gebhart/patrepeval huggingface dataset:
<i>Alternaria alternata</i>serine proteases induce lung inflammation and airway epithelial cell activation via PAR<sub>2</sub> (2011)

Allergens are diverse proteins from mammals, birds, arthropods, plants, and fungi. Allergens associated with asthma (asthmagens) share a common protease activity that may directly impact respiratory epithelial biology and lead to symptoms of asthma. Alternaria alternata is a strong asthmagen in semiarid regions. We examined the impact of proteases from A. alternata on lung inflammation in vivo and on cleaving protease-activated receptor-2 (PAR(2)) in vitro. A. alternata filtrate applied to the airway in nonsensitized Balb/c mice induced a protease-dependent lung inflammation. Moreover, A. alternata filtrate applied to human bronchial epithelial cells (16HBE14o-) induced changes in intracellular Ca(2+) concentration ([Ca(2+)](i)), consistent with PAR(2) activation. These effects were blocked by heat inactivation or by serine protease inhibition of A. alternata filtrates, and mimicked by PAR(2) specific ligands SLIGRL-NH(2) or 2-furoyl-LIGRLO-NH(2), but not the PAR(1)-specific ligand TFLLR-NH(2). Desensitization of PAR(2) in 16HBE14o- cells with 2-furoyl-LIGRLO-NH(2) or trypsin prevented A. alternata-induced [Ca(2+)](i) changes while desensitization of PAR(1), PAR(3), and PAR(4) with thrombin had no effect on A. alternata-induced Ca(2+) responses. Furthermore, the Ca(2+) response to A. alternata filtrates was dependent on PAR(2) expression in stably transfected HeLa cell models. These data demonstrate that A. alternata proteases act through PAR(2) to induce rapid increases in human airway epithelial [Ca(2+)](i) in vitro and cell recruitment in vivo. These responses are likely critical early steps in the development of allergic asthma.
Exosome-dependent Trafficking of HSP70 (2005)

The heat shock proteins (HSPs) are a family of intracellular proteins found in all eukaryotes and prokaryotes. Their functions are well characterized and are central to maintaining cellular homeostasis and in promoting cell survival in response to stressful cellular conditions. However, several studies provide evidence that specific members of the HSP family might be secreted via an unidentified exocytotic pathway. Here we show that exosomes, small membrane vesicles that are secreted by numerous cell types, contribute to the release of HSP70 from human peripheral blood mononuclear cells (PBMCs) in both basal and stress-induced (heat shock at 40 or 43 degrees C for 1 h) states. HSP70 release from PBMCs is independent of the common secretory pathway because Brefeldin A, an inhibitor of the classical protein transport pathway, did not block HSP70 release. Furthermore, we show that HSP70 release from PBMCs does not occur via a lipid raft-dependent pathway, because treatment with methyl-beta-cyclodextrin, a raft-disrupting drug, had no affect on HSP70 release. To examine whether exosomes contributed to HSP70 release from PBMCs, exosomes were purified from PBMC cultures, and exosomal number and HSP70 content were determined. We demonstrate that although heat shock does not influence the exosomal secretory rate, the HSP70 content of exosomes isolated from heat shocked PBMCs is significantly higher than control. These data identify a novel secretory pathway by which HSP70 can be actively released from cells in both the basal and stress-induced state.
A glucose sensor utilising tetracyanoquinodimethane as a mediator. (1988)

This paper describes an amperometric enzyme electrode for glucose analysis. The electrode utilised the mediator tetracyanoquinodimethane (TCNQ) to facilitate electron transfer from glucose oxidase to a pyrolytic graphite carbon electrode. The electrode demonstrated a response to glucose in a clinically relevant range (0-70 mM). Results concerning the direct current cyclic voltammetry of TCNQ and the electrodes' response to glucose, pH profile and the effect of temperature are presented.
Interobserver Agreement on Clinical Judgment of Work of Breathing in Spontaneously Breathing Children in the Pediatric Intensive Care Unit (2019)

Clinical assessment of the work of breathing (WOB) remains a cornerstone in respiratory support decision-making in the pediatric intensive care unit (PICU). In this study, we determined the interobserver agreement of 30 observers (PICU physicians and nurses) on WOB and multiple signs of effort of breathing in 10 spontaneously breathing children admitted to the PICU. By reliability analysis, the agreement on overall WOB was poor to moderate, and only three separate signs of effort of breathing (breathing rate, stridor, and grunting) showed moderate-to-good interobserver reliability. We conclude that the interobserver agreement on the clinical WOB judgment among PICU physicians and nurses is low.
Improving the Dependability of Machine Learning Applications (2008)

As machine learning (ML) applications become prevalent in various aspects of everyday life, their dependability takes on increasing importance. It is challenging to test such applications, however, because they are intended to learn properties of data sets where the correct answers are not already known. Our work is not concerned with testing how well an ML algorithm learns, but rather seeks to ensure that an application using the algorithm implements the specification correctly and fulfills the users' expectations. These are critical to ensuring the application's dependability. This paper presents three approaches to testing these types of applications. In the first, we create a set of limited test cases for which it is, in fact, possible to predict what the correct output should be. In the second approach, we use random testing to generate large data sets according to parameterization based on the application's equivalence classes. Our third approach is based on metamorphic testing, in which properties of the application are exploited to define transformation functions on the input, such that the new output can easily be predicted based on the original output. Here we discuss these approaches, and our findings from testing the dependability of three real-world ML applications.
Tetanus toxin receptor Specific cross‐linking of tetanus toxin to a protein of NGF‐differentiated PC 12 cells (1991)

A subclone of rat pheochromocytoma cells expresses high affinity receptors for tetanus toxin on differentiation with NGF [Walton, K.M., Sandberg, K., Rogers, T.B. and Schnaar, R.L. (1988) J. Biol. Chem. 263, 2055-2063]. In the presence of protein cross-linking agents, [125I]tetanus toxin, bound to these cells at 0 degree C, forms a cross-linked product with apparent molecular weight of 120 kDa. The formation of [125I]tetanus toxin conjugate involves the heavy chain of the toxin, is prevented by cold toxin and it is largely reduced by pretreating cells with proteases. The cross-linked product is formed only upon incubation of the toxin with NGF-differentiated cells. These results suggest that a protein with apparent molecular weight of 20 kDa is involved in the neurospecific binding of tetanus toxin.
New Uses of Sulfur—II (1978)

Because of its unique chemical and physical properties, elemental sulfur has interesting potential applications, particularly in the construction industry. Despite years of research and developmental activities, little sulfur has been consumed in these applications. One reason for this is that sulfur atoms combine with each other to form the extremely complicated and complex system of chain or ring molecules, Sx. Depending on x, the physical and chemical properties of sulfur molecules and the molecular equilibria mixtures change rather drastically. For practical applications, the correlations between molecular size, molecular geometry, chemical and physical stability, and other common properties of sulfur must be known. Stereochemical aspects may indicate the performance of Sx in different applications.
Blood Substitutes: 1995 in the Literature (1996)

The published literature related to blood substitutes and associated topics continues to increase, in peer-reviewed journals, books, edited volumes, meeting proceedings and various editorials. A review of the 1994 literature was presented at the March, 1995, Current Issues in Blood Substitute Research and Development course in San Diego, and this was perceived to be quite useful to those who attended the course. Thus a similar review is presented in the current volume, intended to reach a wider audience. One consequence of presenting the review as part of this book rather than distributing it at the course is that it will be somewhat less up-to-date in March, 1996.
Control of hysteretic systems through inverse compensation (2009)

Inverse compensation is a fundamental technique in the control of systems with hysteresis. In this expository article, we present algorithms for constructing the inverse of the Preisach operator, a hysteresis model with application to magnetics, smart materials, terrestrial hydrology, and economics. Adaptive inverse control is discussed for cases where hysteresis parameters are not known precisely. To meet the demand of highly dynamic applications, an embedded inversion approach is presented that exploits the parallelism offered by FPGAs.
Simulating Yarn-Based Cloth (2011)

Cloth is an important material to model and simulate correctly, both in computer graphics and other industrial applications. The commonly used models for cloth in computer graphics typically approximate the cloth as an elastic sheet with linear isotropic behavior inspired by the construction of woven fabrics. However, they do a poor job of predicting the behavior of knits, which are driven by the complex interactions of yarn loops pulled through each other. This thesis presents a yarn-based model for cloth where yarns in the fabric are explicitly modeled as inextensible but flexible spline curves. Yarn dynamics are dictated by both energy terms and hard constraints, while friction interactions, a critical component of correct yarn behavior, are approximated using a velocity filter that penalizes locally non-rigid motion. Qualitative comparison of the model to observed deformations of hand-knitted samples in the laboratory showed that the model predicts key mechanical properties of different knits. Since this model is slower than sheet-based approaches, further work looked at accelerating the model through both localized rigidification and adaptive contact
Challenges in transcatheter aortic valve implantation (2012)

Although safety and efficacy of TAVI was improved with next-generation equipment, experience, and careful patient selection, some worrisome complications associated with the procedure remain. Current hot topics in transcatheter aortic valve implantation include patient selection, valve sizing, paravalvular regurgitation, cerebrovascular accidents, vascular complications and need for a permanent pacemaker. In this article we review the pathophysiology, avoidance and treatment options for these complications.
Feature Extraction and Pattern Recognition for Human Motion by a Deep Sparse Autoencoder (2014)

Human motion data is high-dimensional time-series data, and it usually contains measurement error and noise. Recognizing human motion on the basis of such high-dimensional measurement row data is often difficult and cannot be expected for high generalization performance. To increase generalization performance in a human motion pattern recognition task, we employ a deep sparse auto encoder to extract low-dimensional features, which can efficiently represent the characteristics of each motion, from the high-dimensional human motion data. After extracting low-dimensional features by using the deep sparse auto encoder, we employ random forests to classify low-dimensional features representing human motion. In experiments, we compared using the row data and three types of feature extraction methods - principal component analysis, a shallow sparse auto encoder, and a deep sparse auto encoder - for pattern recognition. The experimental results show that the deep sparse auto encoder outperformed the other methods with the highest average recognition accuracy, 75.1%, and the lowest standard deviation, ±3.30%. The proposed method, application of a deep sparse auto encoder, thus enabled higher recognition accuracy, better generalization and more stability than could be achieved with the other methods.
UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities (1989)

Escherichia coli endonuclease III and mammalian repair enzymes cleave UV-irradiated DNA at AP sites formed by the removal of cytosine photoproducts by the DNA glycosylase activity of these enzymes. Poly(dG-[3H]dC) was UV irradiated and incubated with purified endonuclease III. 3H-Containing material was released in a fashion consistent with Michaelis-Menten kinetics. This 3H material was determined to be cytosine by chromatography in two independent systems and microderivatization. 3H-Containing material was not released from nonirradiated copolymer. When poly(dA-[3H]dU) was UV irradiated, endonuclease III released 3H-containing material that coeluted with uracil hydrate (6-hydroxy-5,6-dihydrouracil). Similar results are obtained by using extracts of HeLa cells. There results indicate that the modified cytosine residue recognized by endonuclease III and the mammalian enzyme is cytosine hydrate (6-hydroxy-5,6-dihydrocytosine). Once released from DNA through DNA-glycosylase action, the compound eliminates water, reverting to cytosine. This is consistent with the known instability of cytosine hydrate. The repairability of cytosine hydrate in DNA suggests that it is stable in DNA and potentially genotoxic.
Chronic Pepsin Exposure Promotes Anchorage‐Independent Growth and Migration of a Hypopharyngeal Squamous Cell Line (2013)

Hypopharyngeal squamous cell line chronically exposed to pepsin demonstrated increased cell migration and colony-forming ability relative to control cells. These experiments indicate that chronic pepsin exposure acts as a promoter of tumorigenesis and metastasis of airway epithelium, suggesting a role for pepsin in laryngopharyngeal carcinogenesis attributed to gastric reflux.
Asymmetric synthesis of anti-(2S,3S)- and syn-(2R,3S)-diaminobutanoic acidThis is one of a number of contributions from the current members of the Dyson Perrins Laboratory to mark the end of almost 90 years of organic chemistry research in that building, as all its current academic staff move across South Parks Road to a new purpose-built laboratory. (2003)

Conjugate addition of homochiral lithium N-benzyl-N-alpha-methylbenzylamide to tert-butyl (E)-cinnamate or tert-butyl (E)-crotonate and in situ amination with trisyl azide results in the exclusive formation of the corresponding 2-diazo-3-amino esters in > 95% de. Amination of the lithium (E)-enolates of tert-butyl (3S,alphaR)-3-N-benzyl-N-alpha-methylbenzylamino-3-phenylpropanoate or tert-butyl (3S,alphaS)-3-N-benzyl-N-alpha-methylbenzylaminobutanoate with trisyl azide gives the (2R,3R,alphaR)- and (2S,3S,alphaS )-anti-2-azido-3-amino esters in good yields and in 85% de and > 95% de respectively. Alternatively, tert-butyl anti-(2S,3S,alphaS)-2-hydroxy-3-N-benzyl-N-alpha-methylbenzylaminobutanoate may be converted selectively to tert-butyl anti-(2S,3S,alphaS)-2-azido-3-N-benzyl-N-alpha-methylbenzylaminobutanoate by aziridinium ion formation and regioselective opening with azide. Deprotection of tert-butyl (2S,3S,alphaS)-2-azido-3-aminobutanoate via Staudinger reduction, hydrogenolysis and ester hydrolysis furnishes anti-(2S,3S)-diaminobutanoic acid in 98%, de and 98% ee. The asymmetric synthesis of the diastereomeric syn-(2R,3S)-diaminobutanoic acid (98% de and 98% ee) was accomplished via functional group manipulation of tert-butyl anti-(2S,3S,alphaS)-2-hydroxy-3-N-benzyl-N-alpha-methylbenzylaminobutanoate in a protocol involving azide inversion of tert-butyl (2S,3S)-2-mesyloxy-3-N-Boc-butanoate and subsequent deprotection.
Occurrence of a nontypable Helicobacter pylori strain lacking Lewis blood group O antigens and DD-heptoglycan: evidence for the role of the core  1,6-glucan chain in colonization (2003)

The cell envelope of Helicobacter pylori contains a lipopolysaccharide (LPS) essential for the physical integrity and functioning of the bacterial cell membrane. The O-chain of this LPS frequently expresses type 2 Lewis x (Lex) and Lewis y (Ley) blood group antigens that mimic human gastric mucosal cell-surface glycoconjugates. This article describes the isolation and structural analysis of the LPS from a clinical isolate of H. pylori strain PJ2 that lacks Le antigens but is still capable of colonization. Subsequent composition, methylation, and CE-ESMS analyses of LPS revealed its core oligosaccharide structure to be consistent with the previously proposed structural model for H. pylori LPS. In addition, it carries an unusually long side branch alpha1,6-glucan and was devoid of Le O-chain polysaccharide. Its ability to colonize the mouse stomach was essentially identical to that of DD-heptoglycan- and Le antigen- producing H. pylori strains.
An FPGA-oriented HW/SW Codesign of Lucy-Richardson Deconvolution Algorithm for Hyperspectral Images (2019)

Hyperspectral images acquired during remote sensing are usually corrupted by optical blur and additive noise. This article considers a method to reduce the spatial blur in hyperspectral images by applying the Lucy-Richardson deconvolution algorithm. The algorithm is based on convolution with a point-spread function, which is assumed to be known. The complete algorithm is implemented as a HW/Sw Co-Design between the central processing unit and the programmable logic. The convolution, as a time consuming operation, is accelerated in an FPGA. When compared to the software implementation, a speed-up by a factor of 2.7 is achieved when using the accelerated HW/SW Co-Design implementation. Hyperspectral images synthetically distorted by a known Gaussian blur and an additive noise are used for testing. The images are then restored by applying the Lucy-Richardson deconvolution algorithm on each spectral band.
Area-Efficient Error Protection for Caches (2006)

Due to increasing concern about various errors, current processors adopt error protection mechanisms. Especially, protecting L2/L3 caches incur as much as 12.5% area overhead due to error correcting codes. Considering large L2/L3 caches of current processors, the area overhead is very high. This paper proposes an area-efficient error protection scheme for L2/L3 caches. First, it selectively applies ECC (error correcting code) to only dirty cache lines and other clean cache lines are protected using simple parity check codes. Second, the dirty cache lines are periodically cleaned by exploiting the generational behavior of cache lines. Experimental results show that the cleaning technique effectively reduces the number of dirty cache lines per cycle. The ECCs of this reduced number of dirty cache lines can be maintained in a small storage. Our proposed scheme is shown to reduce the area overhead of a 1MB L2 cache for error protection by 59% for SPEC2000 benchmarks running on a typical four-issue superscalar processor
A History-Based Handover Prediction for LTE Systems (2009)

Handover prediction has been considered an effective technology for improvement of LTE Handover performance. Although not a few techniques have been proposed to achieve this goal including handover preparation based on cross-layer optimization and mobility prediction, the fact is that their gains are not usually so high as their cost. To overcome such weaknesses, this paper proposes a simple handover prediction technique which is based on a novel user mobility model to approximate simulation the laws of user mobility actions. We develop a user mobility database to assist the mobility prediction based on the user mobility history records. The simulation results show that the proposed technique minimizes the number of handovers and lower the ping-pang rate in LTE system.
Parallelogram frameworks and flexible quasicrystals (2021)

The first-order flex space of the bar-joint framework G P of a parallelogram tiling P is determined in terms of an explicit free basis. Applications are given to braced parallelogram frameworks and to quasicrystal frameworks associated with multigrids in the sense of de Bruijn and Beenker. In particular we characterise rigid bracing patterns, identify quasicrystal frameworks with finite dimensional flex spaces, and define a zero mode spectrum.
Satellites Separation Method With Eccentricity and Inclination Vector (2009)

With the rapid increasing of application of geostationary satellites,the limited geostationary source is becoming run out.Collocating several satellites within the same longitude/latitude window is proved to be a good way.Successful separation with eccentricity vector of two Chinese geostationary satellites was achieved in 2003.To meet the different collocation requirement,and compensate the drawbacks of the eccentricity vector separation,this paper investigates the collocation strategy with eccentricity vector and inclination vector,which largely increases the relative separation of satellites.East-West Station Keeping(EWSK) and North-South Station Keeping(NSSK) procedures are discussed in the paper;and the separation constraints and implementation for two Chinese satellites are also given.The simulated minimum distance between the satellites within a period is more than 10 km,and these two Chinese geostationary satellites work in orbit with secure operation.
Quantitative Trait Locus Analysis of Flowering Time in Soybean Using a RFLP Linkage Map. (2000)

Flowering time is one of the most important traits in soybean breeding. To analyze the quantitative trait loci (QTLs) related to flowering time in soybean, we constructed a soybean linkage map using an F2 population derived from a cross between two varieties, Misuzudaizu and Moshidou Gong 503. This linkage map consists of 247 RFLP loci, including 92 markers designed in this study using soybean green leaf-derived cDNA clones together with 4 phenotypic loce, covering a total of 33 linkage groups. Based on the number of days from sowing to first flowering of each F2 plant, we identified three QTLs, FT1, FT2 and FT3, for flowering time. The Moshidou Gong 503 alleles of FT1 and FT3, and the Misuzudaizu FT2 allele reduced the flowering time. These QTLs were remarkably effective and accounted for approximately 88% of the total phenotypic variation in this population, based on the multiple-QTL model. The most effective QTL, FT1, accounted for approximately 70% of the total variation and appeared to correspond to the E1, the locus for flowering time and maturity of the classical genetic map.