gebhart/patrepeval huggingface dataset:
Altered Proximal T‐Cell Receptor Signalling Events in Mouse CD4<sup>+</sup> T Cells in the Presence of Anti‐CD4 Monoclonal Antibodies: Evidence for Reduced Phosphorylation of Zap‐70 and LAT (2003)

Anti-CD4 monoclonal antibodies are potential therapeutic agents for the prevention of autoimmune disease and treatment of rejection after organ transplantation and are capable of both restoring tolerance to self-antigens and inducing tolerance to antigens introduced under the cover of the antibody therapy in vivo. Tolerance to donor alloantigens can be induced in vivo by administering donor alloantigen in combination with either depleting (YTA 3.1) or nondepleting (YTS 177) anti-CD4, 28 days before heart transplantation in the mouse. The effect of anti-CD4 on proximal T-cell receptor (TCR) signalling pathways and proliferation was investigated in vitro and in vivo in the presence and absence of YTA 3.1 or YTS 177. Anti-CD4 was found to perturb proximal signalling events upon TCR/CD3 ligation, resulting in reduced tyrosine phosphorylation of Zap-70 and LAT (linker for activation of T cells) and reduced association of tyrosine-phosphorylated LAT with lck. This ultimately resulted in severely reduced proliferation of the responding CD4+ T cells. The signalling profile of the anti-CD4-treated cells resembled that of anergic T cells. This could be a result of a common mechanism involving perturbation in the formation of the central supramolecular activation cluster of the immunological synapse by impaired recruitment of CD4 and CD28, thereby resulting in severely reduced lck activation.
Chicken FK506-binding protein, FKBP65, a member of the FKBP family of peptidylprolyl cis–trans isomerases, is only partially inhibited by FK506 (1998)

The chicken FK506-binding protein FKBP65, a peptidylprolyl cis-trans isomerase, is a rough endoplasmic reticulum protein that contains four domains homologous to FKBP13, another rough endoplasmic reticulum PPIase. Analytical ultracentrifugation suggests that in FKBP65 these four domains are arranged in a linear extended structure with a length of about 26 nm and a diameter of about 3 nm. All four domains are therefore expected to be accessible to substrates. The specificity of FKBP65 towards a number of peptide substrates was determined. The specific activity of FKBP65 is generally lower than that of FKBP12 when expressed as a per domain activity. The substrate specificity of FKBP65 also differs from that of FKBP12. Inhibition studies show that only one of the four domains can be inhibited by FK506, a powerful inhibitor of all other known FKBPs. Furthermore, the same domain seems to be susceptible to inhibition by cyclosporin A. No other FKBPs were shown to be inhibited by cyclosporin A. It is also shown that FKBP65 can catalyse the re-folding of type III collagen in vitro with a kcat/Km = 4.3 x 10(3) M-1.s-1.
Exposing errors related to weak memory in GPU applications (2016)

We present the systematic design of a testing environment that uses stressing and fuzzing to reveal errors in GPU applications that arise due to weak memory effects. We evaluate our approach on seven GPUs spanning three Nvidia architectures, across ten CUDA applications that use fine-grained concurrency. Our results show that applications that rarely or never exhibit errors related to weak memory when executed natively can readily exhibit these errors when executed in our testing environment. Our testing environment also provides a means to help identify the root causes of such errors, and automatically suggests how to insert fences that harden an application against weak memory bugs. To understand the cost of GPU fences, we benchmark applications with fences provided by the hardening strategy as well as a more conservative, sound fencing strategy.
Detection and characterization of low abundance cellular proteins that specifically increase upon loss of the metastatic phenotype (1993)

Human epidermoid carcinoma (HEp-3) cells are highly tumorigenic and metastatic in vivo, but their metastatic phenotype is progressively and uniquely lost upon serial passage in vitro. The nonmetastatic phenotype is fully reversible to the highly metastatic state when HEp-3 cells are passaged back in vivo. To study the complex process of metastasis and its possible negative regulation by specific gene products, the expression of specific proteins between the highly metastatic and nonmetastatic HEp-3 cells was investigated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and subsequent computer assisted analyses. Concomitant with the in vitro loss of metastatic potential of HEp-3 cells is the elevated expression of a subset of low abundance proteins detectable in 2D-PAGE but not apparent in high resolution one dimensional PAGE. When the HEp-3 cells revert to the metastatic state, the expression of these proteins declines. The increased cellular abundance of four distinct proteins directly correlates with the loss of the metastatic phenotype: two of the four proteins are associated with isolated cellular membranes (36kD, pI 5.7; 22kDa, pI 5.6), one protein fractionates with the cytoplasm (65kD, pI 6.2), and one protein is enriched in the nuclei fraction (32kD, pI 5.8). These data indicate that computer-assisted analysis of highly sensitive, large-format, 2D-PAGE can be used to identify specific proteins in subcellular compartments that are candidates for negative regulators of the metastatic process.
Maternal inflammation at midgestation impairs subsequent fetal myoblast function and skeletal muscle growth in rats, resulting in intrauterine growth restriction at term1 (2019)

Maternal inflammation induces intrauterine growth restriction (MI-IUGR) of the fetus, which compromises metabolic health in human offspring and reduces value in livestock. The objective of this study was to determine the effect of maternal inflammation at midgestation on fetal skeletal muscle growth and myoblast profiles at term. Pregnant Sprague-Dawley rats were injected daily with bacterial endotoxin (MI-IUGR) or saline (controls) from the 9th to the 11th day of gestational age (dGA; term = 21 dGA). At necropsy on dGA 20, average fetal mass and upper hindlimb cross-sectional areas were reduced (<i>P</i> < 0.05) in MI-IUGR fetuses compared with controls. MyoD<sup>+</sup> and myf5<sup>+</sup> myoblasts were less abundant (<i>P</i> < 0.05), and myogenin<sup>+</sup> myoblasts were more abundant (<i>P</i> < 0.05) in MI-IUGR hindlimb skeletal muscle compared with controls, indicating precocious myoblast differentiation. Type I and Type II hindlimb muscle fibers were smaller (<i>P</i> < 0.05) in MI-IUGR fetuses than in controls, but fiber type proportions did not differ between experimental groups. Fetal blood plasma TNFα concentrations were below detectable amounts in both experimental groups, but skeletal muscle gene expression for the cytokine receptors <i>TNFR1</i>, <i>IL6R</i>, and <i>FN14</i> was greater (<i>P</i> < 0.05) in MI-IUGR fetuses than controls, perhaps indicating enhanced sensitivity to these cytokines. Maternal blood glucose concentrations at term did not differ between experimental groups, but MI-IUGR fetal blood contained less (<i>P</i> < 0.05) glucose, cholesterol, and triglycerides. Fetal-to-maternal blood glucose ratios were also reduced (<i>P</i> < 0.05), which is indicative of placental insufficiency. Indicators of protein catabolism, including blood plasma urea nitrogen and creatine kinase, were greater (<i>P</i> < 0.05) in MI-IUGR fetuses than in controls. From these findings, we conclude that maternal inflammation at midgestation causes muscle-centric fetal programming that impairs myoblast function, increases protein catabolism, and reduces skeletal muscle growth near term. Fetal muscle sensitivity to inflammatory cytokines appeared to be enhanced after maternal inflammation, which may represent a mechanistic target for improving these outcomes in MI-IUGR fetuses.
Query by humming of midi and audio using locality sensitive hashing (2008)

This paper proposes a query by humming method based on locality sensitive hashing (LSH). The method constructs an index of melodic fragments by extracting pitch vectors from a database of melodies. In retrieval, the method automatically transcribes a sung query into notes and then extracts pitch vectors similarly to the index construction. For each query pitch vector, the method searches for similar melodic fragments in the database to obtain a list of candidate melodies. This is performed efficiently by using LSH. The candidate melodies are ranked by their distance to the entire query and returned to the user. In our experiments, the method achieved mean reciprocal rank of 0.885 for 2797 queries when searching from a database of 6030 MIDI melodies. To retrieve audio signals, we apply an automatic melody transcription method to construct the melody database directly from music recordings and report the corresponding retrieval results.
A Generalized Additional Boundary Condition for Mushroom-Type and Bed-of-Nails-Type Wire Media (2010)

An additional boundary condition (ABC) for mushroom or bed-of-nails metamaterials is generalized for thin 3-D or 2-D material patches or ground planes. It is shown that the usual ABC necessary for the homogenization of these wire-medium metamaterials fails for thin imperfect conductors, and a generalization is presented based on charge conservation. The new ABC leads to results that are in good agreement with full-wave simulations.
Fast placement-dependent full chip thermal simulation (2002)

A general purpose semiconductor device/process simulator, PROPHET, has been adapted for full chip thermal analysis and is capable of quickly (/spl sim/1 minute CPU time) assessing the impact of functional block placement on chip temperature distribution. The key to fast simulation is a new algorithm which maps the heat generation of functional blocks to a coarse mesh while maintaining conservation of heat generating sources. Design of two high-performance CPU chips based on bulk CMOS and SOI technologies, with total power consumption of 100 and 60 watts, respectively, has been evaluated for thermal performance using this approach. Excellent results have been achieved in terms of benchmarked accuracy and computational efficiency. Up to seven interconnect layers have been included in the simulation; effects of packaging are modeled using two capping thermally resistive layers on top and bottom of the chip. Considering the extremely non-uniform nature of interconnect/interleaving-insulating layers, anisotropic thermal conductivity is a critical factor in modeling thermal properties and has been implemented in the simulator. The potential benefit of using pure silicon (Si-28), which has a higher thermal conductivity than that of natural silicon (1.6 times as big at the room temperature), in reducing the peak chip temperature has also been studied. It is shown that with a power consumption level of 100 watts, the peak temperature can be lowered by about 10% (from 136 to 123/spl deg/C).
Surface Anatomy of the Face in Down's Syndrome: Linear and Angular Measurements in the Craniofacial Regions (2001)

Measurements (23 projective linear, 2 angular) taken in the 6 craniofacial regions of 127 patients with Down's syndrome showed that 63.1% (1,836 of 2,908) were within normal limits and 36.9% (1,072) were outside them. Abnormal measurements were subnormal in 90.8% (973) and supernormal in 9.2% (99). All statistical summaries were based on z scores (adjusting for age and sex differences) classified into a small number of ranges to yield a simplified frequency distribution for each measurement. The purpose of the study was to identify the measurements closest to normal and those indicating the most severe degrees of sub- or supernormality. Approximately a quarter of normal measurements were classified as optimal, and half the subnormal or supernormal measurements were classified as severe. Intercanthal width had the highest frequency of optimal measurements (93.7%, 119 of 127), head circumference the smallest (28.6%, 36 of 126). Knowledge of the frequency of extreme abnormalities in the craniofacial regions will help during visual examination of patients with Down's syndrome. This study found the highest percentage of severely subnormal measurements in the orbital region (57.8%, 74 of 128) and the smallest in the labio-oral region (32.7%, 16 of 49). The measurement with the highest proportion of severely subnormal to all subnormal values was the palpebral fissure length (68%, 51 of 75), and the nose width had the smallest proportion (14.3%, 1 of 7).
Cellular and humoral responses of Brucella abortus-infected bovine fetuses (1984)

Fifty-nine bovine fetuses naturally and experimentally infected with Brucella abortus were studied. Lymphoid hyperplasia in multiple lymph nodes, lymphoid depletion in the thymic cortex, adrenal cortical hyperplasia, and disseminated inflammatory foci composed mainly of large mononuclear leukocytes were present in infected fetuses. Histopathologic changes in naturally infected fetuses were indistinguishable from those infected fetuses inoculated in utero. Fetuses inoculated with 1.0 X 10(3) to 1.0 X 10(5) colony-forming units of strain 2308 B abortus were aborted on postinoculation day (PID) 7 to 19. Fetuses obtained by PID 9 and 10 had increased immunoglobulin concentrations and antibody. Increased cortisol values were present in fetuses obtained as early as PID 6. The initial fetal inflammatory response was composed of large mononuclear leukocytes. In fetuses obtained by PID 9 to 10, moderate numbers of neutrophils mixed with mononuclear leukocytes were present in the inflammatory foci. This shift in the initial inflammatory reaction coincided with the appearance of agglutinating antibody.
Crossover between the ballistic and diffusive regime of the spin-conductance and giant magnetoresistance in magnetic multilayered nanostructures (1999)

We analyze the interplay between disorder and band structure in current perpendicular to the planes giant magnetoresistance (GMR). We consider finite magnetic multilayers attached to pure crystalline leads, described by a tight-binding simple cubic two-band model $(s\ensuremath{-}d).$ Several models of disorder are considered, including random on-site potentials, lattice distortions, impurities, vacancies, and cross-section fluctuations. Magnetotransport properties are calculated in the zero-temperature zero-bias limit, within the Landauer-B\"uttiker formalism. Using a very efficient numerical scattering technique, we are able to perform simulations, over large length scales, and to investigate spin transport in the ballistic, diffusive, and localized regimes, as well as the crossover between them. The competition between disorder-induced mean-free-path reduction and disorder-induced spin asymmetry enhancement of the conductance highlights several different regimes of GMR.
Singlet oxygen energy illumination during ischemia preserves high-energy phosphates in a concordant heart xenotransplantation model (2003)

Introduction: We have previously demonstrated that illumination with singlet oxygen energy (SOE) could reduce the generation of reactive oxygen species (ROS) in vitro. We have here investigated whether SOE illumination induced during ischemia could preserve high-energy-phosphate (HEP) levels in an in vivo xenotransplantation heart model. Material and methods: Cervical transplantations between inbred Lewis (RT1 1 ) rats (recipients) and Golden-Syrian hamsters were performed and followed with daily in vivo 31 Phosphorus Magnetic Resonance Spectroscopy ( 31 P MRS) over 4 days. The phosphocreatine (PCr) to beta adenosine triphosphate (β-ATP) ratio was calculated. The recipients were randomized to any of 2 groups (grp.): illumination of the NaC1 and the grafts before reperfusion (r.p.) (grp. A, n = 7) illumination of the NaC1 used during explantation (grp. B, n = 8). SOE was produced as photons at λ 634 nm with the Valkion® equipment, and the grafts were illuminated for 10 min before the onset of reperfusion. The cold ischemia time (+4°C) was standardized to 30 min. Results: The PCr/β-ATP ratio of the illuminated grafts on day 1 was 39% higher (p = 0.002 vs. Grp. 1; 1.99 ± 0.12 vs. 1.43 ± 0.08; mean ± SEM) and similar to the baseline values in situ, 1.80 ± 0.08. Conclusions: We demonstrate for the first time in vivo that SOE illumination, when induced in xenografts before r.p., can preserve the energetic status of concordant hamster grafts and counteract the metabolic effects of short-term ischemia. It remains to be investigated whether reduction of early ischemic events in experimental xenotransplantation, for instance with SOE, has any impact on the survival and future development of chronic rejection in immunosuppressed recipients of xenografts.
Targeting the Tie2–αvβ3 integrin axis with bi-specific reagents for the inhibition of angiogenesis (2018)

Collectively, this study-the first to describe inhibitors targeting all the known functions resulting from Tie2/integrin α<sub>v</sub>β<sub>3</sub> cross-talk-has created new tools for studying Tie2- and integrin α<sub>v</sub>β<sub>3</sub>-dependent molecular pathways and provides the basis for the rational and combinatorial engineering of ligand-Tie2 and ligand-integrin α<sub>v</sub>β<sub>3</sub> receptor interactions. Given the roles of these pathways in cancer angiogenesis and metastasis, this proof of principle study paves the route to create novel Tie2/integrin α<sub>v</sub>β<sub>3</sub>-targeting proteins for clinical use as imaging and therapeutic agents.
Absorption saturation nonlinearity in InGaAs/InP p-i-n photodiodes (2003)

The agreement between the measured nonlinear response and the absorption saturation simulation for different absorber thickness provides strong evidence of an absorption-saturation photodiode nonlinearity. We have improved the linearity of a photonic ADC by developing large-area, thick photodiodes.
Supercritical Fluid Processing of Nutritionally Functional Lipids (2019)

A synergism exists between the development of healthy foods and the use of critical fluid (CF) technology in their production. This chapter proposes the application of CF technology from the perspective of yielding a “healthful” lipid-containing product. It presents how the proper application of CF in their super- and subcritical states can achieve the following: reduce the toxicity of a lipid extract; adjust beneficially the composition of lipid mixture; enrich nutritionally beneficial ingredients, that is, nutraceuticals; and provide a better lipid delivery technology. Hydrogenation in the presence of supercritical fluid (SF) attracted considerable attention recently for both the production of food and industrial lipid products. The application of SF and similar media for the processing of agricultural or natural products traditionally focused on the extraction mode utilizing CO2. The alteration in lipid content using CF is usually accomplished by employing supercritical fluid fractionation and/or supercritical fluid media, or occasionally supercritical fluid extraction.
Examination of Particle Size Distribution of Homogeneous and Conventional Diesel Combustion (2001)

<div class="htmlview paragraph">This paper reports an investigation of the particle size distribution of different homogeneous Diesel combustion systems in comparison to conventional diffusion controlled combustion system. The influence of different operating parameters such as load or degree of homogeneity on the number of particles and the particle size distribution, determined with a Scanning Mobility Particle Sizer, is pointed out.</div> <div class="htmlview paragraph">The homogeneous combustion of Diesel fuel possesses a large potential concerning NO<sub>X</sub>, soot and particle mass, but still a high number of nanoparticles is discharged.</div> <div class="htmlview paragraph">Additional experiments are reported, which were carried out to understand the high emission of nanoparticles at low soot combustion better and to determine the chemical composition of the nanoparticles.</div>
Comparative transcriptome and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids (2019)

Abstract Background: Young wheat plants are continuously exposed to insect herbivorous attack. To maintain their fitness, plants have evolved different defense mechanisms, including the biosynthesis of deterrent compounds named benzoxazinoids, and/or trichome formation that provides physical barriers. It is unclear whether both of these mechanisms are equally critical in providing an efficient defense for wheat seedlings against the bird cherry-oat ( Rhopalosiphum padi ) aphid—an economically costly pest in cereal production. Results: In this study, we compared the transcriptomic, metabolomic, chemical, and physical defenses of three selected wheat genotypes to aphid performance. We chose diverse wheat genotypes, two tetraploid wheat genotypes, domesticated durum ‘Svevo’ and wild emmer ‘Zavitan,’ and one hexaploid bread wheat, ‘Chinese Spring.’ The full transcriptomic analysis revealed a major difference between the three genotypes, while the clustering of significantly different genes suggested a higher similarity between the two domesticated than the wild wheat. A pathway enrichment analysis indicated that genes associated with primary metabolism, as well as the pathways associated with defense such as phytohormones and specialized metabolites, were altered between the three genotypes. Measurement of benzoxazinoid levels at the three time-points (11, 15 and 18 days-after-germination) revealed high abundance levels in the two domesticated genotypes, while the levels were very low in the wild emmer wheat. The Chinese Spring showed a more diverse benzoxazinoid (known and putative) composition than the other two genotypes. In contrast to the benzoxazinoid levels, the trichome density was dramatically higher in the wild emmer than in the domesticated wheat. Evaluation of aphid reproduction indicated that the domesticated bread wheat is more resistant than the tetraploid genotypes. Conclusions: We compared the amount of benzoxazinoids, the trichome number, and aphid reproduction at three time-points, as well as performing a transcriptome analysis. Overall, the results suggested that although wheat seedlings possess both chemical and physical defenses, the chemical defense plays a more significant defensive role than the physical barriers.
Reduced Growth Rate of Transplantable Mammary Adenocarcinoma in C3H Mice Fed Eicosa-5,8,11,14-tetraynoic Acid2 (1977)

Female 3-month-old C3H mice were given sc injections of 5-mg pieces of mammary adenocarcinoma and fed a linoleate-containing (15% corn oil) diet in the presence or absence of eicosa-5,8,11,14-tetraynoic acid (TYA), an inhibitor of prostaglandin synthesis. After 6 weeks, the weights of tumors of mice fed the TYA-free linoleate diet were three to five times greater than those of mice fed the TYA-containing linoleate diet. Dietary TYA caused a reduction in the levels of arachidonate and an elevation in the levels of linoleate in mammary tumors and livers. Aspirin, another known inhibitor of prostaglandin synthesis, when added to the linoleate diet, did not affect the tumor size or the composition of fatty acids in the tumors and livers. Thus we concluded that a) the growth of mammary tumors was not related to prostaglandin synthesis but was related to the availability of arachidonate, and b) TYA was an effective inhibitor for the conversion of linoleate to arachidonate.
Effect of General Anesthesia on Neurodevelopmental Abnormalities in Children Undergoing Treatment of Vascular Anomalies With Laser Surgery: A Retrospective Review (2016)

This is the first report on the prevalence of neurodevelopmental disorders in children undergoing multiple laser treatments under general anesthesia. Although the study sample is small, no increased risks when comparing with prevalence rates reported in the literature were noted.