gebhart/patrepeval huggingface dataset:
Automatic segmentation of liver structure in CT images (1993)

The segmentation and three-dimensional representation of the liver from a computed tomography (CT) scan is an important step in many medical applications, such as in the surgical planning for a living-donor liver transplant and in the automatic detection and documentation of pathological states. A method is being developed to automatically extract liver structure from abdominal CT scans using a priori information about liver morphology and digital image-processing techniques. Segmentation is performed sequentially image-by-image (slice-by-slice), starting with a reference image in which the liver occupies almost the entire right half of the abdomen cross section. Image processing techniques include gray-level thresholding, Gaussian smoothing, and eight-point connectivity tracking. For each case, the shape, size, and pixel density distribution of the liver are recorded for each CT image and used in the processing of other CT images. Extracted boundaries of the liver are smoothed using mathematical morphology techniques and B-splines. Computer-determined boundaries were compared with those drawn by a radiologist. The boundary descriptions from the two methods were in agreement, and the calculated areas were within 10%.
2-Alkoxy-1,3-thiazoles: A new core unit for incorporation into self-organising materials. Synthetic approach, mesomorphism, and electrooptic evaluation (2012)

Abstract The synthesis and transition temperatures of the first series of 2-alkoxy-1,3-thiazole-based liquid crystals are reported. The 2-alkoxy-1,3-thiazole moiety was generated in high yield via a selective SNAr reaction between 2,5-dibromo-1,3-thiazole and the corresponding long-chain alkoxide. The synthesis and mesomorphic properties of the aforementioned chevron-free 2-alkoxy-1,3-thiazole-based liquid crystals are discussed and compared with their 5-alkoxy-1,3-thiazole and phenyl based analogues. Electrooptical properties for both series of alkoxy-1,3-thiazole-based liquid crystals are also presented and discussed. Keywords: 1,3-thiazoleferroelectricchevron-freeSNAr Acknowledgements Financial support for this work through a Research Incentive Grant from the Ohio Board of Regents, and from Kent State University, is gratefully acknowledged. In addition we would like to thank Dr Mahinda Gangoda for assistance in obtaining some of the NMR spectra and Dr Robert J. Twieg for use of his DSC instrument.
Sedimentation Theory and Practical Considerations for the Design of Centrifugal Blood Cell Processes (1984)

This is the first of a five-part series discussing the basic conceptualization and evaluation of techniques for centrifugal separation of blood cells. In this paper, the basic concepts of sedimentation theory will be discussed. The next two papers will discuss the effects of plasma recycle and stagewise separations, respectively, as applied to continuous-flow and semicontinuous-flow processing systems. The subsequent paper will underline the differences between the theoretical approach and our experimental efforts, and the final paper will consider potential future process configurations and areas of expected improvement. A series of calculations is presented for the prediction of sedimentation velocities for red and white cells. The equations are simplified to investigate the regions of high red cell concentration, and are not valid for regions of concentrated platelets or white cells. The intent is to present a sample calculational design approach.
Evaluation of Gas Chromatography/Mini-IMS to Detect VOCs (1999)

The Toxicology Laboratory at Johnson Space Center (JSC) has pioneered the use of gas chromatography-ion mobility spectrometry (GC/IMS) for measuring target volatile organic compounds (VOCs) aboard spacecraft. Graseby Dynamics, under contract to NASA/Wyle, has built several volatile organic analyzers (VOA) based on GC/IMS. Foremost among these have been the volatile organic analyzer-risk mitigation unit and the two flight VOA units for International Space Station (ISS). The development and evaluation of these instruments has been chronicled through presentations at the International Conference on Ion Mobility Spectrometry over the past three years. As the flight VOA from Graseby is prepared for operation on ISS at JSC, it is time to begin evaluations of technologies for the next generation VOA, Although the desired instrument characteristics for the next generation unit are the same as the current unit, the requirements are much more stringent. As NASA looks toward future missions beyond Earth environs, a premium will be placed upon small, light, reliable, autonomous hardware. It is with these visions in mind that the JSC Toxicology Laboratory began a search for the next generation VOA. One technology that is a candidate for the next generation VOA is GC/IMS. The recent miniaturization of IMS technology permits it to compete with other, inherently small, technologies such as chip-sized sensor arrays. This paper will discuss the lessons learned from the VOA experience and how that has shaped the design of a potential second generation VOA based upon GC/IMS technology. Data will be presented from preliminary evaluations of GC technology and the mini-IMS when exposed to VOCs likely to be detected aboard spacecraft. Results from the evaluation of an integrated GC/mini-IMS system will be shown if available.
Heterogeneity of the BALB/c antiphosphorylcholine antibody response at the precursor cell level. (1975)

Immune responsiveness to phosphorylcholine (PC) in BALB/c mice has been characterized by combining (a) usuage of highly sensitive radioimmunoassays for quantitation of antibody, heavy-chain class, and idiotype on a weight basis; (b) isolation of PC-specific B cells in fragment cultures; and (c) stimulation in a carrier-primed environment with the PC hapten coupled to carrier through a tripeptide spacer in order to maximize carrier recognition. The specificity and accuracy of the radioimmunoassays have veen verified by specific inhibition, lack of nonspecific binding, and excellent concordance of values for monoclonal antibody concentration obtained independently for Fab and idiotype content. The latter evidence also serves as strong confirmation of the monoclonality of in vitro monofocal responses as well as the preservation of the idiotype on antibodies of differing immunoglobulin classes. The results indicate that while B cells expressing the TEPC 15 idiotype predominate, other idiotypes may be represented by 2-50% of PC-specific precursors, and monoclonal antibodies even of the TEPC 15 idiotype are produced in both the IgM and IgG1 immunoglobulin classes. These findings are confirmed by the analysis of serum antibodies produced in carrier-primed mice immunized with hapten coupled through a tripeptide spacer, thus re-emphasizint the enhancement of primary responsiveness, particularly IgG1 production, by maximizing carrier recognition. The finding of idiotype diversity in the PC response, as well as diversity of expression in terms of quantity and immunoglobulin class of antibody synthesized by the clonal progeny of B cells within the TEPC 15 clonotype, emphasize the heterogeneity of the B-cell population both in terms of specificity repertoire and the physiological state of cells even within a single clonotype.
The Regions of the Fe65 Protein Homologous to the Phosphotyrosine Interaction/Phosphotyrosine Binding Domain of Shc Bind the Intracellular Domain of the Alzheimer's Amyloid Precursor Protein (1995)

Fe65 is a protein mainly expressed in several districts of the mammalian nervous system. The search of protein sequence data banks revealed that Fe65 contains two phosphotyrosine interaction (PID) or phosphotyrosine binding (PTB) domains, previously identified in the Shc adaptor molecule. The two putative PID/PTB domains of Fe65 were used to construct glutathione S-transferase-Fe65 fusion proteins. Co-precipitation experiments demonstrated that the Fe65 PID/PTB domains interacted with several proteins of apparent molecular mass 135, 115, 105, and 51 kDa. The region of Fe65 containing the PID/PTB domains was used as a bait to screen a human brain cDNA library in yeast by the two-hybrid system. Three different cDNA clones were isolated, two of which contain overlapping segments of the cDNA encoding the COOH terminus of the Alzheimer's beta-amyloid-precursor protein (APP), that represents the short intracellular domain of this membrane protein. The third clone contains a cDNA fragment coding for the COOH terminus of the human counterpart of a mouse beta-amyloid-like precursor protein. The alignment of the three APP encoding cDNA fragments found in the screening suggests that the region of APP involved in the binding is centered on the NPTY sequence, which is analogous to that present in the intracellular domains of the growth factor receptors interacting with the PID/PTB domain of Shc.
Decomposition of Phenoxyalkyl Carboxylic Acids (1962)

Abstract The persistence of phenoxyalkyl carboxylic acids in soil was measured by a bioassay technique using alfalfa seedlings. Acetic, alpha‐propionic and alpha‐ and gammabutyric acid derivatives were toxic when applied to soil planted to alfalfa whereas the beta‐propionic acid derivatives showed no inhibition of the test plant. All 3,4‐dichloro‐ and 2,4,5‐trichlorophenoxyalkyl carboxylic acids exhibited prolonged persistence in soil. The duration of phytotoxicity in soil receiving 4‐chloro‐, 2,4‐dichloro‐ and 2‐methyl‐4‐chlorophenoxyalkyl carboxylic acids was governed by the type and linkage of the aliphatic side chain. A Flavobacterium sp. active in the degradation of phenoxybutyric acids was isolated. The bacterium metabolized only phenoxybutyric acids having no meta chlorine on the aromatic ring. In the decomposition, the organic chlorine was liberated and the aromatic ring cleaved. The results demonstrate that specific structural characteristics of these herbicide molecules govern persistence of the compounds in soil.
EFFECTIVENESS OF SEED AND FOLIAR APPLICATION OF FUNGICIDES TO CONTROL ASCOCHYTA BLIGHT OF FABABEANS (1979)

Control of blight (Ascochyta fabae Speg.) of fababeans (Vicia faba L.) was attempted by using systemic and non-systemic fungicides in laboratory and field tests during 1974–1976. In the laboratory assays, all seed treatments containing the systemic fungicides benomyl or thiabendazole effectively controlled seed-borne Ascochyta but only soaking seeds in benomyl-thiram (0.2% a.i.) for 8 h effected complete eradication. In the field tests none of the seed treatments significantly reduced the seedling infection. When evaluated as foliar sprays, chlorothalonil was the most promising and was evaluated further on V. faba cultivars Erfordia and Ackerperle. One spray of this fungicide (0.1% a.i.) significantly reduced the disease severity in both cultivars. Seed infection was prevented only in Ackerperle by a minimum of two sprays 3 wk apart. In untreated plots, the disease was more severe in Erfordia than in Ackerperle.
Complete nucleotide sequence of wound tumor virus genomic segment Sll (1989)

Journal Article Complete nucleotide sequence of wound tumor virus genomic segment Sll Get access David J. Dall, David J. Dall Roche Institute of Molecular Biology, Roche Research CenterNutley, NJ 07110. USA Search for other works by this author on: Oxford Academic PubMed Google Scholar John V. Anzola, John V. Anzola Roche Institute of Molecular Biology, Roche Research CenterNutley, NJ 07110. USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Zhengkai Xu, Zhengkai Xu Roche Institute of Molecular Biology, Roche Research CenterNutley, NJ 07110. USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Donald L. Nuss Donald L. Nuss Roche Institute of Molecular Biology, Roche Research CenterNutley, NJ 07110. USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 9, 11 May 1989, Page 3599, https://doi.org/10.1093/nar/17.9.3599 Published: 11 May 1989 Article history Received: 23 February 1989 Published: 11 May 1989
Control of glycolytic flux in Zymomonas mobilis by glucose 6‐phosphate dehydrogenase activity (1996)

Glycolytic genes in Zymomonas mobilis are highly expressed and constitute half of the cytoplasmic protein. The first four genes (glf, zwf, edd, glk) in this pathway form an operon encoding a glucose permease, glucose 6-phosphate dehydrogenase (G6-P dehydrogenase), 6-phosphogluconate dehydratase, and glucokinase, respectively. Each gene was overexpressed from a tac promoter to investigate the control of glycolysis during the early stages of batch fermentation when flux (qCO2) is highest. Almost half of flux control appears to reside with G6-P dehydrogenase (CJG6-P dehydrogenase = 0.4). Although Z. mobilis exhibits one of the highest rates of glycolysis known, recombinants with elevated G6-P dehydrogenase had a 10% to 13% higher glycolytic flux than the native organism. A small increase in flux was also observed for recombinants expressing glf. Results obtained did not allow a critical evaluation of glucokinase and this enzyme may also represent an important control point. 6-Phosphogluconate dehydratase appears to be saturating at native levels. With constructs containing the full operon, growth rate and flux were both reduced, complicating interpretations. However, results obtained were also consistent with G6-P dehydrogenase as a primary site of control. Flux was 17% higher in operon constructs which exhibited a 17% increase in G6-P dehydrogenase specific activity, relative to the average of other operon constructs which contain a frameshift mutation in zwf. It is unlikely that all flux control residues solely in G6-P dehydrogenase (calculated CJG6-P dehydrogenase = 1.0) although these results further support the importance of this enzyme. As reported in previous studies, changes in flux were not accompanied by changes in growth rate providing further evidence that ATP production does not limit biosynthesis in rich complex medium. © 1996 John Wiley & Sons, Inc.
Diagnostic stewardship and the 2017 update of the IDSA-SHEA Clinical Practice Guidelines for Clostridium difficile Infection (2018)

Abstract Diagnostic stewardship is an increasingly recognized means to reduce unnecessary tests and diagnostic errors. As a leading cause of healthcare-associated infection for which accurate laboratory diagnosis remains a challenge, Clostridium difficile offers an ideal opportunity to apply the principles of diagnostic stewardship. The recently updated 2017 Infectious Diseases Society of America (IDSA)-Society for Healthcare Epidemiology of America (SHEA) Clinical Practice Guidelines for C. difficile infection now recommend separate diagnostic strategies depending on whether an institution has adopted diagnostic stewardship in test decision making. IDSA-SHEA endorsement of diagnostic stewardship for C. difficile highlights the increasing role of diagnostic stewardship in hospitals. In this opinion piece, we introduce the concept of diagnostic stewardship by discussing the new IDSA-SHEA diagnostic recommendations for laboratory diagnosis of C. difficile . We outline recent examples of diagnostic stewardship, challenges to implementation, potential downsides and propose future areas of study.
Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method (2019)

Succinylation is a type of protein post-translational modification (PTM), which can play important roles in a variety of cellular processes. Due to an increasing number of site-specific succinylated peptides obtained from high-throughput mass spectrometry (MS), various tools have been developed for computationally identifying succinylated sites on proteins. However, most of these tools predict succinylation sites based on traditional machine learning methods. Hence, this work aimed to carry out the succinylation site prediction based on a deep learning model. The abundance of MS-verified succinylated peptides enabled the investigation of substrate site specificity of succinylation sites through sequence-based attributes, such as position-specific amino acid composition, the composition of k-spaced amino acid pairs (CKSAAP), and position-specific scoring matrix (PSSM). Additionally, the maximal dependence decomposition (MDD) was adopted to detect the substrate signatures of lysine succinylation sites by dividing all succinylated sequences into several groups with conserved substrate motifs. According to the results of ten-fold cross-validation, the deep learning model trained using PSSM and informative CKSAAP attributes can reach the best predictive performance and also perform better than traditional machine-learning methods. Moreover, an independent testing dataset that truly did not exist in the training dataset was used to compare the proposed method with six existing prediction tools. The testing dataset comprised of 218 positive and 2621 negative instances, and the proposed model could yield a promising performance with 84.40% sensitivity, 86.99% specificity, 86.79% accuracy, and an MCC value of 0.489. Finally, the proposed method has been implemented as a web-based prediction tool (CNN-SuccSite), which is now freely accessible at http://csb.cse.yzu.edu.tw/CNN-SuccSite/ .
Test/Retest Reliability of Distortion-Product (1992)

Otoacoustic emissions can be used to study cochlear function in an objective and noninvasive manner. These features of emitted responses have stimulated a great deal of investigation into the utility of evoked emissions as clinical tests of hearing. One practical and essential aspect of any clinical measure is the consistency of its result upon repeated testing of the same individual (i.e., its test/retest reliability). The goal of the present work was to conduct a systematic study of the test/retest reliability of the two evoked emission types, the transiently evoked and the distortion-product otoacoustic emissions, that have the greatest promise of becoming clinically useful. Toward this end, the short- and long-term reliabilities of these two response measures were examined in 12 normally hearing adults. The results of these experiments showed that the consistency of both measures of evoked otoacoustic emissions was generally excellent.
Biotin and Protein Synthesis in Rat Liver (1970)

Abstract Biotin administration to biotin-deficient rats enhanced protein synthesis. Time sequence studies indicated that RNA synthesis was stimulated as early as 1 hour after biotin administration to the deficient rat. The synthesis of RNA of liver was stimulated by biotin administration. Nuclear RNA isolated from biotin-injected rats was more active in a protein-synthesizing system in vitro than a similar preparation from the deficient rat liver. It is suggested that biotin has a role in the synthesis of RNA.
Lessons from the withdrawal of rofecoxib: *** (2004)

adverse events before licensing
Quantum Description of High-Resolution NMR in Liquids (1990)

1. Elementary description of NMR 2. Epitome of quantum mechanics 3. Spin and magnetic moment 4. Quantum statistical mechanics 5. Quantum description of NMR 6. Generalities on 2D spectroscopy 7. J Spectroscopy 8. Shift correlation spectroscopy 9. Multiple quantum coherence and applications 10. Fundamentals of relaxation theory
Liver Cell-Selective Targeting Using Glycosylated Liposomes (1999)

To develop liver cell-specific liposomal drug carrier systems, we synthesized novel glycosylated cholesterol derivatives, cholesten-5-yloxy-N-(4-((l-imino-2-β-D-thioglycosylethyl)amino)alkyl) formamide. These glycosylated cholesterols were incorporated into liposomes consisting of DSPC and cholesterol. Mean particle size of all prepared liposomes were about 90 nm. After intravenous injection, these glycosylated liposomes were rapidly taken up by the liver. Fractionation of liver cells revealed that galactosyalted liposomes were taken up mainly by liver parenchymal cells while mannosyalted liposomes by liver non-parenchymal cells. Inhibition studies with galactosylated and mannosylated bovine serum albumin suggested that galactosylated and mannosylated liposomes might be recognized by asialoglycoprotein receptor and mannose receptor, respectively. Then, we studied in vivo distribution of prostaglandin E1 (PGE1) and probucol associated with galactosylated liposomes. Liver accumulation of these drugs were significantly higher than that of non-modified liposomes and drug itself. Moreover, PGE1 associated with galactosylated liposomes was effective for acute hepatitis induced by intraperitoneal injection of carbon tetrachloride.
Orientation and Mobility with Prosthetic Vision - Combination of Luminosity and Depth Information for Scene Representation (2014)

International audience
2-Methyl-N-o-tolylbenzamide (2009)

In the title compound, C(15)H(15)NO, the C-N-C(O)-C amide unit is planar (r.m.s. deviation = 0.003 Å) and subtends dihedral angles of 44.71 (5) and 43.33 (5)° with the two o-tolyl rings. These aromatic rings are inclined at 4.94 (7)° to one another. The ortho-methyl groups of the two tolyl rings are anti to one another. In the crystal structure, N-H⋯O hydrogen bonds augmented by C-H⋯π inter-actions link the mol-ecules in a head-to-head fashion into chains along a. Independent chains pack in a herringbone pattern along c.
Data-flow-based unit testing of aspect-oriented programs (2004)

The current research so far in aspect-oriented software development is focused on problem analysis, software design, and implementation techniques. Even though the importance of software testing is known, it has received little attention in the aspect-oriented paradigm. In this paper, we propose a data-flow-based unit testing approach for aspect oriented programs. Our approach tests two types of units for an aspect-oriented program, i.e., aspects that are modular units of crosscutting implementation of the program, and those classes whose behavior may be affected by one or more aspects. For each aspect or class, our approach performs three levels of testing, i.e., intra-module, inter-module, and intra-aspect or intra-class testing. For an individual module such as apiece of advice, a piece of introduction, and a method, we perform intra-module testing. For a public module along with other modules it calls in an aspect or class, we perform inter-module testing. For modules that can be accessed outside the aspect or class and can be invoked in any order by users of the aspect or class, we perform intra-aspect or intra-class testing. Our approach can handle unit testing problems that are unique to aspect-oriented programs. We use control flow graphs to compute def-use pairs of an aspect or class being tested and use such information to guide the selection of test for the aspect or class.
A Real-Time Rodent Tracking System for Both Light and Dark Cycle Behavior Analysis (2005)

Position tracking of rodents is useful and necessary to help elucidate the behavioral and physiological effects of genetic mutations, drug action, and environmental stimuli. In this paper we describe a real-time system developed to allow continuous overhead video monitoring of rodent behavior in a home cage environment, either in a daylight condition (light-cycle) using standard visible illumination or a night-time condition (dark-cycle), using overhead near infrared illumination (NIR). Due to the lack of research on the effects of NIR on rodent behavior, we also examined open-field locomotor activity under 880 nm and 940 nm wavelengths of NIR, as well as visible white light and a "dark" condition consisting of a very dim level of NIR. The experimental result validated the described system and robustly tracked the target rodent in the light cycle, and for high contrast conditions in the dark cycle.