gebhart/patrepeval huggingface dataset:
Capillary Electrophoresis in Biotechnology and Environmental Analysis (2023)

Part 1 Technological innovations: capillary electrophoresis/mass spectrometry for the determination of bioactive proteins and peptides, K.B. Tomer et al pre-concentration techniques in high-performance capillary electrophoresis, P. Roland-Gosselin et al capillary electrophoresis with laser-induced fluorescence detection - optical design and applications, G. Nouadje, et al. Part 2 HPCE in protein and peptide analysis: analysis of protein folding by capillary electrophoresis, M.A. Strege et al application of HPCE analysis to process monitoring in biotechnology, R. Freitag isoform characterization, peptide mapping and amino-acid analysis of monoclonal antibodies by high-performance capillary electrophoresis, J.F. Veillon et al capillary-zone electrophoresis and isotachophoresis of biologically-active peptides, V. Kasicka and Z. Prusik. Part 3 HPCE in drug abuse and drug interactions: analysis of drugs of abuse by micellar electrokinetic capillary chromatography, V.C. Trenerry and R.J. Wells study of protein-drug binding by capillary-zone electrophoresis - prospects and problems, J.C. Kraak et al HPCE of catecholamines, bioactive molecules and other transmitters, T. Kaneta and S. Tanaka capillary-gel electrophoresis and antisense therapeutics - the analysis of DNA analogs, L.A. DeDionisio and D.H. Lloyd. Part 4 HPCE of carbohydrates, chiral and enantiomers: capillary electrophoresis of heparin-derived carbohydrate chains, J.B.L. Damm chiral separation by HPCE with oligosaccharides - application to acidic compounds, A. D'Hulst and N. Verbeke separation of enantiomers in capillary electrophoresis, T. Schmitt. Part 5 HPCE of anions and cations: negative absorbance - application to the detection of inorganic anions and cations in high-performance capillary electrophoresis, P. Roland-Gosselin et al.
Automatically Evaluating Text Coherence Using Discourse Relations (2011)

We present a novel model to represent and assess the discourse coherence of text. Our model assumes that coherent text implicitly favors certain types of discourse relation transitions. We implement this model and apply it towards the text ordering ranking task, which aims to discern an original text from a permuted ordering of its sentences. The experimental results demonstrate that our model is able to significantly outperform the state-ofthe-art coherence model by Barzilay and Lapata (2005), reducing the error rate of the previous approach by an average of 29 % over three data sets against human upper bounds. We further show that our model is synergistic with the previous approach, demonstrating an error reduction of 73 % when the features from both models are combined for the task. 1
Novel adaptive battery system for integration with multi-level inverters (2017)

A novel adaptive battery system with two battery sources is proposed to provide multiple output levels and increased benefits when integrated with multi-level inverters by improving the batteries' state of health (SOH) and state of charge (SOC). Applications of this topology include dynamic hybrid battery/inverter and photovoltaic/inverter systems. The system has been modeled and validated using Matlab software. Result show the benefits of the prosed system over existing approaches in overall operation and performance of the system.
Deep Convolutional Transfer Learning Network: A New Method for Intelligent Fault Diagnosis of Machines With Unlabeled Data (2018)

The success of intelligent fault diagnosis of machines relies on the following two conditions: 1) labeled data with fault information are available; and 2) the training and testing data are drawn from the same probability distribution. However, for some machines, it is difficult to obtain massive labeled data. Moreover, even though labeled data can be obtained from some machines, the intelligent fault diagnosis method trained with such labeled data possibly fails in classifying unlabeled data acquired from the other machines due to data distribution discrepancy. These problems limit the successful applications of intelligent fault diagnosis of machines with unlabeled data. As a potential tool, transfer learning adapts a model trained in a source domain to its application in a target domain. Based on the transfer learning, we propose a new intelligent method named deep convolutional transfer learning network (DCTLN). A DCTLN consists of two modules: condition recognition and domain adaptation. The condition recognition module is constructed by a one-dimensional (1-D) convolutional neural network (CNN) to automatically learn features and recognize health conditions of machines. The domain adaptation module facilitates the 1-D CNN to learn domain-invariant features by maximizing domain recognition errors and minimizing the probability distribution distance. The effectiveness of the proposed method is verified using six transfer fault diagnosis experiments.
Experimental investigation and empirical modelling of FDM process for compressive strength improvement (2011)

Fused deposition modelling (FDM) is gaining distinct advantage in manufacturing industries because of its ability to manufacture parts with complex shapes without any tooling requirement and human interface. The properties of FDM built parts exhibit high dependence on process parameters and can be improved by setting parameters at suitable levels. Anisotropic and brittle nature of build part makes it important to study the effect of process parameters to the resistance to compressive loading for enhancing service life of functional parts. Hence, the present work focuses on extensive study to understand the effect of five important parameters such as layer thickness, part build orientation, raster angle, raster width and air gap on the compressive stress of test specimen. The study not only provides insight into complex dependency of compressive stress on process parameters but also develops a statistically validated predictive equation. The equation is used to find optimal parameter setting through quantum-behaved particle swarm optimization (QPSO). As FDM process is a highly complex one and process parameters influence the responses in a non linear manner, compressive stress is predicted using artificial neural network (ANN) and is compared with predictive equation.
Defining the Hallmarks of Metastasis (2019)

Metastasis is the primary cause of cancer morbidity and mortality. The process involves a complex interplay between intrinsic tumor cell properties as well as interactions between cancer cells and multiple microenvironments. The outcome is the development of a nearby or distant discontiguous secondary mass. To successfully disseminate, metastatic cells acquire properties in addition to those necessary to become neoplastic. Heterogeneity in mechanisms involved, routes of dissemination, redundancy of molecular pathways that can be utilized, and the ability to piggyback on the actions of surrounding stromal cells makes defining the hallmarks of metastasis extraordinarily challenging. Nonetheless, this review identifies four distinguishing features that are required: motility and invasion, ability to modulate the secondary site or local microenvironments, plasticity, and ability to colonize secondary tissues. By defining these first principles of metastasis, we provide the means for focusing efforts on the aspects of metastasis that will improve patient outcomes.
The adenovirus type 5 i-leader open reading frame functions in cis to reduce the half-life of L1 mRNAs (1990)

The 440-nucleotide adenovirus type 5 i-leader sequence, encoding a 13.6-kilodalton protein, is located between the second and third components of the tripartite leader sequence. It appears primarily on the L1 family of mRNAs. To study its function, we constructed two point mutations within the i leader. pm382 lacks the wild-type i-leader splice acceptor and failed to splice the leader onto L1 mRNAs. pm383 lacks the ATG used for translation of the i-leader protein; it synthesized i-leader-containing mRNAs, but failed to produce detectable levels of the polypeptide. Both mutants exhibited modestly reduced yields in some but not all cell lines tested and accumulated slightly elevated levels of L1 mRNA and L1 52- and 55-kilodalton proteins in infected cells. Mutant phenotypes were consistently more pronounced in pm382- than in pm383-infected cells. In wild-type virus-infected cells, L1 mRNAs lacking the i leader displayed a half-life of about 26 h, whereas L1 mRNAs containing the leader were much less stable, with a half-life of less than 4 h. In pm383-infected cells (ATG mutant), L1 mRNAs containing the i leader exhibited a half-life of 26 h. The abnormally long half-life of pm383-encoded L1 mRNAs containing a mutant i leader was not reduced by coinfection with wild-type virus, suggesting that synthesis of the i-leader protein leads to destabilization of the i-leader-containing L1 mRNA undergoing translation.
PROSPECTIVE 2002-2007 POUR UN PRÉSIDENT : LES RUPTURES PROBABLES (2002)

International audience
Manipulation of the acute inflammatory response by dietary polyunsaturated fatty acid modulation. (1990)

Dietary polyunsaturated fatty acid modulation has been used as an anti-inflammatory strategy in experimental models of disease as well as in clinical trials. To elucidate the mechanisms underlying the anti-inflammatory effects of manipulating dietary polyunsaturated fatty acids, the in vivo effects of essential fatty acid (EFA) deficiency and (n-3) fatty acid supplementation were contrasted using a model of acute inflammation induced by the i.p. injection of zymosan into mice. Both diets led to a substantial decrease in tissue (n-6) fatty acid content. EFA deficiency was also characterized by the accumulation of (n-9) fatty acids, particularly 20:3 (n-9), the fatty acid that uniquely characterizes the deficiency state. Dietary (n-3) fatty acid supplementation led instead to marked increases in (n-3) fatty acids, especially 20:5 (n-3). With respect to the antiinflammatory effects of the two diets, EFA deficiency, but not (n-3) fatty acid supplementation, depleted levels of resident peritoneal macrophages. EFA deficiency was also more effective than (n-3) fatty acid supplementation in inhibiting the influx of polymorphonuclear neutrophils in response to zymosan. The effect of the two diets on the in vivo generation of leukotriene(LT)B also differed markedly. EFA deficiency completely inhibited the synthesis of LTB. Dietary (n-3) fatty acid supplementation, in contrast, reduced the production of LTB4 by only 50%. With (n-3) fatty acid supplementation LTB5 was produced. The more modest effect of (n-3) fatty acid supplementation in decreasing LTB4 generation was not due to blockade of the cyclooxygenase pathway. EFA deficiency, but not (n-3) fatty acid supplementation, was associated with the decreased synthesis of thromboxane. Although dietary fatty acid modulation has been shown to diminish platelet activating factor (PAF) synthesis, studies using the PAF receptor blocker, L659989, established that PAF was not a significant factor in the elicitation of leukocytes in this model of inflammation. In summary, the anti-inflammatory effect of EFA deficiency was more marked that that of dietary (n-3) fatty acid supplementation in acute inflammation. This difference in anti-inflammatory potential appeared to be due to either the greater effect of EFA deficiency in decreasing levels of resident peritoneal macrophages or in suppressing the in vivo generation of LTB4.
An efficient dual-mode floating-point Multiply-Add Fused Unit (2010)

Multiply-Add Fused (MAF) units play a key role in the processor's performance for a variety of applications. Aiming at improving the MAF functionality this paper presents a dual-mode MAF architecture, which is able to perform either one double-precision or two single-precision operations in parallel. The design attains low latency by following a dual-path approach and by combining final addition with rounding. The organization performs a MAF instruction in three cycles, while single floating-point addition in two cycles. The design has been validated and implemented with TSMC 0.13um.
Spleen cells from adult mice given total lymphoid irradiation or from newborn mice have similar regulatory effects in the mixed leukocyte reaction. I. Generation of antigen-specific suppressor cells in the mixed leukocyte reaction after the addition of spleen cells from adult mice given total lymphoid irradiation. (1982)

We added spleen cells from adult BALB/c mice treated with total lymphoid irradiation (TLI) to the mixed leukocyte reaction (MLR) using a variety of responder and stimulator cells. The spleen cells nonspecifically suppressed the uptake of [3H]-thymidine and the generation of cytolytic cells regardless of the responder-stimulator combination used. We also examined the effect of the spleen cells on the generation of antigen-nonspecific and antigen-specific suppressor cells in the MLR. The experimental results suggest that the spleen cells from TLI-treated mice inhibit the generation of nonspecific suppressor cells, but do not inhibit the generation of antigen-specific suppressor cells. Thus, alloantigenic stimulation of normal responder cells in vitro in the presence of spleen cells from TLI-treated mice generates large numbers of antigen-specific suppressor cells, but few cytolytic cells or nonspecific suppressor cells. Similar nonspecific inhibition of the MLR was observed with neonatal spleen cells. This in vitro system provides a regulatory model for the induction and maintenance of tolerance in vivo, in which adult mice given TLI or neonatal mice accept allogeneic bone marrow transplants without graft-vs.-host disease.
Efficient Asymmetric Oxidation of Sulfides and Kinetic Resolution of Sulfoxides Catalyzed by a Vanadium−Salan System (2004)

The asymmetric oxidation of sulfides to chiral sulfoxides with hydrogen peroxide in good yield and high enantioselectivity has been catalyzed very effectively by chiral vanadium-salan [N,N'-alkyl bis(salicylamine)] complex. The salan ligand shows results superior in terms of reactivity and enantioselectivity to those of salen [N,N'-alkylene bis(salicylideneimine)] analogue, and provides the sulfoxide with opposite configuration. The high enantioselectivity of this reaction is the direct result of the asymmetric oxidation. The efficient kinetic resolution of racemic sulfoxides catalyzed by the vanadium-salan system is also described.
Increased claudin‐4 expression is associated with poor prognosis and high tumour grade in breast cancer (2008)

The role of intercellular tight junctions in breast epithelial cells is traditionally thought to be in maintaining polarity and barrier function. However, claudin-4, a tight junction protein, is overexpressed in breast tumour cells compared to normal epithelial cells, which generally corresponds to a loss in polarity. The aim of this study was to investigate the distribution and potential clinical value of claudin-4 in breast cancer, and to evaluate its usefulness as a prognostic and predictive biomarker. Expression of claudin-4 was initially examined by Western blot analysis in a cohort of 88 breast tumours, and was found to correlate positively with tumour grade and negatively with ER. Claudin-4 expression was then evaluated by immunohistochemistry in a larger cohort of 299 tumours represented on a tissue microarray. Claudin-4 expression correlated positively with tumour grade and Her2, and negatively with ER. High claudin-4 expression was also associated with worse breast cancer-specific survival (p = 0.003), recurrence-free survival (p = 0.025) and overall survival (p = 0.034). Multivariate analysis revealed that claudin-4 independently predicted survival in the entire cohort (HR 1.95; 95%CI 1.01-3.79; p = 0.047) and in the ER positive subgroup treated with adjuvant tamoxifen (HR 4.34; 95%CI 1.14-16.53; p = 0.032). This relationship between increased claudin-4 expression and adverse outcome was validated at the mRNA level in a DNA microarray dataset of 295 breast tumours. We conclude that high levels of claudin-4 protein are associated with adverse outcome in breast cancer patients, including the subgroup of patients treated with adjuvant tamoxifen.
Microtexture Determination and Its Applications (2023)

A cornerstone in the study of both natural and technological materials is characterisation of microstructure. In the widest sense this topic encompasses, for all phases present: morphology, including size and shape distributions; chemical composition; crystallographic parameters, including orientation and orientation relationships. A landmark advance for the materials community occurred with the genesis of 'microtexture', which for the first time provided integration of crystallographic parameters and other aspects of the microstructure. A definition of microtexture is: 'a population of crystallographic orientations whose individual components are linked to their location within the microstructure.' The term microtexture also describes any experimental technique used to determine this information. Essentially, a stationary beam of electrons is diffracted by atomic planes in the sampled volume of specimen. Analysis of the resulting diffraction pattern provides crystallographic information which can be related back to its position of origin. An estimated 95 percent of microtexture determination is by 'electron backscatter diffraction' (EBSD) in a scanning electron microscope (SEM), with the remaining 5 percent contributed mainly by transmission electron microscopy (TEM) counterparts to EBSD. Evaluation (indexing) of EBSD diffraction patterns and output of data in a variety of formats is in most cases fully automated. The most exciting EBSD output is an 'orientation map', which is a quantitative depiction of the microstructure in terms of its orientation constituents. Microtexture determination is now firmly established as the most comprehensive experimental tool for quantitative characterisation and analysis of microstructure, and is used extensively in both research and industry. Much has changed since this book was first published and the second edition has been completely rewritten to reflect these changes.
Performance investigation of atmospheric water harvesting systems (2018)

In this paper performance and limitations of commercially-available atmospheric water harvesting (AWH) systems are experimentally investigated. A new experimental setup and test procedure, following the relevant ASHRAE and ANSI/AHRI standards, are developed to measure the water harvesting rate and input electrical power of several residential-size AWHs from different manufacturers. The setup is equipped with an environmental chamber to mimic all climatic conditions in research laboratory at Simon Fraser University and to obtain performance characteristics of AWH systems. The results show the range of water harvesting rate, energy intensity ranging from 1.02 kWh/L for warm and humid to 6.23 kWh/L for cold and humid climates, and climatic limitations of the conventional AWH technology that can be used as a platform for further development of higher efficiency AWH systems in future.
Detection of Helicobacter pylori gene expression in human gastric mucosa (1995)

Mucosal and systemic immunologic recognition of cagA by Helicobacter pylori-infected individuals is associated with peptic ulcer disease; however, in the laboratory, expression of cagA is subject to artificial conditions which may not accurately reflect the conditions in host tissues. Gastric antral and body biopsy specimens and serum for anti-H. pylori immunoglobulin G serology were obtained from 42 patients. Biopsy specimens were studied by histology, culture, and reverse transcription PCR (RT-PCR). Oligonucleotide primers specific for H. pylori (16S rRNA, ureA, and cagA) were used to detect bacterial mRNA in gastric biopsy specimens. PCR was performed on DNA from corresponding H. pylori isolates to detect genomic 16S rRNA, ureA, and cagA. Of the 42 patients from whom clinical specimens were obtained, 25 were infected with H. pylori on the basis of both serology and histology or culture (i.e., tissue positive); 13 were negative by serology, histology, and culture; and 4 were positive by serology only. RT-PCR with 16S rRNA primers detected 24 of 25 tissue-positive and 0 of 17 tissue-negative patients (P < 0.001). RT-PCR with ureA primers detected 16 of 25 tissue-positive and 0 of 17 tissue-negative patients (P < 0.001). CagA mRNA was detected by RT-PCR in 14 of 25 gastric biopsy specimens in the tissue-positive group and in 0 of 17 gastric biopsy specimens in the tissue-negative group. PCR of genomic DNA for the presence of the cagA gene in the corresponding bacterial isolates correlated absolutely with cagA gene expression in gastric tissue. These results indicate that RT-PCR is a sensitive and specific method for the detection of the presence of H. pylori and the expression of H. pylori genes in human gastric tissue. Detection of H. pylori gene expression in vivo by this approach may contribute to improving the diagnosis and understanding the pathogenesis of H. pylori infections.
Analyses of Soft Tissue from <i>Tyrannosaurus rex</i> Suggest the Presence of Protein (2007)

We performed multiple analyses of Tyrannosaurus rex (specimen MOR 1125) fibrous cortical and medullary tissues remaining after demineralization. The results indicate that collagen I, the main organic component of bone, has been preserved in low concentrations in these tissues. The findings were independently confirmed by mass spectrometry. We propose a possible chemical pathway that may contribute to this preservation. The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time.
14,15-Epoxyeicosa-5,8,11-trienoic Acid (14,15-EET) Surrogates: Carboxylate Modifications (2014)

The cytochrome P450 eicosanoid 14,15-epoxyeicosa-5,8,11-trienoic acid (14,15-EET) is a powerful endogenous autacoid that has been ascribed an impressive array of physiologic functions including regulation of blood pressure. Because 14,15-EET is chemically and metabolically labile, structurally related surrogates containing epoxide bioisosteres were introduced and have become useful in vitro pharmacologic tools but are not suitable for in vivo applications. A new generation of EET mimics incorporating modifications to the carboxylate were prepared and evaluated for vasorelaxation and inhibition of soluble epoxide hydrolase (sEH). Tetrazole 19 (ED50 0.18 μM) and oxadiazole-5-thione 25 (ED50 0.36 μM) were 12- and 6-fold more potent, respectively, than 14,15-EET as vasorelaxants; on the other hand, their ability to block sEH differed substantially, i.e., 11 vs >500 nM. These data will expedite the development of potent and specific in vivo drug candidates.
Robust Optimization under Multi-band Uncertainty - Part I: Theory (2013)

The classical single-band uncertainty model introduced by Bertsimas and Sim has represented a breakthrough in the development of tractable robust counterparts of Linear Programs. However, adopting a single deviation band may be too limitative in practice: in many real-world problems, observed deviations indeed present asymmetric distributions over asymmetric ranges, so that getting a higher modeling resolution by partitioning the band into multiple sub-bands is advisable. The critical aim of our work is to close the knowledge gap on the adoption of multi-band uncertainty in Robust Optimization: a general definition and intensive theoretical study of a multi-band model are actually still missing. Our new developments have been also strongly inspired and encouraged by our industrial partners, interested in getting a better modeling of arbitrary shaped distributions, built on historical data about the uncertainty affecting the considered real-world problems.