO4)2 generates H2O2 and •OH; and when included as part of a mixture analogous to the salt composition of samples analyzed at the Mars Phoenix site, the analogue generated O2•-, H2O2, and •OH, with •OH levels 150-fold higher than in the radiolyzed Mg(ClO4)2 samples. Radiolyzed Mars Phoenix site salt analogue that did not contain Mg(ClO4)2 generated only •OH also at 150-fold higher concentration than Mg(ClO4)2 alone. Additionally, UV photolysis of the perchlorate γ radiolysis product chlorite (ClO2-) generated the oxychlorine products trihalide (Cl3-), chlorine dioxide (ClO2•), and hypochlorite (ClO-), with the formation of •OH by UV photolysis of ClO-. While the generation of ROS may have contributed in part to 14CO2 production in the Viking Labeled Release (LR) experiment and O2 (g) release in the Viking Gas Exchange (GEx) experiment, our results indicate that they are not likely to be the major contributor to the LR and GEx results. However, due to their highly reactive nature, they are expected to play a significant role in the alteration of organics on Mars. Additionally, experiments with hypochlorite show that the thermal stability of NaClO is in the range of the thermal stability observed for thermally liable oxidant responsible for the Viking LR results.

Extracting transient Rayleigh wave and its application in detecting quality of highway roadbed

USGS Publications Warehouse

Liu, J.; Xia, J.; Luo, Y.; Li, X.; Xu, S.; ,

2004-01-01

This paper first explains the tau-p mapping method of extracting Rayleigh waves (LR waves) from field shot gathers. It also explains a mathematical model of physical character parameters of quality of high-grade roads. This paper then discusses an algorithm of computing dispersion curves using adjacent channels. Shear velocity and physical character parameters are obtained by inversion of dispersion curves. The algorithm using adjacent channels to calculating dispersion curves eliminates average effects that exist by using multi-channels to obtain dispersion curves so that it improves longitudinal and transverse resolution of LR waves and precision of non-invasive detection, and also broadens its application fields. By analysis of modeling results of detached computation of the ground roll and real examples of detecting density and pressure strength of a high-grade roadbed, and by comparison of shallow seismic image method with borehole cores, we concluded that: 1 the abnormal scale and configuration obtained by LR waves are mostly the same as the result of shallow seismic image method; 2 an average relative error of density obtained from LR waves inversion is 1.6% comparing with borehole coring; 3 transient LR waves in detecting density and pressure strength of a high-grade roadbed is feasible and effective.

Prospective evaluation of IOTA logistic regression models LR1 and LR2 in comparison with subjective pattern recognition for diagnosis of ovarian cancer in an outpatient setting.

PubMed

Nunes, N; Ambler, G; Foo, X; Widschwendter, M; Jurkovic, D

2018-06-01

To determine whether International Ovarian Tumor Analysis (IOTA) logistic regression models LR1 and LR2 developed for the preoperative diagnosis of ovarian cancer could also be used to differentiate between benign and malignant adnexal tumors in the population of women attending gynecology outpatient clinics. This was a single-center prospective observational study of consecutive women attending our gynecological diagnostic outpatient unit, recruited between May 2009 and January 2012. All the women were first examined by a Level-II ultrasound operator. In those diagnosed with adnexal tumors, the IOTA-LR1/2 protocol was used to evaluate the masses. The LR1 and LR2 models were then used to assess the risk of malignancy. Subsequently, the women were also examined by a Level-III examiner, who used pattern recognition to differentiate between benign and malignant tumors. Women with an ultrasound diagnosis of malignancy were offered surgery, while asymptomatic women with presumed benign lesions were offered conservative management with a minimum follow-up of 12 months. The initial diagnosis was compared with two reference standards: histological findings and/or a comparative assessment of tumor morphology on follow-up ultrasound scans. All women for whom the tumor classification on follow-up changed from benign to malignant were offered surgery. In the final analysis, 489 women who had either or both of the reference standards were included. Their mean age was 50 years (range, 16-91 years) and 45% were postmenopausal. Of the included women, 342/489 (69.9%) had surgery and 147/489 (30.1%) were managed conservatively. The malignancy rate was 137/489 (28.0%). Overall, sensitivities of LR1 and LR2 for the diagnosis of malignancy were 97.1% (95% CI, 92.7-99.2%) and 94.9% (95% CI, 89.8-97.9%) and specificities were 77.3% (95% CI, 72.5-81.5%) and 76.7% (95% CI, 71.9-81.0%), respectively (P > 0.05). In comparison with pattern recognition (sensitivity 94.2% (95% CI, 88.8-97.4%), specificity 96.3% (95% CI, 93.8-98.0%)), the specificities of the IOTA models were significantly lower (P < 0.0001). A significantly higher number of women would have been offered surgery for suspected cancer if the women had been assessed using the IOTA models instead of pattern recognition (213/489 (43.6%) vs 142/489 (29.0%); P < 0.001). The IOTA models maintained their high sensitivity when used in an outpatient setting. Specificity was relatively low, which indicates that a significant proportion of the women would have been offered unnecessary surgery for suspected ovarian cancer. These findings show that the IOTA models could be used as a first-stage test to diagnose ovarian cancer in an outpatient setting, but a different second-stage test is required to minimize the number of false-positive findings. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression.

PubMed

Chen, Carla Chia-Ming; Schwender, Holger; Keith, Jonathan; Nunkesser, Robin; Mengersen, Kerrie; Macrossan, Paula

2011-01-01

Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.

Unilateral vs bilateral hip bone mineral density measurement for the diagnosis of osteoporosis.

PubMed

Ikegami, Shota; Kamimura, Mikio; Uchiyama, Shigeharu; Mukaiyama, Keijiro; Kato, Hiroyuki

2014-01-01

It has not been established whether unilateral or bilateral hip dual-energy X-ray absorptiometry (DXA) is preferable for the diagnosis of osteoporosis. We investigated the discordance in DXA measurements in bilateral hips to determine whether unilateral DXA is valid for osteoporosis diagnosis. The subjects were 2964 Japanese patients without a previous diagnosis of primary osteoporosis. We measured bilateral femoral bone mineral density (BMD) and calculated indices, related to the unilateral results, for predicting contralateral hip osteoporosis. A likelihood ratio (LR) of a negative test (LR [-]) of less than 0.2 was considered to exclude the diagnosis. In the normal spinal BMD group, the sensitivity of unilateral DXA for women was 27-73% and LR (-) was 0.28-0.73; the sensitivity for men was 0-50% and LR (-) was 0.51-1.00; the diagnosis of contralateral osteoporosis was not excluded. Sensitivity increased and LR (-) increased with worsening spinal BMD status; however, LR (-) did not meet the cutoff for exclusion. We could exclude unilateral hip osteoporosis, in women only, by performing contralateral femoral DXA; this necessitated lowering the T-score cutoff from -2.5 to -2.0. Unilateral femoral DXA is not useful for excluding the diagnosis of contralateral hip osteoporosis. Copyright © 2014 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

Attenuated migration by green tea extract (-)-epigallocatechin gallate (EGCG): involvement of 67 kDa laminin receptor internalization in macrophagic cells.

PubMed

Ren, Xuezhi; Guo, Xingzhi; Chen, Li; Guo, Minxia; Peng, Ning; Li, Rui

2014-08-01

Excessive activation of the microglia in the brain is involved in the development of several neurodegenerative diseases. Previous studies have indicated that (-)-epigallocatechin gallate (EGCG), a major active constituent of green tea, exhibits potent suppressive effects on the activation of microglia. As the 67 kDa laminin receptor (67LR) is a key element in cellular activation and migration, we investigated the effect of EGCG on cell migration and 67LR in lipopolysaccharide (LPS)-activated macrophagic RAW264.7 cells. The presence of EGCG (1-25 μM) markedly attenuated LPS-induced cell migration in a dose-dependent manner. However, the total amount of 67LR protein in the RAW264.7 cells was unaffected by EGCG, as revealed by Western blot analysis. In addition, confocal immunofluorescence microscopy indicated that EGCG caused a marked membrane translocation of 67LR from the membrane surface towards the cytoplasm. Cell-surface biotinylation analysis confirmed that EGCG induced a significant internalization of 67LR by 24-68% in a dose-dependent manner. This study helps to explain the pharmacological action of EGCG on 67LR, suggesting its potential use in the treatment of diseases associated with macrophage/microglia activation, such as neurodegenerative diseases and cancer.

Target-regulated proximity hybridization with three-way DNA junction for in situ enhanced electronic detection of marine biotoxin based on isothermal cycling signal amplification strategy.

PubMed

Liu, Bingqian; Chen, Jinfeng; Wei, Qiaohua; Zhang, Bing; Zhang, Lan; Tang, Dianping

2015-07-15

A new signal amplification strategy based on target-regulated DNA proximity hybridization (TRPH) reaction accompanying formation of three-way DNA junction was designed for electronic detection of Microcystin-LR (MC-LR used in this case), coupling with junction-induced isothermal cycling signal amplification. Initially, a sandwiched-type immunoreaction was carried out in a low-cost PCR tube between anti-MC-LR mAb1 antibody-labeled DNA1 (mAb1-DNA1) and anti-MC-LR mAb2-labeled DNA2 (mAb2-DNA2) in the presence of target to form a three-way DNA junction. Then, the junction could undergo an unbiased strand displacement reaction on an h-like DNA nanostructure-modified electrode (labeled with methylene blue redox tag on the short DNA strand), thereby resulting in the dissociation of methylene blue-labeled signal DNA from the electrode. The newly formed double-stranded DNA could be cleaved again by exonuclease III, and the released three-way DNA junction retriggered the strand-displacement reaction with h-like DNA nanostructures for junction recycling. During the strand-displacement reaction, numerous methylene blue-labeled DNA strands were far away from the electrode, thus decreasing the detectable electrochemical signal within the applied potentials. Under optimal conditions, the TRPH-based immunosensing system exhibited good electrochemical responses for detecting target MC-LR at a concentration as low as 1.0ngkg(-1) (1.0ppt). Additionally, the precision, reproducibility, specificity and method accuracy were also investigated with acceptable results. Copyright © 2015 Elsevier B.V. All rights reserved.

Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

PubMed

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis; Pestel-Caron, Martine

2014-10-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

76 FR 62457 - Atomic Safety and Licensing Board; Nextera Energy Seabrook, LLC (Seabrook Station, Unit 1...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-07

... NUCLEAR REGULATORY COMMISSION [Docket No. 50-443-LR; ASLBP No. 10-906-02-LR-BD01] Atomic Safety and Licensing Board; Nextera Energy Seabrook, LLC (Seabrook Station, Unit 1); Notice of Hearing Before... subsequent notice or order. \\2\\ Id. at 63. It is so ordered. For the Atomic Safety and Licensing Board. Dated...

75 FR 75704 - Pacific Gas and Electric Company (Diablo Canyon Nuclear Power Plant, Units 1 And 2); Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-06

... NUCLEAR REGULATORY COMMISSION [Docket Nos. 50-275-LR; 50-323-LR] Pacific Gas and Electric Company (Diablo Canyon Nuclear Power Plant, Units 1 And 2); Notice of Appointment of Adjudicatory Employee... of 10 CFR 2.347 and 2.348 in their communications with Dr. Cao. It is so ordered. Dated at Rockville...

The Atypical Cadherin Dachsous Controls Left-Right Asymmetry in Drosophila.

PubMed

González-Morales, Nicanor; Géminard, Charles; Lebreton, Gaëlle; Cerezo, Delphine; Coutelis, Jean-Baptiste; Noselli, Stéphane

2015-06-22

Left-right (LR) asymmetry is essential for organ development and function in metazoans, but how initial LR cue is relayed to tissues still remains unclear. Here, we propose a mechanism by which the Drosophila LR determinant Myosin ID (MyoID) transfers LR information to neighboring cells through the planar cell polarity (PCP) atypical cadherin Dachsous (Ds). Molecular interaction between MyoID and Ds in a specific LR organizer controls dextral cell polarity of adjoining hindgut progenitors and is required for organ looping in adults. Loss of Ds blocks hindgut tissue polarization and looping, indicating that Ds is a crucial factor for both LR cue transmission and asymmetric morphogenesis. We further show that the Ds/Fat and Frizzled PCP pathways are required for the spreading of LR asymmetry throughout the hindgut progenitor tissue. These results identify a direct functional coupling between the LR determinant MyoID and PCP, essential for non-autonomous propagation of early LR asymmetry. Copyright © 2015 Elsevier Inc. All rights reserved.

Predicting and Reducing Driving Mishaps Among Drivers With Type 1 Diabetes

PubMed Central

Gonder-Frederick, Linda A.; Singh, Harsimran; Ingersoll, Karen S.; Banton, Tom; Grabman, Jesse H.; Schmidt, Karen; Clarke, William

2017-01-01

OBJECTIVE Two aims of this study were to develop and validate A) a metric to identify drivers with type 1 diabetes at high risk of future driving mishaps and B) an online intervention to reduce mishaps among high-risk drivers. RESEARCH DESIGN AND METHODS To achieve aim A, in study 1, 371 drivers with type 1 diabetes from three U.S. regions completed a series of established questionnaires about diabetes and driving. They recorded their driving mishaps over the next 12 months. Questionnaire items that uniquely discriminated drivers who did and did not have subsequent driving mishaps were assembled into the Risk Assessment of Diabetic Drivers (RADD) scale. In study 2, 1,737 drivers with type 1 diabetes from all 50 states completed the RADD online. Among these, 118 low-risk (LR) and 372 high-risk (HR) drivers qualified for and consented to participate in a 2-month treatment period followed by 12 monthly recordings of driving mishaps. To address aim B, HR participants were randomized to receive either routine care (RC) or the online intervention “DiabetesDriving.com” (DD.com). Half of the DD.com participants received a motivational interview (MI) at the beginning and end of the treatment period to boost participation and efficacy. All of the LR participants were assigned to RC. In both studies, the primary outcome variable was driving mishaps. RESULTS Related to aim A, in study 1, the RADD demonstrated 61% sensitivity and 75% specificity. Participants in the upper third of the RADD distribution (HR), compared with those in the lower third (LR), reported 3.03 vs. 0.87 mishaps/driver/year, respectively (P < 0.001). In study 2, HR and LR participants receiving RC reported 4.3 and 1.6 mishaps/driver/year, respectively (P < 0.001). Related to aim B, in study 2, MIs did not enhance participation or efficacy, so the DD.com and DD.com + MI groups were combined. DD.com participants reported fewer hypoglycemia-related driving mishaps than HR participants receiving RC (P = 0.01), but more than LR participants receiving RC, reducing the difference between the HR and LR participants receiving RC by 63%. HR drivers differed from LR drivers at baseline across a variety of hypoglycemia and driving parameters. CONCLUSIONS The RADD identified higher-risk drivers, and identification seemed relatively stable across time, samples, and procedures. This 11-item questionnaire could inform patients at higher risk, and their clinicians, that they should take preventive steps to reduce driving mishaps, which was accomplished in aim B using DD.com. PMID:28404657

Quantifying predictive capability of electronic health records for the most harmful breast cancer

NASA Astrophysics Data System (ADS)

Wu, Yirong; Fan, Jun; Peissig, Peggy; Berg, Richard; Tafti, Ahmad Pahlavan; Yin, Jie; Yuan, Ming; Page, David; Cox, Jennifer; Burnside, Elizabeth S.

2018-03-01

Improved prediction of the "most harmful" breast cancers that cause the most substantive morbidity and mortality would enable physicians to target more intense screening and preventive measures at those women who have the highest risk; however, such prediction models for the "most harmful" breast cancers have rarely been developed. Electronic health records (EHRs) represent an underused data source that has great research and clinical potential. Our goal was to quantify the value of EHR variables in the "most harmful" breast cancer risk prediction. We identified 794 subjects who had breast cancer with primary non-benign tumors with their earliest diagnosis on or after 1/1/2004 from an existing personalized medicine data repository, including 395 "most harmful" breast cancer cases and 399 "least harmful" breast cancer cases. For these subjects, we collected EHR data comprised of 6 components: demographics, diagnoses, symptoms, procedures, medications, and laboratory results. We developed two regularized prediction models, Ridge Logistic Regression (Ridge-LR) and Lasso Logistic Regression (Lasso-LR), to predict the "most harmful" breast cancer one year in advance. The area under the ROC curve (AUC) was used to assess model performance. We observed that the AUCs of Ridge-LR and Lasso-LR models were 0.818 and 0.839 respectively. For both the Ridge-LR and LassoLR models, the predictive performance of the whole EHR variables was significantly higher than that of each individual component (p<0.001). In conclusion, EHR variables can be used to predict the "most harmful" breast cancer, providing the possibility to personalize care for those women at the highest risk in clinical practice.

Quantifying predictive capability of electronic health records for the most harmful breast cancer.

PubMed

Wu, Yirong; Fan, Jun; Peissig, Peggy; Berg, Richard; Tafti, Ahmad Pahlavan; Yin, Jie; Yuan, Ming; Page, David; Cox, Jennifer; Burnside, Elizabeth S

2018-02-01

Improved prediction of the "most harmful" breast cancers that cause the most substantive morbidity and mortality would enable physicians to target more intense screening and preventive measures at those women who have the highest risk; however, such prediction models for the "most harmful" breast cancers have rarely been developed. Electronic health records (EHRs) represent an underused data source that has great research and clinical potential. Our goal was to quantify the value of EHR variables in the "most harmful" breast cancer risk prediction. We identified 794 subjects who had breast cancer with primary non-benign tumors with their earliest diagnosis on or after 1/1/2004 from an existing personalized medicine data repository, including 395 "most harmful" breast cancer cases and 399 "least harmful" breast cancer cases. For these subjects, we collected EHR data comprised of 6 components: demographics, diagnoses, symptoms, procedures, medications, and laboratory results. We developed two regularized prediction models, Ridge Logistic Regression (Ridge-LR) and Lasso Logistic Regression (Lasso-LR), to predict the "most harmful" breast cancer one year in advance. The area under the ROC curve (AUC) was used to assess model performance. We observed that the AUCs of Ridge-LR and Lasso-LR models were 0.818 and 0.839 respectively. For both the Ridge-LR and Lasso-LR models, the predictive performance of the whole EHR variables was significantly higher than that of each individual component (p<0.001). In conclusion, EHR variables can be used to predict the "most harmful" breast cancer, providing the possibility to personalize care for those women at the highest risk in clinical practice.

Diagnostic accuracy of the gravity stress test and clinical signs in cases of isolated supination-external rotation-type lateral malleolar fractures.

PubMed

Nortunen, S; Flinkkilä, T; Lantto, I; Kortekangas, T; Niinimäki, J; Ohtonen, P; Pakarinen, H

2015-08-01

We prospectively assessed the diagnostic accuracy of the gravity stress test and clinical findings to evaluate the stability of the ankle mortise in patients with supination-external rotation-type fractures of the lateral malleolus without widening of the medial clear space. The cohort included 79 patients with a mean age of 44 years (16 to 82). Two surgeons assessed medial tenderness, swelling and ecchymosis and performed the external rotation (ER) stress test (a reference standard). A diagnostic radiographer performed the gravity stress test. For the gravity stress test, the positive likelihood ratio (LR) was 5.80 with a 95% confidence interval (CI) of 2.75 to 12.27, and the negative LR was 0.15 (95% CI 0.07 to 0.35), suggesting a moderate change from the pre-test probability. Medial tenderness, both alone and in combination with swelling and/or ecchymosis, indicated a small change (positive LR, 2.74 to 3.25; negative LR, 0.38 to 0.47), whereas swelling and ecchymosis indicated only minimal changes (positive LR, 1.41 to 1.65; negative LR, 0.38 to 0.47). In conclusion, when gravity stress test results are in agreement with clinical findings, the result is likely to predict stability of the ankle mortise with an accuracy equivalent to ER stress test results. When clinical examination suggests a medial-side injury, however, the gravity stress test may give a false negative result. ©2015 The British Editorial Society of Bone & Joint Surgery.

Units in the VO Version 1.0

NASA Astrophysics Data System (ADS)

Derriere, Sebastien; Gray, Norman; Demleitner, Markus; Louys, Mireille; Ochsenbein, Francois; Derriere, Sebastien; Gray, Norman

2014-05-01

This document describes a recommended syntax for writing the string representation of unit labels ("VOUnits"). In addition, it describes a set of recognised and deprecated units, which is as far as possible consistent with other relevant standards (BIPM, ISO/IEC and the IAU). The intention is that units written to conform to this specification will likely also be parsable by other well-known parsers. To this end, we include machine-readable grammars for other units syntaxes.

Development of the gateway recycling cloning system for multiple linking of expression cassettes in a defined order, and direction on gateway compatible binary vectors.

PubMed

Kimura, Tetsuya; Nakao, Akihide; Murata, Sachiko; Kobayashi, Yasuyuki; Tanaka, Yuji; Shibahara, Kenta; Kawazu, Tetsu; Nakagawa, Tsuyoshi

2013-01-01

We developed the Gateway recycling cloning system, which allows multiple linking of expression cassettes by multiple rounds of the Gateway LR reaction. Employing this system, the recycling donor vector pRED419 was subjected to the first LR reaction with an attR1-attR2 type destination vector. Then conversion vector pCON was subjected to an LR reaction to restore the attR1-attR2 site on the destination vector for the next cloning cycle. By repetition of these two simple steps, we linked four expression cassettes of a reporter gene in Gateway binary vector pGWB1, introduced the constructs into tobacco BY-2 cells, and observed the expression of transgenes.

77 FR 13158 - Sunshine Act Meeting Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-05

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0002] Sunshine Act Meeting Notice DATE: Weeks of March 5...-11-2 (Feb. 15, 2011), Docket No. 50-443-LR (Tentative) b. Entergy Nuclear Generation Co. and Entergy Nuclear Operations, Inc. (Pilgrim Nuclear Power Station), Commonwealth of Massachusetts' Notice of Appeal...

Automatic Parsing of Parental Verbal Input

PubMed Central

Sagae, Kenji; MacWhinney, Brian; Lavie, Alon

2006-01-01

To evaluate theoretical proposals regarding the course of child language acquisition, researchers often need to rely on the processing of large numbers of syntactically parsed utterances, both from children and their parents. Because it is so difficult to do this by hand, there are currently no parsed corpora of child language input data. To automate this process, we developed a system that combined the MOR tagger, a rule-based parser, and statistical disambiguation techniques. The resultant system obtained nearly 80% correct parses for the sentences spoken to children. To achieve this level, we had to construct a particular processing sequence that minimizes problems caused by the coverage/ambiguity trade-off in parser design. These procedures are particularly appropriate for use with the CHILDES database, an international corpus of transcripts. The data and programs are now freely available over the Internet. PMID:15190707

Incremental Refinement of FAÇADE Models with Attribute Grammar from 3d Point Clouds

NASA Astrophysics Data System (ADS)

Dehbi, Y.; Staat, C.; Mandtler, L.; Pl¨umer, L.

2016-06-01

Data acquisition using unmanned aerial vehicles (UAVs) has gotten more and more attention over the last years. Especially in the field of building reconstruction the incremental interpretation of such data is a demanding task. In this context formal grammars play an important role for the top-down identification and reconstruction of building objects. Up to now, the available approaches expect offline data in order to parse an a-priori known grammar. For mapping on demand an on the fly reconstruction based on UAV data is required. An incremental interpretation of the data stream is inevitable. This paper presents an incremental parser of grammar rules for an automatic 3D building reconstruction. The parser enables a model refinement based on new observations with respect to a weighted attribute context-free grammar (WACFG). The falsification or rejection of hypotheses is supported as well. The parser can deal with and adapt available parse trees acquired from previous interpretations or predictions. Parse trees derived so far are updated in an iterative way using transformation rules. A diagnostic step searches for mismatches between current and new nodes. Prior knowledge on façades is incorporated. It is given by probability densities as well as architectural patterns. Since we cannot always assume normal distributions, the derivation of location and shape parameters of building objects is based on a kernel density estimation (KDE). While the level of detail is continuously improved, the geometrical, semantic and topological consistency is ensured.

GBParsy: a GenBank flatfile parser library with high speed.

PubMed

Lee, Tae-Ho; Kim, Yeon-Ki; Nahm, Baek Hie

2008-07-25

GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is required and is performed according to a given grammar for the sequence and the description in a GBF. Currently, several parser libraries for the GBF have been developed. However, with the accumulation of DNA sequence information from eukaryotic chromosomes, parsing a eukaryotic genome sequence with these libraries inevitably takes a long time, due to the large GBF file and its correspondingly large genomic nucleotide sequence and related feature information. Thus, there is significant need to develop a parsing program with high speed and efficient use of system memory. We developed a library, GBParsy, which was C language-based and parses GBF files. The parsing speed was maximized by using content-specified functions in place of regular expressions that are flexible but slow. In addition, we optimized an algorithm related to memory usage so that it also increased parsing performance and efficiency of memory usage. GBParsy is at least 5-100x faster than current parsers in benchmark tests. GBParsy is estimated to extract annotated information from almost 100 Mb of a GenBank flatfile for chromosomal sequence information within a second. Thus, it should be used for a variety of applications such as on-time visualization of a genome at a web site.

Disambiguating the species of biomedical named entities using natural language parsers

PubMed Central

Wang, Xinglong; Tsujii, Jun'ichi; Ananiadou, Sophia

2010-01-01

Motivation: Text mining technologies have been shown to reduce the laborious work involved in organizing the vast amount of information hidden in the literature. One challenge in text mining is linking ambiguous word forms to unambiguous biological concepts. This article reports on a comprehensive study on resolving the ambiguity in mentions of biomedical named entities with respect to model organisms and presents an array of approaches, with focus on methods utilizing natural language parsers. Results: We build a corpus for organism disambiguation where every occurrence of protein/gene entity is manually tagged with a species ID, and evaluate a number of methods on it. Promising results are obtained by training a machine learning model on syntactic parse trees, which is then used to decide whether an entity belongs to the model organism denoted by a neighbouring species-indicating word (e.g. yeast). The parser-based approaches are also compared with a supervised classification method and results indicate that the former are a more favorable choice when domain portability is of concern. The best overall performance is obtained by combining the strengths of syntactic features and supervised classification. Availability: The corpus and demo are available at http://www.nactem.ac.uk/deca_details/start.cgi, and the software is freely available as U-Compare components (Kano et al., 2009): NaCTeM Species Word Detector and NaCTeM Species Disambiguator. U-Compare is available at http://-compare.org/ Contact: xinglong.wang@manchester.ac.uk PMID:20053840

Ecological risk assessment of microcystin-LR in the upstream section of the Haihe River based on a species sensitivity distribution model.

PubMed

Niu, Zhiguang; Du, Lei; Li, Jiafu; Zhang, Ying; Lv, Zhiwei

2018-02-01

The eutrophication of surface water has been the main problem of water quality management in recent decades, and the ecological risk of microcystin-LR (MC-LR), which is the by-product of eutrophication, has drawn more attention worldwide. The aims of our study were to determine the predicted no effect concentration (PNEC) of MC-LR and to assess the ecological risk of MC-LR in the upstream section of the Haihe River. HC 5 (hazardous concentration for 5% of biological species) and PNEC were obtained from a species sensitivity distribution (SSD) model, which was constructed with the acute toxicity data of MC-LR on aquatic organisms. The concentrations of MC-LR in the upstream section of the Haihe River from April to August of 2015 were analysed, and the ecological risk characteristics of MC-LR were evaluated based on the SSD model. The results showed that the HC 5 of MC-LR in freshwater was 17.18 μg/L and PNEC was 5.73 μg/L. The concentrations of MC-LR ranged from 0.68 μg/L to 32.21 μg/L and were obviously higher in summer than in spring. The values of the risk quotient (RQ) ranged from 0.12 to 5.62, suggesting that the risk of MC-LR for aquatic organisms in the river was at a medium or high level during the study period. Compared with other waterbodies in the world, the pollution level of MC-LR in the Haihe River was at a moderate level. This research could promote the study of the ecological risk of MC-LR at the ecosystem level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Validity of the MMPI-2-RF (restructured form) L-r and K-r scales in detecting underreporting in clinical and nonclinical samples.

PubMed

Sellbom, Martin; Bagby, R Michael

2008-12-01

In the current investigation, the authors examined the validity of the L-r and K-r scales on the recently developed Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Y. S. Ben-Porath & A. Tellegen, in press) in measuring underreported response bias. Three archival samples previously collected for examining MMPI-2 validity scales were reanalyzed in 2 studies. In Study 1 L-r and K-r significantly differentiated 2 groups of participants (patients with schizophrenia and university students) who had been instructed to underreport on the MMPI-2 from participants who took the test under standard instructions. L-r and K-r also added incremental predictive variance to one another in differentiating these groups. In Study 2 a similar set of outcomes emerged through the use of a differential prevalence design in which L-r and K-r significantly differentiated a group of child custody litigants who were administered the MMPI-2 from university students taking the test under standard instructions. (c) 2008 APA, all rights reserved.

Does elimination of planned postoperative radiation to the primary bed in p16-positive, transorally-resected oropharyngeal carcinoma associate with poorer outcomes?

PubMed

Sinha, Parul; Pipkorn, Patrik; Thorstad, Wade L; Gay, Hiram A; Haughey, Bruce H

2016-10-01

The purpose of our study is to compare oncologic and functional outcomes of p16-positive oropharyngeal squamous cell carcinoma (OPSCC) patients, in the presence and absence of planned radiation to the primary bed following transoral surgery (TOS), stratified by T-classification. Retrospective cohort study of 261, T1-T4, consecutively TOS-treated OPSCC patients. At a median follow-up of 61months, local recurrence (LR) occurred in 6 (2.3%)patients (3 each in T1-T2 and T3-T4 groups), of which 5 had tumors in the tongue base and one in the tonsil. Of patients not receiving planned primary bed radiation, LR occurred in 3% of T1-T2s versus 17% of T3-T4s. In patients with T1-T2 tumors, Absolute Risk Reduction of LR with primary bed radiation was 3.26% (95% CI: -0.37%, 7%); Number Needed to Treat to prevent one LR was 31 (95% CI: 14.5, 271). Absolute Risk Increase for gastrostomy-tube with primary bed radiation was 34.4% (95% CI: 24%, 45%); Number Needed to Harm was 3 (95% CI: 2.2, 4.2), i.e., for every three patients with T1-T2 tumors receiving primary bed radiation, one had a gastrostomy-tube. Elimination of primary bed radiation in margin-negative resected, T1-T2 p16-positive OPSCC was not associated with significant compromise of local control, and correlated with superior swallowing preservation, assessed using gastrostomy rate as a surrogate. Lack of primary bed radiation in T3-T4 tumors associated with significantly increased LR rates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of sexually transmitted disease risk assessment algorithms for selection of intrauterine device candidates.

PubMed

Morrison, C S; Sekadde-Kigondu, C; Miller, W C; Weiner, D H; Sinei, S K

1999-02-01

Sexually transmitted diseases (STD) are an important contraindication for intrauterine device (IUD) insertion. Nevertheless, laboratory testing for STD is not possible in many settings. The objective of this study is to evaluate the use of risk assessment algorithms to predict STD and subsequent IUD-related complications among IUD candidates. Among 615 IUD users in Kenya, the following algorithms were evaluated: 1) an STD algorithm based on US Agency for International Development (USAID) Technical Working Group guidelines: 2) a Centers for Disease Control and Prevention (CDC) algorithm for management of chlamydia; and 3) a data-derived algorithm modeled from study data. Algorithms were evaluated for prediction of chlamydial and gonococcal infection at 1 month and complications (pelvic inflammatory disease [PID], IUD removals, and IUD expulsions) over 4 months. Women with STD were more likely to develop complications than women without STD (19% vs 6%; risk ratio = 2.9; 95% CI 1.3-6.5). For STD prediction, the USAID algorithm was 75% sensitive and 48% specific, with a positive likelihood ratio (LR+) of 1.4. The CDC algorithm was 44% sensitive and 72% specific, LR+ = 1.6. The data-derived algorithm was 91% sensitive and 56% specific, with LR+ = 2.0 and LR- = 0.2. Category-specific LR for this algorithm identified women with very low (< 1%) and very high (29%) infection probabilities. The data-derived algorithm was also the best predictor of IUD-related complications. These results suggest that use of STD algorithms may improve selection of IUD users. Women at high risk for STD could be counseled to avoid IUD, whereas women at moderate risk should be monitored closely and counseled to use condoms.

Diagnostic test accuracy of nutritional tools used to identify undernutrition in patients with colorectal cancer: a systematic review.

PubMed

Håkonsen, Sasja Jul; Pedersen, Preben Ulrich; Bath-Hextall, Fiona; Kirkpatrick, Pamela

2015-05-15

Effective nutritional screening, nutritional care planning and nutritional support are essential in all settings, and there is no doubt that a health service seeking to increase safety and clinical effectiveness must take nutritional care seriously. Screening and early detection of malnutrition is crucial in identifying patients at nutritional risk. There is a high prevalence of malnutrition in hospitalized patients undergoing treatment for colorectal cancer. To synthesize the best available evidence regarding the diagnostic test accuracy of nutritional tools (sensitivity and specificity) used to identify malnutrition (specifically undernutrition) in patients with colorectal cancer (such as the Malnutrition Screening Tool and Nutritional Risk Index) compared to reference tests (such as the Subjective Global Assessment or Patient Generated Subjective Global Assessment). Patients with colorectal cancer requiring either (or all) surgery, chemotherapy and/or radiotherapy in secondary care. Focus of the review: The diagnostic test accuracy of validated assessment tools/instruments (such as the Malnutrition Screening Tool and Nutritional Risk Index) in the diagnosis of malnutrition (specifically under-nutrition) in patients with colorectal cancer, relative to reference tests (Subjective Global Assessment or Patient Generated Subjective Global Assessment). Types of studies: Diagnostic test accuracy studies regardless of study design. Studies published in English, German, Danish, Swedish and Norwegian were considered for inclusion in this review. Databases were searched from their inception to April 2014. Methodological quality was determined using the Quality Assessment of Diagnostic Accuracy Studies checklist. Data was collected using the data extraction form: the Standards for Reporting Studies of Diagnostic Accuracy checklist for the reporting of studies of diagnostic accuracy. The accuracy of diagnostic tests is presented in terms of sensitivity, specificity, positive and negative predictive values. In addition, the positive likelihood ratio (sensitivity/ [1 - specificity]) and negative likelihood ratio (1 - sensitivity)/ specificity), were also calculated and presented in this review to provide information about the likelihood that a given test result would be expected when the target condition is present compared with the likelihood that the same result would be expected when the condition is absent. Not all trials reported true positive, true negative, false positive and false negative rates, therefore these rates were calculated based on the data in the published papers. A two-by-two truth table was reconstructed for each study, and sensitivity, specificity, positive predictive value, negative predictive value positive likelihood ratio and negative likelihood ratio were calculated for each study. A summary receiver operator characteristics curve was constructed to determine the relationship between sensitivity and specificity, and the area under the summary receiver operator characteristics curve which measured the usefulness of a test was calculated. Meta-analysis was not considered appropriate, therefore data was synthesized in a narrative summary. 1. One study evaluated the Malnutrition Screening Tool against the reference standard Patient-Generated Subjective Global Assessment. The sensitivity was 56% and the specificity 84%. The positive likelihood ratio was 3.100, negative likelihood ratio was 0.59, the diagnostic odds ratio (CI 95%) was 5.20 (1.09-24.90) and the Area Under the Curve (AUC) represents only a poor to fair diagnostic test accuracy. A total of two studies evaluated the diagnostic accuracy of Malnutrition Universal Screening Tool (MUST) (index test) compared to both Subjective Global Assessment (SGA) (reference standard) and PG-SGA (reference standard) in patients with colorectal cancer. In MUST vs SGA the sensitivity of the tool was 96%, specificity was 75%, LR+ 3.826, LR- 0.058, diagnostic OR (CI 95%) 66.00 (6.61-659.24) and AUC represented excellent diagnostic accuracy. In MUST vs PG-SGA the sensitivity of the tool was 72%, specificity 48.9%, LR+ 1.382, LR- 0.579, diagnostic OR (CI 95%) 2.39 (0.87-6.58) and AUC indicated that the tool failed as a diagnostic test to identify patients with colorectal cancer at nutritional risk,. The Nutrition Risk Index (NRI) was compared to SGA representing a sensitivity of 95.2%, specificity of 62.5%, LR+ 2.521, LR- 0.087, diagnostic OR (CI 95%) 28.89 (6.93-120.40) and AUC represented good diagnostic accuracy. In regard to NRI vs PG-SGA the sensitivity of the tool was 68%, specificity 64%, LR+ 1.947, LR- 0.487, diagnostic OR (CI 95%) 4.00 (1.23-13.01) and AUC indicated poor diagnostic test accuracy. There are no single, specific tools used to screen or assess the nutritional status of colorectal cancer patients. All tools showed varied diagnostic accuracies when compared to the reference standards SGA and PG-SGA. Hence clinical judgment combined with perhaps the SGA or PG-SGA should play a major role. The PG-SGA offers several advantages over the SGA tool: 1) the patient completes the medical history component, thereby decreasing the amount of time involved; 2) it contains more nutrition impact symptoms, which are important to the patient with cancer; and 3) it has a scoring system that allows patients to be triaged for nutritional intervention. Therefore, the PG-SGA could be used as a nutrition assessment tool as it allows quick identification and prioritization of colorectal cancer patients with malnutrition in combination with other parameters. This systematic review highlights the need for the following: Further studies needs to investigate the diagnostic accuracy of already existing nutritional screening tools in the context of colorectal cancer patients. If new screenings tools are developed, they should be developed and validated in the specific clinical context within the same patient population (colorectal cancer patients). The Joanna Briggs Institute.

Midazolam treatment before re-exposure to contextual fear reduces freezing behavior and amygdala activity differentially in high- and low-anxiety rats.

PubMed

Skórzewska, Anna; Lehner, Małgorzata; Wisłowska-Stanek, Aleksandra; Turzyńska, Danuta; Sobolewska, Alicja; Krząścik, Paweł; Płaźnik, Adam

2015-02-01

The aim of this study was to examine the effects of benzodiazepine (midazolam) administration on rat conditioned fear responses and on local brain activity (c-Fos and CRF expressions) of low- (LR) and high- (HR)anxiety rats after the first and second contextual fear test sessions. The animals were divided into LR and HR groups based on the duration of their conditioned freezing response in the first contextual fear test. The fear-re-conditioned LR and HR animals (28 days later) had increased freezing durations compared with those durations during the first conditioned fear test. These behavioral effects were accompanied by increased c-Fos expression in the medial amygdala (MeA), the basolateral amygdala (BLA), and the paraventricular hypothalamic nuclei and elevated CRF expression in the MeA. All these behavioral and immunochemical effects of fear re-conditioning were stronger in the LR group compared with the effects in the HR group. Moreover, in the LR rats, the re-conditioning led to decreased CRF expression in the primary motor cortex (M1) and to increased CRF expression in the BLA. The pretreatment of rats with midazolam before the second exposure to the aversive context significantly attenuated the conditioned fear response, lowered the serum corticosterone concentration, decreased c-Fos and CRF expressions in the MeA and in the BLA, and increased CRF complex density in M1 area only in the LR group. These studies have demonstrated that LR rats are more sensitive to re-exposure to fear stimuli and that midazolam pretreatment was associated with modified brain activity in the amygdala and in the prefrontal cortex in this group of animals. The current data may facilitate a better understanding of the neurobiological mechanisms responsible for individual differences in the psychopathological processes accompanying some anxiety disorders characterized by stronger reactivity to re-exposure to stressful challenges, e.g., posttraumatic stress disorder. Copyright © 2013 Elsevier Inc. All rights reserved.

Bacterial growth kinetics in ACD-A apheresis platelets: comparison of plasma and PAS III storage.

PubMed

Dumont, Larry J; Wood, Tammara A; Housman, Molly; Herschel, Louise; Brantigan, Barbara; Heber, Cheryl; Houghton, Jaime

2011-05-01

Our objective was to determine the growth kinetics of bacteria in leukoreduced apheresis platelets (LR-AP) in a platelet (PLT) additive solution (PAS; InterSol, Fenwal, Inc.) compared to LR-AP stored in plasma. Hyperconcentrated, double-dose LR-AP were collected from healthy donors with a separator (AMICUS, Fenwal, Inc.). LR-AP were evenly divided, InterSol was added to half (65% InterSol:35% plasma [PAS]), and PLTs in autologous plasma were used for a paired control (PL). Bacteria were inoculated into each LR-AP PAS/PL pair (0.5-1.6 colony-forming units [CFUs]/mL), and bacterial growth was followed for up to 7 days. Time to the end of the lag phase, doubling times, maximum concentration (conc-max), and time to maximum concentration (time-max) were estimated. Streptococcus viridans did not grow to detectable levels in either PAS or PL units. The other bacteria had no significant overall difference in the conc-max (p = 0.47) or time-max (p = 0.7) between PL and PAS LR-AP; PL had a 0.14 hours faster doubling rate (p = 0.023); and PAS had a 4.7 hours shorter lag time (p = 0.016). We observed that five index organisms will grow in LR-AP stored in a 35%:65% ratio of plasma to InterSol where initial bacterial concentrations are 0.5 to 1.6 CFUs/mL. The more rapid initiation of log-phase growth for bacteria within a PAS storage environment resulted in a bacterial concentration up to 4 logs higher in the PAS units compared to the plasma units at 24 hours, but with no difference in the conc-max. This may present an early bacterial detection advantage for PAS-stored PLTs. © 2010 American Association of Blood Banks.

Increasing chloride in rivers of the conterminous U.S. and linkages to potential corrosivity and lead action level exceedances in drinking water.

PubMed

Stets, E G; Lee, C J; Lytle, D A; Schock, M R

2018-02-01

Corrosion in water-distribution systems is a costly problem and controlling corrosion is a primary focus of efforts to reduce lead (Pb) and copper (Cu) in tap water. High chloride concentrations can increase the tendency of water to cause corrosion in distribution systems. The effects of chloride are also expressed in several indices commonly used to describe the potential corrosivity of water, the chloride-sulfate mass ratio (CSMR) and the Larson Ratio (LR). Elevated CSMR has been linked to the galvanic corrosion of Pb whereas LR is indicative of the corrosivity of water to iron and steel. Despite the known importance of chloride, CSMR, and LR to the potential corrosivity of water, monitoring of seasonal and interannual changes in these parameters is not common among water purveyors. We analyzed long-term trends (1992-2012) and the current status (2010-2015) of chloride, CSMR, and LR in order to investigate the short and long-term temporal variability in potential corrosivity of US streams and rivers. Among all sites in the trend analyses, chloride, CSMR, and LR increased slightly, with median changes of 0.9mgL -1 , 0.08, and 0.01, respectively. However, urban-dominated sites had much larger increases, 46.9mgL -1 , 2.50, and 0.53, respectively. Median CSMR and LR in urban streams (4.01 and 1.34, respectively) greatly exceeded thresholds found to cause corrosion in water distribution systems (0.5 and 0.3, respectively). Urbanization was strongly correlated with elevated chloride, CSMR, and LR, especially in the most snow-affected areas in the study, which are most likely to use road salt. The probability of Pb action-level exceedances (ALEs) in drinking water facilities increased along with raw surface water CSMR, indicating a statistical connection between surface water chemistry and corrosion in drinking water facilities. Optimal corrosion control will require monitoring of critical constituents reflecting the potential corrosivity in surface waters. Published by Elsevier B.V.

Effective deep learning training for single-image super-resolution in endomicroscopy exploiting video-registration-based reconstruction.

PubMed

Ravì, Daniele; Szczotka, Agnieszka Barbara; Shakir, Dzhoshkun Ismail; Pereira, Stephen P; Vercauteren, Tom

2018-06-01

Probe-based confocal laser endomicroscopy (pCLE) is a recent imaging modality that allows performing in vivo optical biopsies. The design of pCLE hardware, and its reliance on an optical fibre bundle, fundamentally limits the image quality with a few tens of thousands fibres, each acting as the equivalent of a single-pixel detector, assembled into a single fibre bundle. Video registration techniques can be used to estimate high-resolution (HR) images by exploiting the temporal information contained in a sequence of low-resolution (LR) images. However, the alignment of LR frames, required for the fusion, is computationally demanding and prone to artefacts. In this work, we propose a novel synthetic data generation approach to train exemplar-based Deep Neural Networks (DNNs). HR pCLE images with enhanced quality are recovered by the models trained on pairs of estimated HR images (generated by the video registration algorithm) and realistic synthetic LR images. Performance of three different state-of-the-art DNNs techniques were analysed on a Smart Atlas database of 8806 images from 238 pCLE video sequences. The results were validated through an extensive image quality assessment that takes into account different quality scores, including a Mean Opinion Score (MOS). Results indicate that the proposed solution produces an effective improvement in the quality of the obtained reconstructed image. The proposed training strategy and associated DNNs allows us to perform convincing super-resolution of pCLE images.

Distinct mechanisms determine organ left-right asymmetry patterning in an uncoupled way.

PubMed

Huang, Sizhou; Xu, Wenming; Su, Bingyin; Luo, Lingfei

2014-03-01

Disruption of Nodal in the lateral plate mesoderm (LPM) usually leads to left-right (LR) patterning defects in multiple organs. However, whether the LR patterning of organs is always regulated in a coupled way has largely not yet been elucidated. In addition, whether other crucial regulators exist in the LPM that coordinate with Nodal in regulating organ LR patterning is also undetermined. In this paper, after briefly summarizing the common process of LR patterning, the most puzzling question regarding the initiation of asymmetry is considered and the divergent mechanisms underlying the uncoupled LR patterning in different organs are discussed. On the basis of cases in which different organ LR patterning is determined in an uncoupled way via an independent mechanism or at a different time, we propose that there are other critical factors in the LPM that coordinate with Nodal to regulate heart LR asymmetry patterning during early LR patterning. © 2014 WILEY Periodicals, Inc.

Internal Associations of the Acidic Region of Upstream Binding Factor Control Its Nucleolar Localization.

PubMed

Ueshima, Shuhei; Nagata, Kyosuke; Okuwaki, Mitsuru

2017-11-15

Upstream binding factor (UBF) is a member of the high-mobility group (HMG) box protein family, characterized by multiple HMG boxes and a C-terminal acidic region (AR). UBF is an essential transcription factor for rRNA genes and mediates the formation of transcriptionally active chromatin in the nucleolus. However, it remains unknown how UBF is specifically localized to the nucleolus. Here, we examined the molecular mechanisms that localize UBF to the nucleolus. We found that the first HMG box (HMG box 1), the linker region (LR), and the AR cooperatively regulate the nucleolar localization of UBF1. We demonstrated that the AR intramolecularly associates with and attenuates the DNA binding activity of HMG boxes and confers the structured DNA preference to HMG box 1. In contrast, the LR was found to serve as a nuclear localization signal and compete with HMG boxes to bind the AR, permitting nucleolar localization of UBF1. The LR sequence binds DNA and assists the stable chromatin binding of UBF. We also showed that the phosphorylation status of the AR does not clearly affect the localization of UBF1. Our results strongly suggest that associations of the AR with HMG boxes and the LR regulate UBF nucleolar localization. Copyright © 2017 American Society for Microbiology.

Multi-modal antigen specific therapy for autoimmunity.

PubMed

Legge, K L; Bell, J J; Li, L; Gregg, R; Caprio, J C; Zaghouani, H

2001-10-01

Peripheral tolerance, represents an attractive strategy to down-regulate previously activated T cells and suppress an ongoing disease. Herein, immunoglobulins (Igs) were used to deliver self and altered self peptides for efficient peptide presentation without costimulation to test for modulation of experimental allergic encephalomyelitis (EAE). Accordingly, the encephalitogenic proteolipid protein (PLP) sequence 139-151 (referred to as PLP1) and an altered form of PLP1 known as PLP-LR were genetically expressed on Igs and the resulting Ig-PLP1 and Ig-PLP-LR were tested for efficient presentation of the peptides and for amelioration of ongoing EAE. Evidence is presented indicating that Ig-PLP1 as well as Ig-PLP-LR given in saline to mice with ongoing clinical EAE suppresses subsequent relapses. However, aggregation of both chimeras allows crosslinking of Fcgamma receptors (FcgammaRs) and induction of IL-10 production by APCs but does not promote the up-regulation of costimulatory molecules. Consequently, IL-10 displays bystander suppression and synergizes with presentation without costimulation to drive effective modulation of EAE. As Ig-PLP1 is more potent than Ig-PLP-LR in the down-regulation of T cells, we conclude that peptide affinity plays a critical role in this multi-modal approach of T cell modulation.

An aptamer-based immunoassay in microchannels of a portable analyzer for detection of microcystin-leucine-arginine.

PubMed

Xiang, An; Lei, Xiaoying; Ren, Fengling; Zang, Liuqin; Wang, Qin; Zhang, Ju; Lu, Zifan; Guo, Yanhai

2014-12-01

The rapid detection of microcystin-leucine-arginine (MC-LR), the most highly toxic among MCs, is significantly important to environmental and human health protection and prevention of MC-LR from being used as a bioweapon. Although aptamers offer higher affinity, specificity, and stability with MC-LR than antibodies in the immunodetection of MC-LR due to steric hindrance between two antibodies and limited epitopes of MC-LR for use in a sandwich immunoassay, no sandwich immunoassay using an aptmer has been developed for MC-LR detection. This study is aimed at developing an aptamer-antibody immunoassay (AAIA) to detect MC-LR using a portable analyzer. The aptamers were immobilized onto the glass surface of a microchamber to capture MC-LR. MC-LR and horseradish peroxidase (HRP)-labeled antibody were pulled into the microchamber to react with the immobilized aptamer. The chemiluminescence (CL) catalyzed by HRP was tested by a photodiode-based portable analyzer. MC-LR at 0.5-4.0 μg/L was detected quantitatively by the AAIA, with a CL signal sensitivity of 0.3 μg/L. The assay took less than 35 min for a single sample and demonstrated a high specificity, detecting only MC-LR, but not MC-LA, MC-YR, or nodularin-R. The recovery of two spiked real environmental samples calculated as 94.5-112.7%. Therefore, this AAIA was proved to be a rapid and simple method to detect MC-LR in the field by a single analyst. Copyright © 2014 Elsevier B.V. All rights reserved.

Genome-wide association study using deregressed breeding values for cryptorchidism and scrotal/inguinal hernia in two pig lines.

PubMed

Sevillano, Claudia A; Lopes, Marcos S; Harlizius, Barbara; Hanenberg, Egiel H A T; Knol, Egbert F; Bastiaansen, John W M

2015-03-21

Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS. Heritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia. The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.

Lettuce (Lactuca sativa L.) leaf-proteome profiles after exposure to cylindrospermopsin and a microcystin-LR/cylindrospermopsin mixture: a concentration-dependent response.

PubMed

Freitas, Marisa; Campos, Alexandre; Azevedo, Joana; Barreiro, Aldo; Planchon, Sébastien; Renaut, Jenny; Vasconcelos, Vitor

2015-02-01

The intensification of agricultural productivity is an important challenge worldwide. However, environmental stressors can provide challenges to this intensification. The progressive occurrence of the cyanotoxins cylindrospermopsin (CYN) and microcystin-LR (MC-LR) as a potential consequence of eutrophication and climate change is of increasing concern in the agricultural sector because it has been reported that these cyanotoxins exert harmful effects in crop plants. A proteomic-based approach has been shown to be a suitable tool for the detection and identification of the primary responses of organisms exposed to cyanotoxins. The aim of this study was to compare the leaf-proteome profiles of lettuce plants exposed to environmentally relevant concentrations of CYN and a MC-LR/CYN mixture. Lettuce plants were exposed to 1, 10, and 100 μg/l CYN and a MC-LR/CYN mixture for five days. The proteins of lettuce leaves were separated by two-dimensional electrophoresis (2-DE), and those that were differentially abundant were then identified by matrix-assisted laser desorption/ionization time of flight-mass spectrometry (MALDI-TOF/TOF MS). The biological functions of the proteins that were most represented in both experiments were photosynthesis and carbon metabolism and stress/defense response. Proteins involved in protein synthesis and signal transduction were also highly observed in the MC-LR/CYN experiment. Although distinct protein abundance patterns were observed in both experiments, the effects appear to be concentration-dependent, and the effects of the mixture were clearly stronger than those of CYN alone. The obtained results highlight the putative tolerance of lettuce to CYN at concentrations up to 100 μg/l. Furthermore, the combination of CYN with MC-LR at low concentrations (1 μg/l) stimulated a significant increase in the fresh weight (fr. wt) of lettuce leaves and at the proteomic level resulted in the increase in abundance of a high number of proteins. In contrast, many proteins exhibited a decrease in abundance or were absent in the gels of the simultaneous exposure to 10 and 100 μg/l MC-LR/CYN. In the latter, also a significant decrease in the fr. wt of lettuce leaves was obtained. These findings provide important insights into the molecular mechanisms of the lettuce response to CYN and MC-LR/CYN and may contribute to the identification of potential protein markers of exposure and proteins that may confer tolerance to CYN and MC-LR/CYN. Furthermore, because lettuce is an important crop worldwide, this study may improve our understanding of the potential impact of these cyanotoxins on its quality traits (e.g., presence of allergenic proteins). Copyright © 2014 Elsevier Ltd. All rights reserved.

FLIP for FLAG model visualization

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

Wooten, Hasani Omar

A graphical user interface has been developed for FLAG users. FLIP (FLAG Input deck Parser) provides users with an organized view of FLAG models and a means for efficiently and easily navigating and editing nodes, parameters, and variables.

Python/Lua Benchmarks

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

Busby, L.

This is an adaptation of the pre-existing Scimark benchmark code to a variety of Python and Lua implementations. It also measures performance of the Fparser expression parser and C and C++ code on a variety of simple scientific expressions.

An experimental method for the assessment of color simulation tools.

PubMed

Lillo, Julio; Alvaro, Leticia; Moreira, Humberto

2014-07-22

The Simulcheck method for evaluating the accuracy of color simulation tools in relation to dichromats is described and used to test three color simulation tools: Variantor, Coblis, and Vischeck. A total of 10 dichromats (five protanopes, five deuteranopes) and 10 normal trichromats participated in the current study. Simulcheck includes two psychophysical tasks: the Pseudoachromatic Stimuli Identification task and the Minimum Achromatic Contrast task. The Pseudoachromatic Stimuli Identification task allows determination of the two chromatic angles (h(uv) values) that generate a minimum response in the yellow–blue opponent mechanism and, consequently, pseudoachromatic stimuli (greens or reds). The Minimum Achromatic Contrast task requires the selection of the gray background that produces minimum contrast (near zero change in the achromatic mechanism) for each pseudoachromatic stimulus selected in the previous task (L(R) values). Results showed important differences in the colorimetric transformations performed by the three evaluated simulation tools and their accuracy levels. Vischeck simulation accurately implemented the algorithm of Brettel, Viénot, and Mollon (1997). Only Vischeck appeared accurate (similarity in huv and L(R) values between real and simulated dichromats) and, consequently, could render reliable color selections. It is concluded that Simulcheck is a consistent method because it provided an equivalent pattern of results for huv and L(R) values irrespective of the stimulus set used to evaluate a simulation tool. Simulcheck was also considered valid because real dichromats provided expected huv and LR values when performing the two psychophysical tasks included in this method. © 2014 ARVO.

Transvaginal ultrasound vs magnetic resonance imaging for diagnosing deep infiltrating endometriosis: systematic review and meta-analysis.

PubMed

Guerriero, S; Saba, L; Pascual, M A; Ajossa, S; Rodriguez, I; Mais, V; Alcazar, J L

2018-05-01

To perform a systematic review of studies comparing the accuracy of transvaginal ultrasound (TVS) and magnetic resonance imaging (MRI) in diagnosing deep infiltrating endometriosis (DIE) including only studies in which patients underwent both techniques. An extensive search was carried out in PubMed/MEDLINE and Web of Science for papers from January 1989 to October 2016 comparing TVS and MRI in DIE. Studies were considered eligible for inclusion if they reported on the use of TVS and MRI in the same set of patients for the preoperative detection of endometriosis in pelvic locations in women with clinical suspicion of DIE and using surgical data as a reference standard. Quality was assessed using the QUADAS-2 tool. A random-effects model was used to determine pooled sensitivity, specificity, positive and negative likelihood ratios (LR+ and LR-) and diagnostic odds ratio (DOR). Of 375 citations identified, six studies (n = 424) were considered eligible. For MRI in the detection of DIE in the rectosigmoid, pooled sensitivity was 0.85 (95% CI, 0.78-0.90), specificity was 0.95 (95% CI, 0.83-0.99), LR+ was 18.4 (95% CI, 4.7-72.4), LR- was 0.16 (95% CI, 0.11-0.24) and DOR was 116 (95% CI, 23-585). For TVS in the detection of DIE in the rectosigmoid, pooled sensitivity was 0.85 (95% CI, 0.68-0.94), specificity was 0.96 (95% CI, 0.85-0.99), LR+ was 20.4 (95% CI, 4.7-88.5), LR- was 0.16 (95% CI, 0.07-0.38) and DOR was 127 (95% CI, 14-1126). For MRI in the detection of DIE in the rectovaginal septum, pooled sensitivity was 0.66 (95% CI, 0.51-0.79), specificity was 0.97 (95% CI, 0.89-0.99), LR+ was 22.5 (95% CI, 6.7-76.2), LR- was 0.38 (95% CI, 0.23-0.52) and DOR was 65 (95% CI, 21-204). For TVS in the detection of DIE in the rectovaginal septum, pooled sensitivity was 0.59 (95% CI, 0.26-0.86), specificity was 0.97 (95% CI, 0.94-0.99), LR+ was 23.5 (95% CI, 9.1-60.5), LR- was 0.42 (95% CI, 0.18-0.97) and DOR was 56 (95% CI, 11-275). For MRI in the detection of DIE in the uterosacral ligaments, pooled sensitivity was 0.70 (95% CI, 0.55-0.82), specificity was 0.93 (95% CI, 0.87-0.97), LR+ was 10.4 (95% CI, 5.1-21.2), LR- was 0.32 (95% CI, 0.20-0.51) and DOR was 32 (95% CI, 12-85). For TVS in the detection of DIE in the uterosacral ligaments, pooled sensitivity was 0.67 (95% CI, 0.55-0.77), specificity was 0.86 (95% CI, 0.73-0.93), LR+ was 4.8 (95% CI, 2.6-9.0), LR- was 0.38 (95% CI, 0.29-0.50) and DOR was 12 (95% CI, 7-24). Confidence intervals of pooled sensitivities, specificities and DOR were wide for both techniques in all the locations considered. Heterogeneity was moderate or high for sensitivity and specificity for both TVS and MRI in most locations assessed. According to QUADAS-2, the quality of the included studies was considered good for most domains. The diagnostic performance of TVS and MRI is similar for detecting DIE involving rectosigmoid, uterosacral ligaments and rectovaginal septum. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Mis-Spliced Lr34 Transcript Events in Winter Wheat.

PubMed

Fang, Tilin; Carver, Brett F; Hunger, Robert M; Yan, Liuling

2017-01-01

Lr34 in wheat is a non-race-specific gene that confers resistance against multiple fungal pathogens. The resistant allele Lr34 and the susceptible allele Lr34s can be distinguished by three polymorphisms that cause alternation of deduced amino acid sequences of Lr34 at the protein level. In seedlings of a cultivar carrying the resistant Lr34r allele, only a portion (35%) of its transcripts was correctly spliced and the majority (65%) of its transcripts were incorrectly spliced due to multiple mis-splicing events. Lr34 mis-splicing events were also observed at adult plant age when this gene exerts its function. All of the mis-spliced Lr34r cDNA transcripts observed in this study resulted in a premature stop codon due to a shift of the open reading frame; hence, the mis-spliced Lr34r cDNAs were deduced to encode incomplete proteins. Even if a cultivar has a functional Lr34 gene, its transcripts might not completely splice in a correct pattern. These findings suggested that the partial resistance conferred by a quantitative gene might be due to mis-splicing events in its transcripts; hence, the resistance of the gene could be increased by eliminating or mutating regulators that cause mis-splicing events in wheat.

Comparative Analysis of Aqueous Binders for High-Energy Li-Rich NMC as a Lithium-Ion Cathode and the Impact of Adding Phosphoric Acid.

PubMed

Kazzazi, Arefeh; Bresser, Dominic; Birrozzi, Agnese; von Zamory, Jan; Hekmatfar, Maral; Passerini, Stefano

2018-05-23

Even though electrochemically inactive, the binding agent in lithium-ion electrodes substantially contributes to the performance metrics such as the achievable capacity, rate capability, and cycling stability. Herein, we present an in-depth comparative analysis of three different aqueous binding agents, allowing for the replacement of the toxic N-methyl-2-pyrrolidone as the processing solvent, for high-energy Li 1.2 Ni 0.16 Mn 0.56 Co 0.08 O 2 (Li-rich NMC or LR-NMC) as a potential next-generation cathode material. The impact of the binding agents, sodium carboxymethyl cellulose, sodium alginate, and commercial TRD202A (TRD), and the related chemical reactions occurring during the electrode coating process on the electrode morphology and cycling performance is investigated. In particular, the role of phosphoric acid in avoiding the aluminum current collector corrosion and stabilizing the LR-NMC/electrolyte interface as well as its chemical interaction with the binder is investigated, providing an explanation for the observed differences in the electrochemical performance.

Oxaliplatin but Not Irinotecan Impairs Posthepatectomy Liver Regeneration in a Murine Model

PubMed Central

Soriano, Perry A.; Liu, Nian; Castillo, Erick; Foster, Brock; Artinyan, Avo; Kim, Joseph; Huang, Wendong; Wagman, Lawrence D.

2011-01-01

Introduction. We examined the murine hepatectomy model of liver regeneration (LR) in the setting of neoadjuvant chemotherapy. Methods. C57BL/6 mice were randomized to receive neoadjuvant intraperitoneal (IP) injections of a control, oxaliplatin (15 mg/kg), or irinotecan (100 mg/Kg or 250 mg/Kg) solution. Hepatectomy (70%) was performed 14 days after the final IP treatment. Animals were sacrificed at postoperative day (D) 0, 1, 2, 3, and 7. Liver remnants and serum were collected for analysis. T-tests for independent samples were used for statistical comparisons. Results. For oxaliplatin, percent LR did not differ at D1 or D2 but was significantly less at D3 (89.0% versus 70.0%, P = 0.048) with no difference on D7 (P = 0.21). Irinotecan-treated mice at both dose levels (100 mg/Kg and 250 mg/Kg) showed no significant differences in LR. BrdU incorporation was significantly decreased in oxaliplatin-treated animals (D1,2,3). Conclusions. Neoadjuvant oxaliplatin but not irinotecan impairs early LR in a posthepatectomy murine model which correlates with decreased DNA synthesis. PMID:22164336

Endoscopic resection is cost-effective compared with laparoscopic resection in the management of complex colon polyps: an economic analysis.

PubMed

Law, Ryan; Das, Ananya; Gregory, Dyanna; Komanduri, Srinadh; Muthusamy, Raman; Rastogi, Amit; Vargo, John; Wallace, Michael B; Raju, G S; Mounzer, Rawad; Klapman, Jason; Shah, Janak; Watson, Rabindra; Wilson, Robert; Edmundowicz, Steven A; Wani, Sachin

2016-06-01

Endoscopic resection (ER) is an efficacious treatment for complex colon polyps (CCPs). Many patients are referred for surgical resection because of concerns over procedural safety, incomplete polyp resection, and adenoma recurrence after ER. Efficacy data for both resection strategies are widely available, but a paucity of data exist on the cost-effectiveness of each modality. The aim of this study was to perform an economic analysis comparing ER and laparoscopic resection (LR) strategies in patients with CCP. A decision analysis tree was constructed using decision analysis software. The 2 strategies (ER vs LR) were evaluated in a hypothetical cohort of patients with CCPs. A hybrid Markov model with a 10-year time horizon was used. Patients entered the model after colonoscopic diagnosis at age 50. Under Strategy I, patients underwent ER followed by surveillance colonoscopy at 3 to 6 months and 12 months. Patients with failed ER and residual adenoma at 12 months were referred for LR. Under Strategy II, patients underwent LR as primary treatment. Patients with invasive cancer were excluded. Estimates regarding ER performance characteristics were obtained from a systematic review of published literature. The Centers for Medicare & Medicaid Services (2012-2013) and the 2012 Healthcare Cost and Utilization Project databases were used to determine the costs and loss of utility. We assumed that all procedures were performed with anesthesia support, and patients with adverse events in both strategies required inpatient hospitalization. Baseline estimates and costs were varied by using a sensitivity analysis through the ranges. LR was found to be more costly and yielded fewer quality-adjusted life-years (QALYs) compared with ER. The cost of ER of a CCP was $5570 per patient and yielded 9.640 QALYs. LR of a CCP cost $18,717 per patient and yielded fewer QALYs (9.577). For LR to be more cost-effective, the thresholds of 1-way sensitivity analyses were (1) technical success of ER for complete resection in <75.8% of cases, (2) adverse event rates for ER > 12%, and (3) LR cost of <$14,000. Our data suggest that ER is a cost-effective strategy for removal of CCPs. The effectiveness is driven by high technical success and low adverse event rates associated with ER, in addition to the increased cost of LR. Copyright © 2016 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Azacitidine in Lower-Risk Myelodysplastic Syndromes: A Meta-Analysis of Data from Prospective Studies.

PubMed

Komrokji, Rami; Swern, Arlene S; Grinblatt, David; Lyons, Roger M; Tobiasson, Magnus; Silverman, Lewis R; Sayar, Hamid; Vij, Ravi; Fliss, Albert; Tu, Nora; Sugrue, Mary M

2018-02-01

After erythropoiesis-stimulating agent (ESA) failure, lenalidomide and hypomethylating agents are the only remaining treatment options for most patients with lower-risk myelodysplastic syndromes (LR-MDS). Optimal choice of these agents as front-line therapy in non-del(5q) LR-MDS is unclear. Because azacitidine clinical data mainly describe experience in higher-risk MDS, we performed a meta-analysis of patient-level data to evaluate azacitidine in patients with red blood cell (RBC) transfusion-dependent LR-MDS. We searched English-language articles for prospective phase II and III azacitidine clinical trials and patient registries published between 2000 and 2015, and Embase abstracts from 2015 conferences. Patient-level data from identified relevant studies were provided by investigators. Meta-analyses followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Efficacy endpoints were RBC transfusion independence (TI) and Clinical Benefit (RBC-TI, erythroid response, and complete or partial remission, per International Working Group 2006 criteria for MDS). Data for 233 patients from 6 clinical studies and 1 registry study met criteria for inclusion in analyses. Overall, 90.3% of patients had non-del(5q) LR-MDS. Pooled estimates from random-effects models of RBC-TI and Clinical Benefit were 38.9% and 81.1%, respectively; for the ESA-refractory subgroup, they were 40.5% and 77.3%; and for patients with isolated anemia, they were 41.9% and 82.5%. In multivariate analyses, planned use of ≥6 azacitidine treatment cycles was significantly predictive of response. Azacitidine effects in these patients, most with non-del(5q) LR-MDS, were promising and generally similar to those reported for lenalidomide in similar patients. The choice of initial therapy is important because most patients eventually stop responding to front-line therapy and alternatives are limited. Lower-risk myelodysplastic syndromes (LR-MDS) are primarily characterized by anemia. After erythropoiesis-stimulating agent (ESA) failure, lenalidomide and hypomethylating agents are the only remaining treatment options for most patients. This meta-analysis of 233 azacitidine-treated red blood cell (RBC) transfusion-dependent patients with LR-MDS (92.3% non-del[5q]) from 7 studies showed 38.9% became RBC transfusion-independent. There is no clear guidance regarding the optimal choice of lenalidomide or hypomethylating agents for patients with non-del(5q) LR-MDS following ESA failure. Clinical presentation (e.g., number of cytopenias) and potential outcomes after hypomethylating agent failure are factors to consider when making initial treatment decisions for LR-MDS patients. © AlphaMed Press 2017.

Epigenetic regulation of left-right asymmetry by DNA methylation.

PubMed

Wang, Lu; Liu, Zhibin; Lin, Hao; Ma, Dongyuan; Tao, Qinghua; Liu, Feng

2017-10-16

DNA methylation is a major epigenetic modification; however, the precise role of DNA methylation in vertebrate development is still not fully understood. Here, we show that DNA methylation is essential for the establishment of the left-right (LR) asymmetric body plan during vertebrate embryogenesis. Perturbation of DNA methylation by depletion of DNA methyltransferase 1 ( dnmt1 ) or dnmt3bb.1 in zebrafish embryos leads to defects in dorsal forerunner cell (DFC) specification or collective migration, laterality organ malformation, and disruption of LR patterning. Knockdown of dnmt1 in Xenopus embryos also causes similar defects. Mechanistically, loss of dnmt1 function induces hypomethylation of the lefty2 gene enhancer and promotes lefty2 expression, which consequently represses Nodal signaling in zebrafish embryos. We also show that Dnmt3bb.1 regulates collective DFC migration through cadherin 1 (Cdh1). Taken together, our data uncover dynamic DNA methylation as an epigenetic mechanism to control LR determination during early embryogenesis in vertebrates. © 2017 The Authors.

A simple highly sensitive and selective aptamer-based colorimetric sensor for environmental toxins microcystin-LR in water samples.

PubMed

Li, Xiuyan; Cheng, Ruojie; Shi, Huijie; Tang, Bo; Xiao, Hanshuang; Zhao, Guohua

2016-03-05

A simple and highly sensitive aptamer-based colorimetric sensor was developed for selective detection of Microcystin-LR (MC-LR). The aptamer (ABA) was employed as recognition element which could bind MC-LR with high-affinity, while gold nanoparticles (AuNPs) worked as sensing materials whose plasma resonance absorption peaks red shifted upon binding of the targets at a high concentration of sodium chloride. With the addition of MC-LR, the random coil aptamer adsorbed on Au NPs altered into regulated structure to form MC-LR-aptamer complexes and broke away from the surface of Au NPs, leading to the aggregation of AuNPs, and the color converted from red to blue due to the interparticle plasmon coupling. Results showed that our aptamer-based colorimetric sensor exhibited rapid and sensitive detection performance for MC-LR with linear range from 0.5 nM to 7.5 μM and the detection limit reached 0.37 nM. Meanwhile, the pollutants usually coexisting with MC-LR in pollutant water samples had not demonstrated disturbance for detecting of MC-LR. The mechanism was also proposed suggesting that high affinity interaction between aptamer and MC-LR significantly enhanced the sensitivity and selectivity for MC-LR detection. Besides, the established method was utilized in analyzing real water samples and splendid sensitivity and selectivity were obtained as well. Copyright © 2015 Elsevier B.V. All rights reserved.

Sulforaphane protects Microcystin-LR-induced toxicity through activation of the Nrf2-mediated defensive response

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

Gan Nanqin; Mi Lixin; Sun Xiaoyun

2010-09-01

Microcystins (MCs), a cyclic heptapeptide hepatotoxins, are mainly produced by the bloom-forming cyanobacerium Microcystis, which has become an environmental hazard worldwide. Long term consumption of MC-contaminated water may induce liver damage, liver cancer, and even human death. Therefore, in addition to removal of MCs in drinking water, novel strategies that prevent health damages are urgently needed. Sulforaphane (SFN), a natural-occurring isothiocyanate from cruciferous vegetables, has been reported to reduce and eliminate toxicities from xenobiotics and carcinogens. The purpose of the present study was to provide mechanistic insights into the SFN-induced antioxidative defense system against MC-LR-induced cytotoxicity. We performed cell viabilitymore » assays, including MTS assay, colony formation assay and apoptotic cell sorting, to study MC-LR-induced cellular damage and the protective effects by SFN. The results showed that SFN protected MC-LR-induced damages at a nontoxic and physiological relevant dose in HepG2, BRL-3A and NIH 3 T3 cells. The protection was Nrf2-mediated as evident by transactivation of Nrf2 and activation of its downstream genes, including NQO1 and HO-1, and elevated intracellular GSH level. Results of our studies indicate that pretreatment of cells with 10 {mu}M SFN for 12 h significantly protected cells from MC-LR-induced damage. SFN-induced protective response was mediated through Nrf2 pathway.« less

Oxygen partial pressure modulates 67-kDa laminin receptor expression, leading to altered activity of the green tea polyphenol, EGCG.

PubMed

Tsukamoto, Shuntaro; Yamashita, Shuya; Kim, Yoon Hee; Kumazoe, Motofumi; Huang, Yuhui; Yamada, Koji; Tachibana, Hirofumi

2012-09-21

(-)-Epigallocatechin-3-O-gallate (EGCG) exhibits anti-tumor activity mediated via the 67-kDa laminin receptor (67LR). In this study, we found that 67LR protein levels are reduced by exposure to low O(2) levels (5%), without affecting the expression of HIF-1α. We also found that EGCG-induced anti-cancer activity is abrogated under low O(2) levels (5%) in various cancer cells. Notably, treatment with the proteasome inhibitor, prevented down-regulation of 67LR and restored sensitivity to EGCG under 5% O(2). In summary, 67LR expression is highly sensitive to O(2) partial pressure, and the activity of EGCG can be regulated in cancer cells by O(2) partial pressure. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

The MicroRNA390/TRANS-ACTING SHORT INTERFERING RNA3 Module Mediates Lateral Root Growth under Salt Stress via the Auxin Pathway.

PubMed

He, Fu; Xu, Changzheng; Fu, Xiaokang; Shen, Yun; Guo, Li; Leng, Mi; Luo, Keming

2018-06-01

Salt-induced developmental plasticity in a plant root system strongly depends on auxin signaling. However, the molecular events underlying this process are poorly understood. MicroRNA390 ( miR390 ), trans-actin small interfering RNA s ( tasiRNA s), and AUXIN RESPONSE FACTORs ( ARFs ) form a regulatory module involved in controlling lateral root (LR) growth. Here, we found that miR390 expression was strongly induced by exposure to salt during LR formation in poplar ( Populus spp.) plants. miR390 overexpression stimulated LR development and increased salt tolerance, whereas miR390 knockdown caused by a short tandem target mimic repressed LR growth and compromised salt resistance. ARF3.1 , ARF3.2 , and ARF4 expression was inhibited significantly by the presence of salt, and transcript abundance was decreased dramatically in the miR390 -overexpressing line but increased in the miR390 -knockdown line. Constitutive expression of ARF4m harboring mutated trans-acting small interfering ARF -binding sites removed the salt resistance of the miR390 overexpressors. miR390 positively regulated auxin signaling in LRs subjected to salt, but ARF4 inhibited auxin signaling. Salinity stabilized the poplar Aux/IAA repressor INDOLE-3-ACETIC ACID17.1, and overexpression of an auxin/salt-resistant form of this repressor suppressed LR growth in miR390 -overexpressing and ARF4 -RNA interfering lines in the presence of salt. Thus, the miR390/TAS3/ARFs module is a key regulator, via modulating the auxin pathway, of LR growth in poplar subjected to salt stress. © 2018 American Society of Plant Biologists. All rights reserved.

Enhancement of a culture-based bacterial detection system (eBDS) for platelet products based on measurement of oxygen consumption.

PubMed

Holme, Stein; McAlister, Morven B; Ortolano, Girolamo A; Chong, Chiyong; Cortus, Mary Anne; Jacobs, Michael R; Yomtovian, Roslyn; Freundlich, Lawrence F; Wenz, Barry

2005-06-01

An enhanced bacterial detection system (Pall eBDS) was developed that distinguishes itself from its predecessor (Pall BDS) by removal of the platelet (PLT)-retaining filter allowing for optimal bacterial transfer, modification of the culture tablet to reduce the confounding effects of respiring PLTs while enhancing bacterial growth, and facilitation of nutrients and gas exchange by agitating the sample pouch during incubation at 35 degrees C. The objective was to evaluate the performance of the new eBDS. Leukoreduced whole blood-derived PLT concentrates (LR-PCs) and LR single-donor PLTs (LR-SDPs) were inoculated with 1 to 15 colony-forming units (CFUs) of bacteria per mL in studies of each of 10 bacterial species associated with fatal transfusion-transmitted bacterial infection. Immediately after inoculation and after 24 hours of storage at 22 degrees C, samples of inoculated LR-PCs were aseptically transferred into the eBDS pouches. Pouches were then incubated for 24 hours at 35 degrees C with agitation and oxygen concentration was then measured. Median inoculation levels ranged from 5 to 13 CFUs per mL for each species studied. No significant differences in oxygen concentration were found when comparing LR-PCs with LR-SDPs. When sampling occurred from the PLTs 24 hours after inoculation, all 280 cases (24-33 replicates of each species) were detected as contaminated by the device (100% sensitivity). No false-positives were obtained with 713 uninoculated PLT units. The eBDS demonstrated improved detection sensitivity in the range of 1 to 15 CFUs per mL with no observed false-positives compared to the original BDS (detection range 100 to 500 CFUs/mL) with no false-positives.

Totally robotic vs 3D laparoscopic colectomy: A single centers preliminary experience

PubMed Central

Guerrieri, Mario; Campagnacci, Roberto; Sperti, Pierluigi; Belfiori, Giulio; Gesuita, Rosaria; Ghiselli, Roberto

2015-01-01

AIM: To compare robotic and three-dimensional (3D) laparoscopic colectomy based on the literature and our preliminary experience. METHODS: This retrospective observational study compared operative measures and postoperative outcomes between laparoscopic 3D and robotic colectomy for cancer. From September 2013 to September 2014, 24 robotic colectomies and 23 3D laparoscopic colectomy were performed at our Department. Data were analyzed and reported both by approach and by colectomy side. Robotic left colectomy (RL) vs laparoscopic 3D left colectomy (LL 3D) and Robotic right colectomy (RR) vs laparoscopic 3D (LR 3D). Rectal cancer procedures were not included. RESULTS: There were 18 RR and 11 LR 3D, 6 RL and 12 LL 3D. As regards LR 3D, extracorporeal anastomosis (EA) was performed in 7 patients and intracorporeal anastomosis (IA) in 4; the RR group included 14 IA and 4 EA. There was no mortality. Median operative time was higher for the robotic group while conversion rate (12.5% vs 13%) and lymph nodes removed (14 vs 13) were similar for both. First flatus time was 1 d for RR and 2 d the other patient groups. Oral intake was resumed in 1 d by LR and in 2 d by the other patients (P = 0.012). Overall cost was €4950 and €1950 for RL and LL 3D, and €4450 and €1450 for RR and LR 3D, respectively. CONCLUSION: There were no differences between RR and LR 3D, except that IA was easier with RR, and probably contributed with the learning curve to the longer operative time recorded. Both techniques offer similar advantages for the patient with significantly different costs. In left colectomies robotic colectomy provided better outcomes, especially in resections approaching the rectum. PMID:26674518

The Lr34 adult plant rust resistance gene provides seedling resistance in durum wheat without senescence.

PubMed

Rinaldo, Amy; Gilbert, Brian; Boni, Rainer; Krattinger, Simon G; Singh, Davinder; Park, Robert F; Lagudah, Evans; Ayliffe, Michael

2017-07-01

The hexaploid wheat (Triticum aestivum) adult plant resistance gene, Lr34/Yr18/Sr57/Pm38/Ltn1, provides broad-spectrum resistance to wheat leaf rust (Lr34), stripe rust (Yr18), stem rust (Sr57) and powdery mildew (Pm38) pathogens, and has remained effective in wheat crops for many decades. The partial resistance provided by this gene is only apparent in adult plants and not effective in field-grown seedlings. Lr34 also causes leaf tip necrosis (Ltn1) in mature adult plant leaves when grown under field conditions. This D genome-encoded bread wheat gene was transferred to tetraploid durum wheat (T. turgidum) cultivar Stewart by transformation. Transgenic durum lines were produced with elevated gene expression levels when compared with the endogenous hexaploid gene. Unlike nontransgenic hexaploid and durum control lines, these transgenic plants showed robust seedling resistance to pathogens causing wheat leaf rust, stripe rust and powdery mildew disease. The effectiveness of seedling resistance against each pathogen correlated with the level of transgene expression. No evidence of accelerated leaf necrosis or up-regulation of senescence gene markers was apparent in these seedlings, suggesting senescence is not required for Lr34 resistance, although leaf tip necrosis occurred in mature plant flag leaves. Several abiotic stress-response genes were up-regulated in these seedlings in the absence of rust infection as previously observed in adult plant flag leaves of hexaploid wheat. Increasing day length significantly increased Lr34 seedling resistance. These data demonstrate that expression of a highly durable, broad-spectrum adult plant resistance gene can be modified to provide seedling resistance in durum wheat. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Bioacumulation of cyanotoxins in Hypophthalmichthys molitrix (silver carp) in Paranoá Lake, Brasilia-DF, Brazil.

PubMed

Oliveira, N B; Schwartz, C A; Bloch, C; Paulino, L; Pires, O R

2013-03-01

Three individuals of silver carp (Hypophthalmichthys molitrix) were collected biweekly from Paranoá Lake (DF, Brazil) for analysis of microcystin (MC) concentrations in their muscle and liver tissue. Analysis by high performance liquid chromatography and mass spectrometry revealed MC masses and fragmentation patterns that were identified as MC-LR (995.04 m/z), MC-LA (909.01 m/z) and an unknown MC (987.07 m/z). Concentrations were calculated as MC-LR equivalents using a calibration curve prepared with a standard of MC-LR. May/06 was the month with the highest MC-LR equivalent concentrations in muscle and liver (3.83 ± 2.78, and 12.94 ± 10.51 μg g(-1), respectively). Our results show that during the drought months (April-September), consumption of fish with these MC concentrations would result in exposure to MCs that greatly exceed the World Health Organization's recommended tolerable daily intake limit of 0.04 μg MC kg(-1) body weight.

The Laser Ranging Experiment of the Lunar Reconnaissance Orbiter: Five Years of Operations and Data Analysis

NASA Technical Reports Server (NTRS)

Mao, Dandan; McGarry, Jan F.; Mazarico, Erwan; Neumann, Gregory A.; Sun, Xiaoli; Torrence, Mark H.; Zagwodzki, Thomas W.; Rowlands, David D.; Hoffman, Evan D.; Horvath, Julie E.;

Speed breeding for multiple quantitative traits in durum wheat.

PubMed

Alahmad, Samir; Dinglasan, Eric; Leung, Kung Ming; Riaz, Adnan; Derbal, Nora; Voss-Fels, Kai P; Able, Jason A; Bassi, Filippo M; Christopher, Jack; Hickey, Lee T

2018-01-01

Plant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named 'speed breeding' was successfully deployed in bread wheat ( Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat ( Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F 2 population (n = 1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F 3 progeny derived from 100 'selected' and 100 'unselected' F 2 individuals. Transgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F 2 population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between 'selected' and 'unselected' F 3 families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed. The novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.

Lung recruitment manoeuvres are effective in regaining lung volume and oxygenation after open endotracheal suctioning in acute respiratory distress syndrome

PubMed Central

Dyhr, Thomas; Bonde, Jan; Larsson, Anders

2003-01-01

Introduction Lung collapse is a contributory factor in the hypoxaemia that is observed after open endotracheal suctioning (ETS) in patients with acute lung injury and acute respiratory distress syndrome. Lung recruitment (LR) manoeuvres may be effective in rapidly regaining lung volume and improving oxygenation after ETS. Materials and method A prospective, randomized, controlled study was conducted in a 15-bed general intensive care unit at a university hospital. Eight consecutive mechanically ventilated patients with acute lung injury or acute respiratory distress syndrome were included. One of two suctioning procedures was performed in each patient. In the first procedure, ETS was performed followed by LR manoeuvre and reconnection to the ventilator with positive end-expiratory pressure set at 1 cmH2O above the lower inflexion point, and after 60 min another ETS (but without LR manoeuvre) was performed followed by reconnection to the ventilator with similar positive end-expiratory pressure; the second procedure was the same as the first but conducted in reverse order. Before (baseline) and over 25 min following each ETS procedure, partial arterial oxygen tension (PaO2) and end-expiratory lung volume were measured. Results After ETS, PaO2 decreased by 4.3(0.9–9.7)kPa (median and range; P < 0.005). After LR manoeuvre, PaO2 recovered to baseline. Without LR manoeuvre, PaO2 was reduced (P = 0.05) until 7 min after ETS. With LR manoeuvre end-expiratory lung volume was unchanged after ETS, whereas without LR manoeuvre end-expiratory lung volume was still reduced (approximately 10%) at 5 and 15 min after ETS (P = 0.01). Discussion A LR manoeuvre immediately following ETS was, as an adjunct to positive end-expiratory pressure, effective in rapidly counteracting the deterioration in PaO2 and lung volume caused by open ETS in ventilator-treated patients with acute lung injury or acute respiratory distress syndrome. PMID:12617741

Mercury and drought along the lower Carson River, Nevada: IV. Snowy egret post-fledging dispersal, timing of migration and survival, 2002–2004

USGS Publications Warehouse

Henny, Charles J.; Hill, Elwood F.; Grove, Robert A.; Chelgren, Nathan; Haggerty, Patricia K.

2017-01-01

This telemetry study is an extension of our 1997–2006 research on historical mercury contamination on snowy egrets (Egretta thula) up to ~ 20 days of age. Findings from initial studies at the mercury-contaminated Carson River colony at Lahontan Reservoir (LR) and a similar-sized reference (REF) colony on the Humboldt River included mercury-related physiological, biochemical, histopathological and reproductive effects up to ~20 days of age; with poor water years (2000–04), i.e., reduced prey availability, exacerbating effects. Herein, we compare timing of dispersal and migration at LR vs. REF, but the primary question now addressed is “whether survival of young mercury-exposed snowy egrets from LR would be further compromised beyond ~20 days of age? ” Based upon telemetry signals until 90–110 days of age (including dead bird counts and survival rate estimates), we conclude that mercury did not further compromise survival. Dead bird counts and survival rate estimates included time in the colony when fed by adults, plus the critical period when young dispersed from the colony to forage independently. The extended drought during this 3-year study was most critical in 2002 when production of ~20 d old egrets at LR was only 0.24 young/nest. In 2002, survival rates were low at both colonies and we documented the highest counts of dead egrets for both colonies. We suggest the losses in 2002 beyond 20 days of age were more a function of prey availability influenced by drought than exposure to mercury, especially at LR, because higher mercury concentrations, higher survival rates and fewer dead birds were documented at LR in 2003 when water conditions improved. Furthermore, total mercury (THg) in blood in 2003 was more than double 2002 (geometric mean, 3.39 vs 1.47 µg/g wet weight (ww). This higher THg exposure at LR in 2003 was associated with a redistribution of parent and post-dispersal feeding activities upstream (where there was higher mercury from historic mining) related to slightly improved water levels. When comparing the 3-year telemetry findings based upon ~20 d old young at LR (blood THg, geo. means 1.47, 3.39 and 1.89 µg/g ww), we found no evidence that age at dispersal, Julian date at dispersal, timing of migration, or pre-migration survival (~20 to ~100 days post-hatch) were adversely affected by elevated mercury.

Mercury and drought along the lower Carson River, Nevada: IV. Snowy egret post-fledging dispersal, timing of migration and survival, 2002-2004.

PubMed

Henny, Charles J; Hill, Elwood F; Grove, Robert A; Chelgren, Nathan D; Haggerty, Patricia K

2017-01-01

This telemetry study is an extension of our 1997-2006 research on historical mercury contamination on snowy egrets (Egretta thula) up to ~ 20 days of age. Findings from initial studies at the mercury-contaminated Carson River colony at Lahontan Reservoir (LR) and a similar-sized reference (REF) colony on the Humboldt River included mercury-related physiological, biochemical, histopathological and reproductive effects up to ~20 days of age; with poor water years (2000-04), i.e., reduced prey availability, exacerbating effects. Herein, we compare timing of dispersal and migration at LR vs. REF, but the primary question now addressed is "whether survival of young mercury-exposed snowy egrets from LR would be further compromised beyond ~20 days of age? " Based upon telemetry signals until 90-110 days of age (including dead bird counts and survival rate estimates), we conclude that mercury did not further compromise survival. Dead bird counts and survival rate estimates included time in the colony when fed by adults, plus the critical period when young dispersed from the colony to forage independently. The extended drought during this 3-year study was most critical in 2002 when production of ~20d old egrets at LR was only 0.24 young/nest. In 2002, survival rates were low at both colonies and we documented the highest counts of dead egrets for both colonies. We suggest the losses in 2002 beyond 20 days of age were more a function of prey availability influenced by drought than exposure to mercury, especially at LR, because higher mercury concentrations, higher survival rates and fewer dead birds were documented at LR in 2003 when water conditions improved. Furthermore, total mercury (THg) in blood in 2003 was more than double 2002 (geometric mean, 3.39 vs 1.47µg/g wet weight (ww). This higher THg exposure at LR in 2003 was associated with a redistribution of parent and post-dispersal feeding activities upstream (where there was higher mercury from historic mining) related to slightly improved water levels. When comparing the 3-year telemetry findings based upon ~20d old young at LR (blood THg, geo. means 1.47, 3.39 and 1.89µg/g ww), we found no evidence that age at dispersal, Julian date at dispersal, timing of migration, or pre-migration survival (~20 to ~100 days post-hatch) were adversely affected by elevated mercury. Published by Elsevier Inc.

Correlated peak relative light intensity and peak current in triggered lightning subsequent return strokes

NASA Technical Reports Server (NTRS)

Idone, V. P.; Orville, R. E.

1985-01-01

The correlation between peak relative light intensity L(R) and stroke peak current I(R) is examined for 39 subsequent return strokes in two triggered lightning flashes. One flash contained 19 strokes and the other 20 strokes for which direct measurements were available of the return stroke peak current at ground. Peak currents ranged from 1.6 to 21 kA. The measurements of peak relative light intensity were obtained from photographic streak recordings using calibrated film and microsecond resolution. Correlations, significant at better than the 0.1 percent level, were found for several functional relationships. Although a relation between L(R) and I(R) is evident in these data, none of the analytical relations considered is clearly favored. The correlation between L(R) and the maximum rate of current rise is also examined, but less correlation than between L(R) and I(R) is found. In addition, the peak relative intensity near ground is evaluated for 22 dart leaders, and a mean ratio of peak dart leader to peak return stroke relative light intensity was found to be 0.1 with a range of 0.02-0.23. Using two different methods, the peak current near ground in these dart leaders is estimated to range from 0.1 to 6 kA.

Analysis of WRKY transcription factors and characterization of two Botrytis cinerea-responsive LrWRKY genes from Lilium regale.

PubMed

Cui, Qi; Yan, Xiao; Gao, Xue; Zhang, Dong-Mei; He, Heng-Bin; Jia, Gui-Xia

2018-06-01

A major constraint in producing lilies is gray mold caused by Botrytis elliptica and B. cinerea. WRKY transcription factors play important roles in plant immune responses. However, limited information is available about the WRKY gene family in lily plants. In this study, 23 LrWRKY genes with complete WRKY domains were identified from the Botrytis-resistant species Lilium regale. The putative WRKY genes were divided into seven subgroups (Group I, IIa-e, and III) according to their structural features. Sequence alignment revealed that LrWRKY proteins have a highly conserved WRKYGQK domain and a variant, the WRKYGKK domain, and these proteins generally contained similar motif compositions throughout the same subgroup. Functional annotation predicted they might be involved in biological processes related to abiotic and biotic stresses. A qRT-PCR analysis confirmed that expression of six LrWRKY genes in L. regale or the susceptible Asian hybrid 'Yale' was induced by B. cinerea infection. Among these genes, LrWRKY4, LrWRKY8 and LrWRKY10 were expressed at a higher level in L. regale than 'Yale', while the expression of LrWRKY6 and LrWRKY12 was lower in L. regale. Furthermore, LrWRKY4 and LrWRKY12 genes, which also respond to salicylic acid (SA) and methyl jasmonate (MeJA) treatments, were isolated from L. regale. Subcellular localization analysis determined that they were targeted to the nucleus. Constitutive expression of LrWRKY4 and LrWRKY12 in Arabidopsis resulted in plants that were more resistant to B. cinerea than wild-type plants. This resistance was coupled with the transcriptional changes of SA and JA-responsive genes. Overall, our study provides valuable information about the structural and functional characterization of LrWRKY genes that will not only deepen our understanding of the molecular mechanisms underlying the defense of lily against B. cinerea but also offer potential targets for cultivar improvement via biotechnology. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Visible Light-activated TiO2 photocatalytic Films; Synthesis, Characterization and Environmental Application for the Destruction of Microcystin-LR

EPA Science Inventory

Titanium dioxide (TiO2) photocatalysis has become one of the most effective advanced oxidation technologies (AOTs) for the treatment of persistent organic contaminants. To generate hydroxyl radicals, a non-selective, reactive oxidizing species and responsible for the oxidation of...

Kidney transplantation: evaluation and clinical outcome of 237 recipients at low, medium, high, or strong immunological risk of rejection.

PubMed

Nascimento, E; Fabreti de Oliveira, R A; Maciel, M D; Pereira, A B; das Mercêz de Lucas, F; Salomão-Filho, A; Pereira, W A; Moreira, J B; Vilaça, S S; de Castro Gontijo, R; Lasmar, M F; Vianna, H R; Magalhâes, A; Calazans, C A C; Simão-Filho, C; Vilela, B

2014-01-01

Donor-specific antibodies (DSAs) play a fundamental role in kidney transplantation. The identification of DSAs is an essential rejection parameter. We evaluated a protocol in 237 patients receiving kidneys from living (LDs) and deceased donors (DDs). Recipients were classified as being at low (LR), medium (MR), high (HR), or strong (SR) risk of rejection based on Luminex panel reactive antibody (PRA)-single antigen beads (SABs). Grafts that survived for 1 year were evaluated. Of the 237 transplanted patients, 129 (54.43%) received a kidney from an LD and 108 (45.57%) from a DD. Of 95 LR recipients receiving kidneys from LDs, 2 patients lost the graft due to non-immunological causes. Of 34 MR recipients, 13 had rejection episodes, and 2 lost the graft by AMR and one by cellular rejection (CR). Of 108 recipients receiving a kidney from a DD, 59 (54.63%) were LR, 31 (28.70%) MR, 11 (10.19%) HR, and 7 (6.48%) SR. Twenty of all transplanted recipients lost their grafts; 4 were due to clinical causes, 4 by cellular rejection, and 12 by antibody-mediated rejection (AMR) with PRA-SAB mean fluorescent intensity of 530 to 12,591. One-year graft survival for LD transplanted LR and MR patients was 97.6% and 94.1%, respectively (P = .004). In DD recipients, the LR vs MR SD was P = .011, and for LR vs HR + SR it was P = .001. For MR vs HR+SR no SD was found (P = .323). Rejections were detected in 51 patients (21.52%). Graft failure occurred in 16 patients (6.75%). A total of 218 (91.98%) recipients maintained good kidney function after 1 year. This protocol based on fluxogram risk assessment of AMR provided fast and precise immunological evaluation of recipients and donors and stratification by immunological risk of AMR. Copyright © 2014 Elsevier Inc. All rights reserved.

Changes in the rotational axes of the tibiofemoral joint caused by resection of the anterior cruciate ligament.

PubMed

Bonny, Daniel P; Howell, Stephen M; Hull, Maury L

2017-04-01

Kinematic alignment is a method of aligning implants in total knee arthroplasty (TKA) that strives to restore the native flexion-extension (F-E) and longitudinal rotation (LR) axes of the tibiofemoral joint. The anterior cruciate ligament (ACL) is typically resected at the time of TKA, which might change the position, and orientation of these axes from that of the native knee. Our objective was to determine whether resecting the ACL causes changes in the F-E and LR axes. A custom designed and validated instrumented spatial linkage (ISL) measured the F-E and LR axes in nine cadaveric knees before and after ACL resection. Changes in these axes were computed for knee flexion from 0° to 120°. For the F-E axis, the two statistically significant yet relatively small changes were internal rotation of 0.5° (p = 0.02) and posterior translation of 0.3 mm (p = 0.04). For the LR axis, the statistically significant and relatively large change was medial translation of 2.1 mm (p = 0.01). Changes to the LR axis in both medial-lateral position and varus-valgus orientation varied widely; 77% of a population of knees would have a medial-lateral position change greater than 1 mm, and 53% of a population of knees would have a varus-valgus orientation change greater than 1°. Knowledge of changes of the F-E and LR axes caused by resecting the ACL provides an important baseline for determining the changes in these axes caused by kinematic alignment and mechanical alignment of bi-cruciate retaining, posterior cruciate retaining, and posterior cruciate substituting implants. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:886-893, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Stability of reconstituted parecoxib for injection with commonly used diluents.

PubMed

Crane, I M; Mulhern, M G; Nema, S

2003-10-01

The purpose of this study was to evaluate the effect of diluent type, storage conditions and the nature of package on the stability of reconstituted Parecoxib sodium for injection (PSI). Parecoxib sodium for injection is a lyophilized product for single use. It is intended for the management of acute pain. Six diluent types were initially evaluated for physical compatibility with PSI. Reconstituted PSI was visually inspected at 8, 24 and 48 h after reconstitution with 0.9% sodium chloride injection (NS), lactated ringers injection (LR), bacteriostatic 0.9% NaCl injection (BNS), lactated ringers and 5% dextrose injection (LR + D5W), 5% dextrose injection (D5W), and 5% dextrose + 0.45% NaCl injection (D5W + 1/2NS). Reconstituted PSI, stored in glass vials and glass or plastic syringes at 5 degrees and 25 degrees C, under 500 lx light intensity for 48 h or subjected to freeze-thaw cycles, were tested for chemical stability by high-performance liquid chromatography (HPLC). The PSI reconstituted with NS, BNS, D5W, and D5W + 1/2NS met visual acceptance criteria and showed almost no (<0.5% total) degradation under all storage conditions. No significant differences were seen between storage in glass vials or polypropylene/glass syringes. PSI reconstituted with LR and LR + D5W showed visual precipitation in many vials which was confirmed by the decrease in the HPLC assay values at all time points. The needlelike crystals (precipitate), analyzed by Infrared Spectroscopy and Scanning Electron Microscopy-Energy Dispersive Spectrometry (SEM-EDS) analyses, were identified as the free acid form of the active drug. PSI is stable after reconstitution, with NS, BNS, D5W, and D5W + 1/2NS, when stored at room temperature in glass vials or glass/plastic syringes for up to 48 h* LR and LR + D5W are not recommended for reconstitution because of crystallization of the drug (free acid).

Roles of miRNAs in microcystin-LR-induced Sertoli cell toxicity

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

Zhou, Yuan; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu 210093; Wang, Hui

2015-08-15

Microcystin (MC)-LR, a cyclic heptapeptide, is a potent reproductive system toxin. To understand the molecular mechanisms of MC-induced reproductive system cytotoxicity, we evaluated global changes of miRNA and mRNA expression in mouse Sertoli cells following MC-LR treatment. Our results revealed that the exposure to MC-LR resulted in an altered miRNA expression profile that might be responsible for the modulation of mRNA expression. Bio-functional analysis indicated that the altered genes were involved in specific cellular processes, including cell death and proliferation. Target gene analysis suggested that junction injury in Sertoli cells exposed to MC-LR might be mediated by miRNAs through themore » regulation of the Sertoli cell-Sertoli cell pathway. Collectively, these findings may enhance our understanding on the modes of action of MC-LR on mouse Sertoli cells as well as the molecular mechanisms underlying the toxicity of MC-LR on the male reproductive system. - Highlights: • miRNAs were altered in Sertoli cells exposed to MC-LR. • Alerted genes were involved in different cell functions including the cell morphology. • MC-LR adversely affected Sertoli cell junction formation through the regulating miRNAs.« less

Role of Surgical Margin on Local Recurrence in High Risk Extremity Osteosarcoma: A Case-Controlled Study

PubMed Central

Song, Won Seok; Kong, Chang-Bae; Cho, Wan Hyeong; Cho, Sang Hyun; Lee, Jeong Dong; Lee, Soo-Yong

2013-01-01

Background The relationship between surgical margin and local recurrence (LR) in osteosarcoma patients with poor responses to chemotherapy is unclear. Moreover, the incidences of LR according to three different resection planes (bone, soft tissue, and perineurovascular) are not commonly known. Methods We evaluated the incidence of LR in three areas. To assess whether there is a role of surgical margin on LR in patients resistant to preoperative chemotherapy, we designed a case (35 patients with LR) and control (70 patients without LR) study. Controls were matched for age, location, initial tumor volume, and tumor volume change during preoperative chemotherapy. Results LR occurred at the soft tissues in 18 cases (51.4%), at the perineurovascular tissues in 11 cases (31.4%), and at the bones in six cases (17.2%). The proportion of inadequate perineurovascular margin was higher in the case group than in the control group (p = 0.01). Within case-control group (105 patients), a correlation between each margin status and LR at corresponding area was found in the bone (p < 0.001) and perineurovascular area (p = 0.001). Conclusions LR is most common in soft tissues. In patients showing similar unfavorable responses to chemotherapy, the losses of perineurovascular fat plane on preoperative magnetic resonance imaging may be a valuable finding in predicting LR. PMID:24009908

Resuscitation with lactated ringer's does not increase inflammatory response in a Swine model of uncontrolled hemorrhagic shock.

PubMed

Watters, Jennifer M; Brundage, Susan I; Todd, S Rob; Zautke, Nathan A; Stefater, J A; Lam, J C; Muller, Patrick J; Malinoski, Darren; Schreiber, Martin A

2004-09-01

Lactated Ringer's (LR) and normal saline (NS) are widely and interchangeably used for resuscitation of trauma victims. Studies show LR to be superior to NS in the physiologic response to resuscitation. Recent in vitro studies demonstrate equivalent effects of LR and NS on leukocytes. We aimed to determine whether LR resuscitation would produce an equivalent inflammatory response compared with normal saline (NS) resuscitation in a clinically relevant swine model of uncontrolled hemorrhagic shock. Thirty-two swine were randomized. Control animals (n = 6) were sacrificed following induction of anesthesia for baseline data. Sham animals (n = 6) underwent laparotomy and 2 h of anesthesia. Uncontrolled hemorrhagic shock animals (n = 10/group) underwent laparotomy, grade V liver injury, and blinded resuscitation with LR or NS to maintain baseline blood pressure for 1.5 h before sacrifice. Lung was harvested, and tissue mRNA levels of interleukin-6 (IL-6), granulocyte colony-stimulating factor (G-CSF), and tumor necrosis factor-alpha (TNF-alpha) were determined using quantitative reverse transcriptase polymerase chain reaction (Q-RT-PCR). Sections of lung were processed and examined for neutrophils sequestered within the alveolar walls. Cytokine analysis showed no difference in IL-6 gene transcription in any group (P = 0.99). Resuscitated swine had elevated G-CSF and TNF-alpha gene transcription, but LR and NS groups were not different from each other (P= 0.96 and 0.10, respectively). Both resuscitation groups had significantly more alveolar neutrophils present than controls (P < 0.01) and shams (P < 0.05) but were not different from one another (P= 0.83). LR and NS resuscitation have equivalent effects on indices of inflammation in the lungs in our model of uncontrolled hemorrhagic shock.

Exposure of Lycopersicon Esculentum to Microcystin-LR: Effects in the Leaf Proteome and Toxin Translocation from Water to Leaves and Fruits

PubMed Central

Gutiérrez-Praena, Daniel; Campos, Alexandre; Azevedo, Joana; Neves, Joana; Freitas, Marisa; Guzmán-Guillén, Remédios; Cameán, Ana María; Renaut, Jenny; Vasconcelos, Vitor

2014-01-01

Natural toxins such as those produced by freshwater cyanobacteria have been regarded as an emergent environmental threat. However, the impact of these water contaminants in agriculture is not yet fully understood. The aim of this work was to investigate microcystin-LR (MC-LR) toxicity in Lycopersicon esculentum and the toxin accumulation in this horticultural crop. Adult plants (2 month-old) grown in a greenhouse environment were exposed for 2 weeks to either pure MC-LR (100 μg/L) or Microcystis aeruginosa crude extracts containing 100 μg/L MC-LR. Chlorophyll fluorescence was measured, leaf proteome investigated with two-dimensional gel electrophoresis and Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF)/TOF, and toxin bioaccumulation assessed by liquid chromatography-mass spectrometry (LC-MS)/MS. Variations in several protein markers (ATP synthase subunits, Cytochrome b6-f complex iron-sulfur, oxygen-evolving enhancer proteins) highlight the decrease of the capacity of plants to synthesize ATP and to perform photosynthesis, whereas variations in other proteins (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and ribose-5-phosphate isomerase) suggest an increase of carbon fixation and decrease of carbohydrate metabolism reactions in plants exposed to pure MC-LR and cyanobacterial extracts, respectively. MC-LR was found in roots (1635.21 μg/kg fw), green tomatoes (5.15–5.41 μg/kg fw), mature tomatoes (10.52–10.83 μg/kg fw), and leaves (12,298.18 μg/kg fw). The results raise concerns relative to food safety and point to the necessity of monitoring the bioaccumulation of water toxins in agricultural systems affected by cyanotoxin contamination. PMID:24921194

Exposure of Lycopersicon esculentum to microcystin-LR: effects in the leaf proteome and toxin translocation from water to leaves and fruits.

PubMed

Gutiérrez-Praena, Daniel; Campos, Alexandre; Azevedo, Joana; Neves, Joana; Freitas, Marisa; Guzmán-Guillén, Remédios; Cameán, Ana María; Renaut, Jenny; Vasconcelos, Vitor

2014-06-11

Natural toxins such as those produced by freshwater cyanobacteria have been regarded as an emergent environmental threat. However, the impact of these water contaminants in agriculture is not yet fully understood. The aim of this work was to investigate microcystin-LR (MC-LR) toxicity in Lycopersicon esculentum and the toxin accumulation in this horticultural crop. Adult plants (2 month-old) grown in a greenhouse environment were exposed for 2 weeks to either pure MC-LR (100 μg/L) or Microcystis aeruginosa crude extracts containing 100 μg/L MC-LR. Chlorophyll fluorescence was measured, leaf proteome investigated with two-dimensional gel electrophoresis and Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF)/TOF, and toxin bioaccumulation assessed by liquid chromatography-mass spectrometry (LC-MS)/MS. Variations in several protein markers (ATP synthase subunits, Cytochrome b6-f complex iron-sulfur, oxygen-evolving enhancer proteins) highlight the decrease of the capacity of plants to synthesize ATP and to perform photosynthesis, whereas variations in other proteins (ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit and ribose-5-phosphate isomerase) suggest an increase of carbon fixation and decrease of carbohydrate metabolism reactions in plants exposed to pure MC-LR and cyanobacterial extracts, respectively. MC-LR was found in roots (1635.21 μg/kg fw), green tomatoes (5.15-5.41 μg/kg fw), mature tomatoes (10.52-10.83 μg/kg fw), and leaves (12,298.18 μg/kg fw). The results raise concerns relative to food safety and point to the necessity of monitoring the bioaccumulation of water toxins in agricultural systems affected by cyanotoxin contamination.

The bZIP dimer localizes at DNA full-sites where each basic region can alternately translocate and bind to subsites at the half-site

PubMed Central

Chan, I-San; Al-Sarraj, Taufik; Shahravan, S. Hesam; Fedorova, Anna V.; Shin, Jumi A.

2012-01-01

Crystal structures of the GCN4 bZIP (basic region/leucine zipper) with the AP-1 or CRE site show how each GCN4 basic region binds to a 4-bp cognate half-site as a single DNA target; however, this may not always fully describe how bZIP proteins interact with their target sites. Previously, we showed that the GCN4 basic region interacts with all 5 bp in half-site TTGCG (termed 5H-LR), and that 5H-LR comprises two 4-bp subsites, TTGC and TGCG, which individually are also target sites of the basic region. In this work, we explored how the basic region interacts with 5H-LR when the bZIP dimer localizes to full-sites. Using AMBER molecular modeling, we simulated GCN4 bZIP complexes with full-sites containing 5H-LR to investigate in silico the interface between the basic region and 5H-LR. We also performed in vitro investigation of bZIP–DNA interactions at a number of full-sites that contain 5H-LR vs. either subsite: we analyzed results from DNase I footprinting and electrophoretic mobility shift assay (EMSA) and from EMSA titrations to quantify binding affinities. Our computational and experimental results together support a highly dynamic DNA-binding model: when a bZIP dimer localizes to its target full-site, the basic region can alternately recognize either subsite as a distinct target at 5H-LR and translocate between the subsites, potentially by sliding and hopping. This model provides added insights into how α-helical DNA-binding domains of transcription factors can localize to their gene regulatory sequences in vivo. PMID:22856882

The bZIP dimer localizes at DNA full-sites where each basic region can alternately translocate and bind to subsites at the half-site.

PubMed

Chan, I-San; Al-Sarraj, Taufik; Shahravan, S Hesam; Fedorova, Anna V; Shin, Jumi A

2012-08-21

Crystal structures of the GCN4 bZIP (basic region/leucine zipper) with the AP-1 or CRE site show how each GCN4 basic region binds to a 4 bp cognate half-site as a single DNA target; however, this may not always fully describe how bZIP proteins interact with their target sites. Previously, we showed that the GCN4 basic region interacts with all 5 bp in half-site TTGCG (termed 5H-LR) and that 5H-LR comprises two 4 bp subsites, TTGC and TGCG, which individually are also target sites of the basic region. In this work, we explore how the basic region interacts with 5H-LR when the bZIP dimer localizes to full-sites. Using AMBER molecular modeling, we simulated GCN4 bZIP complexes with full-sites containing 5H-LR to investigate in silico the interface between the basic region and 5H-LR. We also performed in vitro investigation of bZIP-DNA interactions at a number of full-sites that contain 5H-LR versus either subsite: we analyzed results from DNase I footprinting and electrophoretic mobility shift assay (EMSA) and from EMSA titrations to quantify binding affinities. Our computational and experimental results together support a highly dynamic DNA-binding model: when a bZIP dimer localizes to its target full-site, the basic region can alternately recognize either subsite as a distinct target at 5H-LR and translocate between the subsites, potentially by sliding and hopping. This model provides added insights into how α-helical DNA-binding domains of transcription factors can localize to their gene regulatory sequences in vivo.

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

Wong, Philip; Lambert, Christine, E-mail: christine.lambert@muhc.mcgill.ca; Agnihotram, Ramanakumar V.

Purpose: Local recurrence (LR) of ductal carcinoma in situ (DCIS) is reduced by whole-breast irradiation after breast-conserving surgery (BCS). However, the benefit of adding a radiotherapy boost to the surgical cavity for DCIS is unclear. We sought to determine the impact of the boost on LR in patients with DCIS treated at the McGill University Health Centre. Methods and Materials: A total of 220 consecutive cases of DCIS treated with BCS and radiotherapy between January 2000 and December 2006 were reviewed. Of the patients, 36% received a radiotherapy boost to the surgical cavity. Median follow-up was 46 months for themore » boost and no-boost groups. Kaplan-Meier survival analyses and Cox regression analyses were performed. Results: Compared with the no-boost group, patients in the boost group more frequently had positive and <0.1-cm margins (48% vs. 8%) (p < 0.0001) and more frequently were in higher-risk categories as defined by the Van Nuys Prognostic (VNP) index (p = 0.006). Despite being at higher risk for LR, none (0/79) of the patients who received a boost experienced LR, whereas 8 of 141 patients who did not receive a boost experienced an in-breast LR (log-rank p = 0.03). Univariate analysis of prognostic factors (age, tumor size, margin status, histological grade, necrosis, and VNP risk category) revealed only the presence of necrosis to significantly correlate with LR (log-rank p = 0.003). The whole-breast irradiation dose and fractionation schedule did not affect LR rate. Conclusions: Our results suggest that the use of a radiotherapy boost improves local control in DCIS and may outweigh the poor prognostic effect of necrosis.« less

Stealth life detection instruments aboard Curiosity

NASA Astrophysics Data System (ADS)

Levin, Gilbert V.

2012-10-01

NASA has often stated (e.g. MSL Science Corner1) that it's Mars Science Laboratory (MSL), "Curiosity," Mission to Mars carries no life detection experiments. This is in keeping with NASA's 36-year explicit ban on such, imposed immediately after the 1976 Viking Mission to Mars. The space agency attributes the ban to the "ambiguity" of that Mission's Labeled Release (LR) life detection experiment, fearing an adverse effect on the space program should a similar "inconclusive" result come from a new robotic quest. Yet, despite the NASA ban, this author, the Viking LR Experimenter, contends there are "stealth life detection instruments" aboard Curiosity. These are life detection instruments in the sense that they can free the Viking LR from the pall of ambiguity that has held it prisoner so long. Curiosity's stealth instruments are those seeking organic compounds, and the mission's high-resolution camera system. Results from any or all of these devices, coupled with the Viking LR data, can confirm the LR's life detection claim. In one possible scenario, Curiosity can, of itself, completely corroborate the finding of life on Mars. MSL has just successfully landed on Mars. Hopefully, its stealth confirmations of life will be reported shortly.

Design, calibration and validation of a novel 3D printed instrumented spatial linkage that measures changes in the rotational axes of the tibiofemoral joint.

PubMed

Bonny, Daniel P; Hull, M L; Howell, S M

2014-01-01

An accurate axis-finding technique is required to measure any changes from normal caused by total knee arthroplasty in the flexion-extension (F-E) and longitudinal rotation (LR) axes of the tibiofemoral joint. In a previous paper, we computationally determined how best to design and use an instrumented spatial linkage (ISL) to locate the F-E and LR axes such that rotational and translational errors were minimized. However, the ISL was not built and consequently was not calibrated; thus the errors in locating these axes were not quantified on an actual ISL. Moreover, previous methods to calibrate an ISL used calibration devices with accuracies that were either undocumented or insufficient for the device to serve as a gold-standard. Accordingly, the objectives were to (1) construct an ISL using the previously established guidelines,(2) calibrate the ISL using an improved method, and (3) quantify the error in measuring changes in the F-E and LR axes. A 3D printed ISL was constructed and calibrated using a coordinate measuring machine, which served as a gold standard. Validation was performed using a fixture that represented the tibiofemoral joint with an adjustable F-E axis and the errors in measuring changes to the positions and orientations of the F-E and LR axes were quantified. The resulting root mean squared errors (RMSEs) of the calibration residuals using the new calibration method were 0.24, 0.33, and 0.15 mm for the anterior-posterior, medial-lateral, and proximal-distal positions, respectively, and 0.11, 0.10, and 0.09 deg for varus-valgus, flexion-extension, and internal-external orientations, respectively. All RMSEs were below 0.29% of the respective full-scale range. When measuring changes to the F-E or LR axes, each orientation error was below 0.5 deg; when measuring changes in the F-E axis, each position error was below 1.0 mm. The largest position RMSE was when measuring a medial-lateral change in the LR axis (1.2 mm). Despite the large size of the ISL, these calibration residuals were better than those for previously published ISLs, particularly when measuring orientations, indicating that using a more accurate gold standard was beneficial in limiting the calibration residuals. The validation method demonstrated that this ISL is capable of accurately measuring clinically important changes (i.e. 1 mm and 1 deg) in the F-E and LR axes.

Dynamical resonance shift and unification of resonances in short-pulse laser-cluster interaction

NASA Astrophysics Data System (ADS)

Mahalik, S. S.; Kundu, M.

2018-06-01

Pronounced maximum absorption of laser light irradiating a rare-gas or metal cluster is widely expected during the linear resonance (LR) when Mie-plasma wavelength λM of electrons equals the laser wavelength λ . On the contrary, by performing molecular dynamics (MD) simulations of an argon cluster irradiated by short 5-fs (FWHM) laser pulses it is revealed that, for a given laser pulse energy and a cluster, at each peak intensity there exists a λ —shifted from the expected λM—that corresponds to a unified dynamical LR at which evolution of the cluster happens through very efficient unification of possible resonances in various stages, including (i) the LR in the initial time of plasma creation, (ii) the LR in the Coulomb expanding phase in the later time, and (iii) anharmonic resonance in the marginally overdense regime for a relatively longer pulse duration, leading to maximum laser absorption accompanied by maximum removal of electrons from cluster and also maximum allowed average charge states for the argon cluster. Increasing the laser intensity, the absorption maxima is found to shift to a higher wavelength in the band of λ ≈(1 -1.5 ) λM than permanently staying at the expected λM. A naive rigid sphere model also corroborates the wavelength shift of the absorption peak as found in MD and unequivocally proves that maximum laser absorption in a cluster happens at a shifted λ in the marginally overdense regime of λ ≈(1 -1.5 ) λM instead of λM of LR. The present study is important for guiding an optimal condition laser-cluster interaction experiment in the short-pulse regime.

SU-E-J-103: Setup Errors Analysis by Cone-Beam CT (CBCT)-Based Imaged-Guided Intensity Modulated Radiotherapy for Esophageal Cancer

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

Yang, H; Wang, W; Hu, W

2014-06-01

Purpose: To quantify setup errors by pretreatment kilovolt cone-beam computed tomography(KV-CBCT) scans for middle or distal esophageal carcinoma patients. Methods: Fifty-two consecutive middle or distal esophageal carcinoma patients who underwent IMRT were included this study. A planning CT scan using a big-bore CT simulator was performed in the treatment position and was used as the reference scan for image registration with CBCT. CBCT scans(On-Board Imaging v1. 5 system, Varian Medical Systems) were acquired daily during the first treatment week. A total of 260 CBCT scans was assessed with a registration clip box defined around the PTV-thorax in the reference scanmore » based on(nine CBCTs per patient) bony anatomy using Offline Review software v10.0(Varian Medical Systems). The anterior-posterior(AP), left-right(LR), superiorinferior( SI) corrections were recorded. The systematic and random errors were calculated. The CTV-to-PTV margins in each CBCT frequency was based on the Van Herk formula (2.5Σ+0.7σ). Results: The SD of systematic error (Σ) was 2.0mm, 2.3mm, 3.8mm in the AP, LR and SI directions, respectively. The average random error (σ) was 1.6mm, 2.4mm, 4.1mm in the AP, LR and SI directions, respectively. The CTV-to-PTV safety margin was 6.1mm, 7.5mm, 12.3mm in the AP, LR and SI directions based on van Herk formula. Conclusion: Our data recommend the use of 6 mm, 8mm, and 12 mm for esophageal carcinoma patient setup in AP, LR, SI directions, respectively.« less

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model

PubMed Central

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software “Kongoh” for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1–4 persons’ contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI’s contribution in true contributors and non-contributors by using 2–4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI’s contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples. PMID:29149210

Development and validation of open-source software for DNA mixture interpretation based on a quantitative continuous model.

PubMed

Manabe, Sho; Morimoto, Chie; Hamano, Yuya; Fujimoto, Shuntaro; Tamaki, Keiji

2017-01-01

In criminal investigations, forensic scientists need to evaluate DNA mixtures. The estimation of the number of contributors and evaluation of the contribution of a person of interest (POI) from these samples are challenging. In this study, we developed a new open-source software "Kongoh" for interpreting DNA mixture based on a quantitative continuous model. The model uses quantitative information of peak heights in the DNA profile and considers the effect of artifacts and allelic drop-out. By using this software, the likelihoods of 1-4 persons' contributions are calculated, and the most optimal number of contributors is automatically determined; this differs from other open-source software. Therefore, we can eliminate the need to manually determine the number of contributors before the analysis. Kongoh also considers allele- or locus-specific effects of biological parameters based on the experimental data. We then validated Kongoh by calculating the likelihood ratio (LR) of a POI's contribution in true contributors and non-contributors by using 2-4 person mixtures analyzed through a 15 short tandem repeat typing system. Most LR values obtained from Kongoh during true-contributor testing strongly supported the POI's contribution even for small amounts or degraded DNA samples. Kongoh correctly rejected a false hypothesis in the non-contributor testing, generated reproducible LR values, and demonstrated higher accuracy of the estimated number of contributors than another software based on the quantitative continuous model. Therefore, Kongoh is useful in accurately interpreting DNA evidence like mixtures and small amounts or degraded DNA samples.

Characterization of Lr75: a partial, broad-spectrum leaf rust resistance gene in wheat.

PubMed

Singla, Jyoti; Lüthi, Linda; Wicker, Thomas; Bansal, Urmil; Krattinger, Simon G; Keller, Beat

2017-01-01

Here, we describe a strategy to improve broad-spectrum leaf rust resistance by marker-assisted combination of two partial resistance genes. One of them represents a novel partial adult plant resistance gene, named Lr75. Leaf rust caused by the fungal pathogen Puccinia triticina is a damaging disease of wheat (Triticum aestivum L.). The combination of several, additively-acting partial disease resistance genes has been proposed as a suitable strategy to breed wheat cultivars with high levels of durable field resistance. The Swiss winter wheat cultivar 'Forno' continues to show near-immunity to leaf rust since its release in the 1980s. This resistance is conferred by the presence of at least six quantitative trait loci (QTL), one of which is associated with the morphological trait leaf tip necrosis. Here, we used a marker-informed strategy to introgress two 'Forno' QTLs into the leaf rust-susceptible Swiss winter wheat cultivar 'Arina'. The resulting backcross line 'ArinaLrFor' showed markedly increased leaf rust resistance in multiple locations over several years. One of the introgressed QTLs, QLr.sfr-1BS, is located on chromosome 1BS. We developed chromosome 1B-specific microsatellite markers by exploiting the Illumina survey sequences of wheat cv. 'Chinese Spring' and mapped QLr.sfr-1BS to a 4.3 cM interval flanked by the SSR markers gwm604 and swm271. QLr.sfr-1BS does not share a genetic location with any of the described leaf rust resistance genes present on chromosome 1B. Therefore, QLr.sfr-1BS is novel and was designated as Lr75. We conclude that marker-assisted combination of partial resistance genes is a feasible strategy to increase broad-spectrum leaf rust resistance. The identification of Lr75 adds a novel and highly useful gene to the small set of known partial, adult plant leaf rust resistance genes.

Lettuce irrigated with contaminated water: Photosynthetic effects, antioxidative response and bioaccumulation of microcystin congeners.

PubMed

Bittencourt-Oliveira, Maria do Carmo; Cordeiro-Araújo, Micheline Kézia; Chia, Mathias Ahii; Arruda-Neto, João Dias de Toledo; de Oliveira, Ênio Tiago; dos Santos, Flávio

2016-06-01

The use of microcystins (MCs) contaminated water to irrigate crop plants represents a human health risk due to their bioaccumulation potential. In addition, MCs cause oxidative stress and negatively influence photosynthetic activities in plants. The present study was aimed at investigating the effect of MCs on photosynthetic parameters and antioxidative response of lettuce. Furthermore, the bioaccumulation factor (BAF) of total MCs, MC-LR and MC-RR in the vegetable after irrigation with contaminated water was determined. Lettuce crops were irrigated for 15 days with water containing cyanobacterial crude extracts (Microcystis aeruginosa) with MC-LR (0.0, 0.5, 2.0, 5.0 and 10.0 µg L(-1)), MC-RR (0.0, 0.15, 0.5, 1.5 and 3.0 µg L(-1)) and total MCs (0.0, 0.65, 2.5, 6.5 and 13.0 µg L(-1)). Increased net photosynthetic rate, stomatal conductance, leaf tissue transpiration and intercellular CO2 concentration were recorded in lettuce exposed to different MCs concentrations. Antioxidant response showed that glutathione S-transferase activity was down-regulated in the presence of MCs. On the other hand, superoxide dismutase, catalase and peroxidase activities were upregulated with increasing MCs concentrations. The bioaccumulation factor (BAF) of total MCs and MC-LR was highest at 6.50 and 5.00 µg L(-1), respectively, while for MC-RR, the highest BAF was recorded at 1.50 µg L(-1) concentration. The amount of total MCs, MC-LR and MC-RR bioacumulated in lettuce was highest at the highest exposure concentrations. However, at the lowest exposure concentration, there were no detectable levels of MC-LR, MC-RR and total MCs in lettuce. Thus, the bioaccumulation of MCs in lettuce varies according to the exposure concentration. In addition, the extent of physiological response of lettuce to the toxins relies on exposure concentrations. Copyright © 2016 Elsevier Inc. All rights reserved.

Vulnerabilities in Bytecode Removed by Analysis, Nuanced Confinement and Diversification (VIBRANCE)

DTIC Science & Technology

2015-06-01

VIBRANCE tool starts with a vulnerable Java application and automatically hardens it against SQL injection, OS command injection, file path traversal...7 2.2 Java Front End...7 2.2.2 Java Byte Code Parser

LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

EPA Science Inventory

Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

The wheat Lr34 multipathogen resistance gene confers resistance to anthracnose and rust in sorghum.

PubMed

Schnippenkoetter, Wendelin; Lo, Clive; Liu, Guoquan; Dibley, Katherine; Chan, Wai Lung; White, Jodie; Milne, Ricky; Zwart, Alexander; Kwong, Eunjung; Keller, Beat; Godwin, Ian; Krattinger, Simon G; Lagudah, Evans

2017-11-01

The ability of the wheat Lr34 multipathogen resistance gene (Lr34res) to function across a wide taxonomic boundary was investigated in transgenic Sorghum bicolor. Increased resistance to sorghum rust and anthracnose disease symptoms following infection with the biotrophic pathogen Puccinia purpurea and the hemibiotroph Colletotrichum sublineolum, respectively, occurred in transgenic plants expressing the Lr34res ABC transporter. Transgenic sorghum lines that highly expressed the wheat Lr34res gene exhibited immunity to sorghum rust compared to the low-expressing single copy Lr34res genotype that conferred partial resistance. Pathogen-induced pigmentation mediated by flavonoid phytoalexins was evident on transgenic sorghum leaves following P. purpurea infection within 24-72 h, which paralleled Lr34res gene expression. Elevated expression of flavone synthase II, flavanone 4-reductase and dihydroflavonol reductase genes which control the biosynthesis of flavonoid phytoalexins characterized the highly expressing Lr34res transgenic lines 24-h post-inoculation with P. purpurea. Metabolite analysis of mesocotyls infected with C. sublineolum showed increased levels of 3-deoxyanthocyanidin metabolites were associated with Lr34res expression, concomitant with reduced symptoms of anthracnose. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Detection of trace microcystin-LR on a 20 MHz QCM sensor coated with in situ self-assembled MIPs.

PubMed

He, Hao; Zhou, Lianqun; Wang, Yi; Li, Chuanyu; Yao, Jia; Zhang, Wei; Zhang, Qingwen; Li, Mingyu; Li, Haiwen; Dong, Wen-fei

2015-01-01

A 20 MHz quartz crystal microbalance (QCM) sensor coated with in situ self-assembled molecularly imprinted polymers (MIPs) was presented for the detection of trace microcystin-LR (MC-LR) in drinking water. The sensor performance obtained using the in situ self-assembled MIPs was compared with traditionally synthesized MIPs on 20 MHz and normal 10 MHz QCM chip. The results show that the response increases by more than 60% when using the in situ self-assembly method compared using the traditionally method while the 20 MHz QCM chip provides four-fold higher response than the 10 MHz one. Therefore, the in situ self-assembled MIPs coated on a high frequency QCM chip was used in the sensor performance test to detect MC-LR in tap water. It showed a limit of detection (LOD) of 0.04 nM which is lower than the safety guideline level (1 nM MC-LR) of drinking water in China. The low sensor response to other analogs indicated the high specificity of the sensor to MC-LR. The sensor showed high stability and low signal variation less than 2.58% after regeneration. The lake water sample analysis shows the sensor is possible for practical use. The combination of the higher frequency QCM with the in situ self-assembled MIPs provides a good candidate for the detection of other small molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

An Experiment to Detect Lunar Horizon Glow with the Lunar Orbit Laser Altimeter Laser Ranging Telescope

NASA Astrophysics Data System (ADS)

Smith, David E.; Zuber, Maria T.; Barker, Michael; Mazarico, Erwan; Neumann, Gregory A.; McClanahan, Timothy P.; Sun, Xiaoli

2016-04-01

Lunar horizon glow (LHG) was an observation by the Apollo astronauts of a brightening of the horizon around the time of sunrise. The effect has yet to be fully explained or confirmed by instruments on lunar orbiting spacecraft despite several attempts. The Lunar Reconnaissance Orbiter (LRO) spacecraft carries the laser altimeter (LOLA) instrument which has a 2.5 cm aperture telescope for Earth-based laser ranging (LR) mounted and bore-sighted with the high gain antenna (HGA). The LR telescope is connected to LOLA by a fiber-glass cable to one of its 5 detectors. For the LGH experiments the LR telescope is pointed toward the horizon shortly before lunar sunrise with the intent of observing any forward scattering of sunlight due to the presence of dust or particles in the field of view. Initially, the LR telescope is pointed at the dark lunar surface, which provides a measure of the dark count, and moves toward the lunar limb so as to measure the brightness of the sky just above the lunar limb immediately prior to lunar sunrise. At no time does the sun shine directly into the LR telescope, although the LR telescope is pointed as close to the sun as the 1.75-degree field of view permits. Experiments show that the LHG signal seen by the astronauts can be detected with a four-second integration of the noise counts.

Loading rate increases during barefoot running in habitually shod runners: Individual responses to an unfamiliar condition.

PubMed

Tam, Nicholas; Astephen Wilson, Janie L; Coetzee, Devon R; van Pletsen, Leanri; Tucker, Ross

2016-05-01

The purpose of this study was to examine the effect of barefoot running on initial loading rate (LR), lower extremity joint kinematics and kinetics, and neuromuscular control in habitually shod runners with an emphasis on the individual response to this unfamiliar condition. Kinematics and ground reaction force data were collected from 51 habitually shod runners during overground running in a barefoot and shod condition. Joint kinetics and stiffness were calculated with inverse dynamics. Inter-individual initial LR variability was explored by separating individuals by a barefoot/shod ratio to determine acute responders/non-responders. Mean initial LR was 54.1% greater in the barefoot when compared to the shod condition. Differences between acute responders/non-responders were found at peak and initial contact sagittal ankle angle and at initial ground contact. Correlations were found between barefoot sagittal ankle angle at initial ground contact and barefoot initial LR. A large variability in biomechanical responses to an acute exposure to barefoot running was found. A large intra-individual variability was found in initial LR but not ankle plantar-dorsiflexion between footwear conditions. A majority of habitually shod runners do not exhibit previously reported benefits in terms of reduced initial LRs when barefoot. Lastly, runners who increased LR when barefoot reduced LRs when wearing shoes to levels similar seen in habitually barefoot runners who do adopt a forefoot-landing pattern, despite increased dorsiflexion. Copyright © 2016 Elsevier B.V. All rights reserved.

Anatomic and physiological characteristics of the ferret lateral rectus muscle and abducens nucleus.

PubMed

Bishop, Keith N; McClung, J Ross; Goldberg, Stephen J; Shall, Mary S

2007-11-01

The ferret has become a popular model for physiological and neurodevelopmental research in the visual system. We believed it important, therefore, to study extraocular whole muscle as well as single motor unit physiology in the ferret. Using extracellular stimulation, 62 individual motor units in the ferret abducens nucleus were evaluated for their contractile characteristics. Of these motor units, 56 innervated the lateral rectus (LR) muscle alone, while 6 were split between the LR and retractor bulbi (RB) muscle slips. In addition to individual motor units, the whole LR muscle was evaluated for twitch, tetanic peak force, and fatigue. The abducens nucleus motor units showed a twitch contraction time of 15.4 ms, a mean twitch tension of 30.2 mg, and an average fusion frequency of 154 Hz. Single-unit fatigue index averaged 0.634. Whole muscle twitch contraction time was 16.7 ms with a mean twitch tension of 3.32 g. The average fatigue index of whole muscle was 0.408. The abducens nucleus was examined with horseradish peroxidase conjugated with the subunit B of cholera toxin histochemistry and found to contain an average of 183 motoneurons. Samples of LR were found to contain an average of 4,687 fibers, indicating an LR innervation ratio of 25.6:1. Compared with cat and squirrel monkeys, the ferret LR motor units contract more slowly yet more powerfully. The functional visual requirements of the ferret may explain these fundamental differences.

Role of polymorphic Fc receptor Fc gammaRIIa in cytokine release and adverse effects of murine IgG1 anti-CD3/T cell receptor antibody (WT31).

PubMed

Tax, W J; Tamboer, W P; Jacobs, C W; Frenken, L A; Koene, R A

1997-01-15

Anti-CD3 monoclonal antibody (mAb) OKT3 is immunosuppressive, but causes severe adverse effects during the first administration ("first-dose reaction"). These adverse effects are presumably caused by cytokine release that results from T-cell activation. In vitro, T-cell activation by anti-CD3 mAb requires interaction with monocyte Fc receptors. The Fc receptor for murine IgG1, Fc gammaRIIa, is polymorphic. In some individuals, murine IgG1 anti-CD3 mAb causes T-cell proliferation and cytokine release in vitro (high responders [HR]), whereas in individuals with the low-responder (LR) phenotype it does not. We have now investigated the role of this Fc gammaRIIa polymorphism in the release of cytokines in vivo and the occurrence of adverse effects after the administration of WT31, a murine IgG1 anti-CD3/T cell receptor mAb. WT31 caused an increase of plasma tumor necrosis factor-alpha in all four HR patients and none of the five LR patients. In all HR patients except one, plasma gamma-interferon and interleukin 6 also increased, and a first-dose response was observed, whereas no cytokine release or adverse effects occurred in any of the LR patients. WT31 caused lymphopenia in all HR and none of the LR patients. FACS analysis demonstrated that in HR patients, after the initial disappearance of CD3+ cells from peripheral blood, modulation of CD3 occurred, whereas in LR patients a high degree of coating of the lymphocytes was observed. Surprisingly, WT31 also induced a marked granulocytopenia, as well as a decrease of thrombocytes, in three of the four HR patients (and in none of the LR patients). These data provide direct clinical evidence that Fc receptor interaction determines the release of cytokines and the occurrence of adverse effects after administration of anti-CD3/T cell receptor mAb. Furthermore, these data suggest that tumor necrosis factor-alpha by itself is not sufficient to induce the first-dose reaction.

Toxic threshold of dietary microcystin (-LR) for quart medaka.

PubMed

Deng, Dong-Fang; Zheng, Keke; Teh, Foo-Ching; Lehman, Peggy W; Teh, Swee J

2010-04-01

This study was designed to estimate the toxic threshold of male and female fish to microcystins based on different biomarkers. Japanese medaka (Oryzias latipes) were fed dietary Microcystin-LR (0, 0.46, 0.85, 2.01 and 3.93 microg MC-LR/g dry diet for 8 weeks at 25 degrees C. The results revealed that dietary MC-LR inhibited growth at the end of 8 weeks. The survival of embryos and the RNA/DNA ratio of whole fish decreased significantly (P < 0.05) in fish fed 3.93 microg MC-LR/g dry diet. Heat shock protein (Hsp60) expression was induced in the liver of female and male fish fed diets containing > or =0.85 and 0.46 microg MC-LR/g diet, respectively. The activity of liver caspase 3/7 was significantly higher in female fish fed 3.93 microg MC-LR/g diet and in males fed 2.01 MC-LR microg/g dry diet than fish fed the control diet. The threshold for inhibition of liver protein phosphatase expression was lower in female (2.01 microg/g diet) than that in male fish (3.93 microg/g diet). Histopathological examination showed significant single-cell necrosis in female and male medaka fed diets containing 0.85 and 3.93 microg MC-LR/g diet, respectively. Based on different biomarkers, this study demonstrated that dietary MC-LR is toxic to Medaka and the effects are gender dependent. Published by Elsevier Ltd.

Predicting complex syntactic structure in real time: Processing of negative sentences in Russian.

PubMed

Kazanina, Nina

2017-11-01

In Russian negative sentences the verb's direct object may appear either in the accusative case, which is licensed by the verb (as is common cross-linguistically), or in the genitive case, which is licensed by the negation (Russian-specific "genitive-of-negation" phenomenon). Such sentences were used to investigate whether case marking is employed for anticipating syntactic structure, and whether lexical heads other than the verb can be predicted on the basis of a case-marked noun phrase. Experiment 1, a completion task, confirmed that genitive-of-negation is part of Russian speakers' active grammatical repertoire. In Experiments 2 and 3, the genitive/accusative case manipulation on the preverbal object led to shorter reading times at the negation and verb in the genitive versus accusative condition. Furthermore, Experiment 3 manipulated linear order of the direct object and the negated verb in order to distinguish whether the abovementioned facilitatory effect was predictive or integrative in nature, and concluded that the parser actively predicts a verb and (otherwise optional) negation on the basis of a preceding genitive-marked object. Similarly to a head-final language, case-marking information on preverbal noun phrases (NPs) is used by the parser to enable incremental structure building in a free-word-order language such as Russian.

A single-nucleotide polymorphism that accounts for allelic variation in the Lr34 gene and leaf rust reaction in hard winter wheat.

PubMed

Cao, Shuanghe; Carver, Brett F; Zhu, Xinkai; Fang, Tilin; Chen, Yihua; Hunger, Robert M; Yan, Liuling

2010-07-01

Leaf rust, caused by Puccinia triticina Eriks, is one of the most common and persistent wheat diseases in the US Great Plains. We report that the Lr34 gene was mapped in the center of a QTL for leaf rust reaction and explained 18-35% of the total phenotypic variation in disease severity of adult plants in a Jagger x 2174 population of recombinant inbred lines (RILs) field-tested for 3 years. The sequence of the complete Lr34 gene was determined for the susceptible Jagger allele and for the resistant 2174 allele. The two alleles had exactly the same sequence as the resistant allele reported previously in Chinese Spring at three polymorphic sites in intron 4, exon 11, and exon 12. A G/T polymorphism was found in exon 22, where a premature stop codon was found in the susceptible Jagger allele (Lr34E22s), confirming a previous report, due to a point mutation compared with the resistant 2174 allele (Lr34E22r). We have experimentally demonstrated a tight association between the point mutation at exon 22 of Lr34 and leaf rust susceptibility in a segregating biparental population. A PCR marker was developed to distinguish between the Lr34E22r and Lr34E22s alleles. A survey of 33 local hard winter wheat cultivars indicated that 7 cultivars carry the Lr34E22s allele and 26 cultivars carry the Lr34E22r allele. This study significantly improves our genetic understanding of allelic variation in the Lr34 gene and provides a functional molecular tool to improve leaf rust resistance in a major US wheat gene pool.

Task Context Influences Brain Activation during Music Listening

PubMed Central

Markovic, Andjela; Kühnis, Jürg; Jäncke, Lutz

2017-01-01

In this paper, we examined brain activation in subjects during two music listening conditions: listening while simultaneously rating the musical piece being played [Listening and Rating (LR)] and listening to the musical pieces unconstrained [Listening (L)]. Using these two conditions, we tested whether the sequence in which the two conditions were fulfilled influenced the brain activation observable during the L condition (LR → L or L → LR). We recorded high-density EEG during the playing of four well-known positively experienced soundtracks in two subject groups. One group started with the L condition and continued with the LR condition (L → LR); the second group performed this experiment in reversed order (LR → L). We computed from the recorded EEG the power for different frequency bands (theta, lower alpha, upper alpha, lower beta, and upper beta). Statistical analysis revealed that the power in all examined frequency bands increased during the L condition but only when the subjects had not had previous experience with the LR condition (i.e., L → LR). For the subjects who began with the LR condition, there were no power increases during the L condition. Thus, the previous experience with the LR condition prevented subjects from developing the particular mental state associated with the typical power increase in all frequency bands. The subjects without previous experience of the LR condition listened to the musical pieces in an unconstrained and undisturbed manner and showed a general power increase in all frequency bands. We interpret the fact that unconstrained music listening was associated with increased power in all examined frequency bands as a neural indicator of a mental state that can best be described as a mind-wandering state during which the subjects are “drawn into” the music. PMID:28706480

A right-handed signalling pathway drives heart looping in vertebrates

PubMed Central

Ocaña, Oscar H.; Coskun, Hakan; Minguillón, Carolina; Murawala, Prayag; Tanaka, Elly M.; Galcerán, Joan; Muñoz-Chapuli, Ramón; Nieto, M. Angela

2017-01-01

The majority of animals show external bilateral symmetry, precluding the observation of multiple internal left-right (L/R) asymmetries that are fundamental for organ packaging and function1,2. In vertebrates, left identity is mediated by the left-specific Nodal-Pitx2 axis that is repressed on the right-hand side by the epithelial-mesenchymal transition (EMT) inducer Snail13,4. Despite some existing evidence3,5, it remains unclear whether an equivalent instructive pathway provides right-hand specific information to the embryo. Here we show that in zebrafish, BMP mediates the L/R asymmetric activation of another EMT inducer, Prrx1a, in the lateral plate mesoderm (LPM) with higher levels on the right. Prrx1a drives L/R differential cell movements towards the midline leading to a leftward displacement of the cardiac posterior pole through an actomyosin-dependent mechanism. Downregulation of Prrx1a prevents heart looping and leads to mesocardia. Two parallel and mutually repressed pathways, respectively driven by Nodal and BMP on the left and right LPM, converge on the asymmetric activation of Pitx2 and Prrx1, two transcription factors that integrate left and right information to govern heart morphogenesis. This mechanism is conserved in the chicken embryo and, in the mouse, Snail1 fulfills the role played by Prrx1 in fish and chick. Thus, a differential L/R EMT produces asymmetric cell movements and forces, more prominent from the right, that drive heart laterality in vertebrates. PMID:28880281

Natural Language Sourcebook

DTIC Science & Technology

1990-01-01

Identification of Syntactic Units Exemplar I.A. (#l) Problem (1) The tough coach the young. (2) The tough coach married a star. (3) The tough coach married ...34the tough" vs. "the tough coach" and (b) "people" vs. " married people." The problem could also be considered a problem of determining lexical...and " married " in example (2). Once the parser specifies a verb, the structure of the rest of the sentence is determined: specifying "coach" as a

Probiotics as an environment-friendly approach to enhance red sea bream, Pagrus major growth, immune response and oxidative status.

PubMed

Dawood, Mahmoud A O; Koshio, Shunsuke; Ishikawa, Manabu; El-Sabagh, Mabrouk; Esteban, M Angeles; Zaineldin, Amr I

2016-10-01

A usual strategy in modern aquaculture to combat production bottlenecks associated with intensification is preventive health care through the use of consumer and environment-friendly alternatives including probiotics. The current study evaluates the influence of Lactobacillus rhamnosus (LR), a lyophilized probiotic bacterium, on health status and performance of red sea bream (Pagrus major). Probiotics were incorporated in the diets at four different concentrations: 0 (control diet, LR0), 10(2) (LR1), 10(4) (LR2) and 10(6) (LR3) cells g(-1) and diets were administered to the fish for a period of 8 weeks. After the feeding trial, final body weight, body weight gain, specific growth rate, protease activity, protein digestibility, Lactobacillus sp. intestinal count, and superoxide dismutase were significantly higher in all probiotic-fed groups (P < 0.05). In addition, lipid and dry matter digestibility, reactive oxygen metabolites, biological antioxidant potential, and humoral and mucosal immune parameters including (total serum protein, alternative complement pathway, bactericidal and peroxidase activities) were also significantly elevated in fish fed probiotic supplementations being the effects dose-dependent. All growth, feed utilization, immune and oxidative parameters were significantly improved following probiotic administration. Present results revealed that L. rhamnosus is a promising probiotic candidate employed to help red sea bream protect themselves, thus promoting safe farming that would be less dependent on chemotherapy against infectious diseases. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oxidative elimination of cyanotoxins: comparison of ozone, chlorine, chlorine dioxide and permanganate.

PubMed

Rodríguez, Eva; Onstad, Gretchen D; Kull, Tomas P J; Metcalf, James S; Acero, Juan L; von Gunten, Urs

2007-08-01

As the World Health Organization (WHO) progresses with provisional Drinking Water Guidelines of 1 microg/L for microcystin-LR and a proposed Guideline of 1 microg/L for cylindrospermopsin, efficient treatment strategies are needed to prevent cyanotoxins such as these from reaching consumers. A kinetic database has been compiled for the oxidative treatment of three cyanotoxins: microcystin-LR (MC-LR), cylindrospermopsin (CYN), and anatoxin-a (ANTX) with ozone, chlorine, chlorine dioxide and permanganate. This kinetic database contains rate constants not previously reported and determined in the present work (e.g. for permanganate oxidation of ANTX and chlorine dioxide oxidation of CYN and ANTX), together with previously published rate constants for the remaining oxidation processes. Second-order rate constants measured in pure aqueous solutions of these toxins could be used in a kinetic model to predict the toxin oxidation efficiency of ozone, chlorine, chlorine dioxide and permanganate when applied to natural waters. Oxidants were applied to water from a eutrophic Swiss lake (Lake Greifensee) in static-dose testing and dynamic time-resolved experiments to confirm predictions from the kinetic database, and to investigate the effects of a natural matrix on toxin oxidation and by-product formation. Overall, permanganate can effectively oxidize ANTX and MC-LR, while chlorine will oxidize CYN and MC-LR and ozone is capable of oxidizing all three toxins with the highest rate. The formation of trihalomethanes (THMs) in the treated water may be a restriction to the application of sufficiently high-chlorine doses.

Radiation-Driven Formation of Reactive Oxygen Species in Oxychlorine-Containing Mars Surface Analogues.

PubMed

Georgiou, Christos D; Zisimopoulos, Dimitrios; Kalaitzopoulou, Electra; Quinn, Richard C

2017-04-01

The present study demonstrates that γ-radiolyzed perchlorate-containing Mars soil salt analogues (in a CO 2 atmosphere) generate upon H 2 O wetting the reactive oxygen species (ROS) superoxide radical (O 2 •- ), hydrogen peroxide (H 2 O 2 ), and hydroxyl radicals ( • OH). This study also validates that analogue radiolysis forms oxychlorine species that, in turn, can UV-photolyze to • OH upon UV photolysis. This investigation was made possible by the development of a new assay for inorganic-origin O 2 •- and H 2 O 2 determination and by the modification of a previous assay for soil • OH. Results show that radiolyzed Mg(ClO 4 ) 2 generates H 2 O 2 and • OH; and when included as part of a mixture analogous to the salt composition of samples analyzed at the Mars Phoenix site, the analogue generated O 2 •- , H 2 O 2 , and • OH, with • OH levels 150-fold higher than in the radiolyzed Mg(ClO 4 ) 2 samples. Radiolyzed Mars Phoenix site salt analogue that did not contain Mg(ClO 4 ) 2 generated only • OH also at 150-fold higher concentration than Mg(ClO 4 ) 2 alone. Additionally, UV photolysis of the perchlorate γ radiolysis product chlorite (ClO 2 - ) generated the oxychlorine products trihalide (Cl 3 - ), chlorine dioxide (ClO 2 • ), and hypochlorite (ClO - ), with the formation of • OH by UV photolysis of ClO - . While the generation of ROS may have contributed in part to 14 CO 2 production in the Viking Labeled Release (LR) experiment and O 2 (g) release in the Viking Gas Exchange (GEx) experiment, our results indicate that they are not likely to be the major contributor to the LR and GEx results. However, due to their highly reactive nature, they are expected to play a significant role in the alteration of organics on Mars. Additionally, experiments with hypochlorite show that the thermal stability of NaClO is in the range of the thermal stability observed for thermally liable oxidant responsible for the Viking LR results. Key Words: Mars-Oxygen-Salts-Radiation-Habitability. Astrobiology 17, 319-336.

Homology and homoplasy of swimming behaviors and neural circuits in the Nudipleura (Mollusca, Gastropoda, Opisthobranchia)

PubMed Central

Newcomb, James M.; Sakurai, Akira; Lillvis, Joshua L.; Gunaratne, Charuni A.; Katz, Paul S.

2012-01-01

How neural circuit evolution relates to behavioral evolution is not well understood. Here the relationship between neural circuits and behavior is explored with respect to the swimming behaviors of the Nudipleura (Mollusca, Gastropoda, Opithobranchia). Nudipleura is a diverse monophyletic clade of sea slugs among which only a small percentage of species can swim. Swimming falls into a limited number of categories, the most prevalent of which are rhythmic left–right body flexions (LR) and rhythmic dorsal–ventral body flexions (DV). The phylogenetic distribution of these behaviors suggests a high degree of homoplasy. The central pattern generator (CPG) underlying DV swimming has been well characterized in Tritonia diomedea and in Pleurobranchaea californica. The CPG for LR swimming has been elucidated in Melibe leonina and Dendronotus iris, which are more closely related. The CPGs for the categorically distinct DV and LR swimming behaviors consist of nonoverlapping sets of homologous identified neurons, whereas the categorically similar behaviors share some homologous identified neurons, although the exact composition of neurons and synapses in the neural circuits differ. The roles played by homologous identified neurons in categorically distinct behaviors differ. However, homologous identified neurons also play different roles even in the swim CPGs of the two LR swimming species. Individual neurons can be multifunctional within a species. Some of those functions are shared across species, whereas others are not. The pattern of use and reuse of homologous neurons in various forms of swimming and other behaviors further demonstrates that the composition of neural circuits influences the evolution of behaviors. PMID:22723353

Molecular characterization of swine leukocyte antigen gene diversity in purebred Pietrain pigs.

PubMed

Essler, Sabine E; Ertl, Werner; Deutsch, Julia; Ruetgen, Barbara C; Groiss, Sandra; Stadler, Maria; Wysoudil, Bhuma; Gerner, Wilhelm; Ho, Chak-Sum; Saalmueller, Armin

2013-04-01

The porcine major histocompatibility complex (MHC) harbors the highly polymorphic swine leukocyte antigen (SLA) class I and II gene clusters encoding glycoproteins that present antigenic peptides to T cells in the adaptive immune response. In Austria, the majority of commercial pigs are F 2 descendants of F 1 Large White/Landrace hybrids paired with Pietrain boars. Therefore, the repertoire of SLA alleles and haplotypes present in Pietrain pigs has an important influence on that of their descendants. In this study, we characterized the SLA class I ( SLA-1 , SLA-2 , SLA-3 ) and class II ( SLA-DRB1 , SLA-DQB1 , SLA-DQA ) genes of 27 purebred Pietrain pigs using a combination of the high-resolution sequence-based typing (SBT) method and a low-resolution (Lr) PCR-based method using allele-group, sequence-specific primers (PCR-SSP). A total of 15 class I and 13 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotype Lr-43.0 ( SLA-1 *11XX- SLA-3 *04XX- SLA-2 *04XX) was identified in 11 animals with a frequency of 20%. For SLA class II, the most prevalent haplotype, Lr-0.14 [ SLA-DRB1 *0901- SLA-DQB1 *0801- SLA-DQA *03XX], was found in 14 animals with a frequency of 26%. Two class II haplotypes, tentatively designated as Lr-Pie-0.1 [ SLA-DRB1 *01XX/be01/ha04- SLA-DQB1 *05XX- SLA - DQA*blank] and Lr-Pie-0.2 [ SLA-DRB1 *06XX- SLA-DQB1 *03XX- SLA-DQA *03XX], appeared to be novel and have never been reported so far in other pig populations. We showed that SLA genotyping using PCR-SSP-based assays represents a rapid and cost-effective way to study SLA diversity in outbred commercial pigs and may facilitate the development of more effective vaccines or identification of disease-resistant pigs in the context of SLA antigens to improve overall swine health. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

The utility of clinical measures for the diagnosis of achilles tendon injuries: a systematic review with meta-analysis.

PubMed

Reiman, Michael; Burgi, Ciara; Strube, Eileen; Prue, Kevin; Ray, Keaton; Elliott, Amanda; Goode, Adam

2014-01-01

To summarize and evaluate the current diagnostic accuracy of clinical measures used to diagnose Achilles tendon injuries. A literature search of MEDLINE, CINAHL, and EMBASE databases was conducted with key words related to diagnostic accuracy and Achilles tendon injuries. Original research articles investigating Achilles tendon injuries against an acceptable reference standard were included. Three studies met the inclusion criteria. Quality assessment was conducted using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. DerSimonian-Laird random-effects models were used to pool sensitivity (SN), specificity (SP), and diagnostic odds ratios with their 95% confidence intervals (CIs). The SN and negative likelihood ratio (-LR) values for Achilles tendon rupture measures ranged from 0.73 (95% CI = 0.65, 0.81) and 0.30 (95% CI = 0.23, 0.40) to 0.96 (95% CI = 0.93, 0.99) and 0.04 (95% CI = 0.02, 0.10), respectively, whereas SP and positive likelihood ratio (+LR) values ranged from 0.85 (95% CI = 0.72, 0.98) and 6.29 (95% CI = 2.33, 19.96) to 0.93 (95% CI = 0.84, 1.00) and 13.71 (95% CI = 3.54, 51.24), respectively, with the highest SN and SP both reported in the calf-squeeze test. The SN and -LR values for Achilles tendinopathy measures ranged from 0.03 (95% CI = 0.00, 0.08) and 0.97 (95% CI = not reported) to 0.89 (95% CI = 0.75, 0.98) and 0.19 (95% CI = not reported), whereas SP and +LR values ranged from 0.58 (95% CI = 0.38, 0.77) and 2.12 (95% CI = not reported) to 1.00 (95% CI = 1.00, 1.00) and infinity, respectively, with the highest SN and SP reported for morning stiffness and palpation for crepitus. Pooled analyses demonstrated similar diagnostic properties in all 3 clinical measures (arc sign, palpation, and Royal London Hospital test), with SN and -LR ranging from 0.42 (95% CI = 0.23, 0.62) and 0.68 (95% CI = 0.50, 0.93), respectively, for the arc sign, to 0.64 (95% CI = 0.44, 0.81) and 0.48 (95% CI = 0.29, 0.80), respectively, for palpation. Pooled SP and +LR ranged from 0.81 (95% CI = 0.65, 0.91) and 3.15 (95% CI = 1.61, 6.18), respectively, for palpation, to 0.88 (95% CI = 0.74, 0.96) SP for the arc sign and 3.84 (95% CI = 1.69, 8.73) +LR for the Royal London Hospital test. Most clinical measures for Achilles tendon injury have greater diagnostic than screening capability.

The Utility of Clinical Measures for the Diagnosis of Achilles Tendon Injuries: A Systematic Review With Meta-Analysis

PubMed Central

Reiman, Michael; Burgi, Ciara; Strube, Eileen; Prue, Kevin; Ray, Keaton; Elliott, Amanda; Goode, Adam

2014-01-01

Objective: To summarize and evaluate the current diagnostic accuracy of clinical measures used to diagnose Achilles tendon injuries. Data Sources: A literature search of MEDLINE, CINAHL, and EMBASE databases was conducted with key words related to diagnostic accuracy and Achilles tendon injuries. Study Selection: Original research articles investigating Achilles tendon injuries against an acceptable reference standard were included. Data Extraction: Three studies met the inclusion criteria. Quality assessment was conducted using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. DerSimonian-Laird random-effects models were used to pool sensitivity (SN), specificity (SP), and diagnostic odds ratios with their 95% confidence intervals (CIs). Data Synthesis: The SN and negative likelihood ratio (−LR) values for Achilles tendon rupture measures ranged from 0.73 (95% CI = 0.65, 0.81) and 0.30 (95% CI = 0.23, 0.40) to 0.96 (95% CI = 0.93, 0.99) and 0.04 (95% CI = 0.02, 0.10), respectively, whereas SP and positive likelihood ratio (+LR) values ranged from 0.85 (95% CI = 0.72, 0.98) and 6.29 (95% CI = 2.33, 19.96) to 0.93 (95% CI = 0.84, 1.00) and 13.71 (95% CI = 3.54, 51.24), respectively, with the highest SN and SP both reported in the calf-squeeze test. The SN and −LR values for Achilles tendinopathy measures ranged from 0.03 (95% CI = 0.00, 0.08) and 0.97 (95% CI = not reported) to 0.89 (95% CI = 0.75, 0.98) and 0.19 (95% CI = not reported), whereas SP and +LR values ranged from 0.58 (95% CI = 0.38, 0.77) and 2.12 (95% CI = not reported) to 1.00 (95% CI = 1.00, 1.00) and infinity, respectively, with the highest SN and SP reported for morning stiffness and palpation for crepitus. Pooled analyses demonstrated similar diagnostic properties in all 3 clinical measures (arc sign, palpation, and Royal London Hospital test), with SN and −LR ranging from 0.42 (95% CI = 0.23, 0.62) and 0.68 (95% CI = 0.50, 0.93), respectively, for the arc sign, to 0.64 (95% CI = 0.44, 0.81) and 0.48 (95% CI = 0.29, 0.80), respectively, for palpation. Pooled SP and +LR ranged from 0.81 (95% CI = 0.65, 0.91) and 3.15 (95% CI = 1.61, 6.18), respectively, for palpation, to 0.88 (95% CI = 0.74, 0.96) SP for the arc sign and 3.84 (95% CI = 1.69, 8.73) +LR for the Royal London Hospital test. Conclusions: Most clinical measures for Achilles tendon injury have greater diagnostic than screening capability. PMID:25243736