gebhart/patrepeval huggingface dataset:
Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins (2016)

Microbial pathogens may express a wide range of carbohydrate-specific adhesion proteins that mediate adherence to host tissues. Pathogen attachment to host cells is achieved through the binding of these lectin-like adhesins to glycans on human glycoproteins. In only a few cases have the human receptors of pathogenic adhesins been described. We developed a new strategy to predict these interacting receptors. Therefore, we developed a novel LGI network that would allow the mapping of potential adhesin binding receptors in the host with prioritization, based on the experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins (bacterial uroepithelial FimH from E. coli and fungal Epa and Als adhesins from C. glabrata and C. albicans) were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with human-pathogenic viruses and to discover whether FimH adhesin has anti-HIV activity.
Field emission from amorphous carbon and silicon-carbon films, prepared by VHF CVD (2002)

The aim of this work was to study field emission from carbon and silicon-carbon films prepared by Very High Frequency Chemical Vapour Deposition (VHF CVD). The films were prepared by capacitive discharge at a frequency f=58 MHz from argon-methane, hexane, hexane-hydrogen and hexane-silane-hydrogen mixtures on substrates of silicon, quartz and titanium-coated ceramics at temperatures of 200-250/spl deg/C. The films were characterised by AFM, Raman spectroscopy and conductivity measurements. Field electron emission was measured for an anode-to-cathode distance of 40 micron. Scanning secondary electron emission microscopy (SSEEM) measurements over sample area were performed before and after field emission measurements.
Proximal Sequences of the Aldolase A Fast Muscle-specific Promoter Direct Nerve- and Activity-dependent Expression in Transgenic Mice (1998)

Muscle activity is known to modulate the muscle fiber phenotype. Changes in muscle activity (normal or experimentally induced) lead to modifications of the expression status of several muscle-specific genes. However, the transcription regulatory elements involved in the adaptative response are mainly unknown. The aldolase A muscle-specific promoter, pM, is expressed in adult fast twitch muscle with a preferential expression in fast glycolytic-2B fibers. Its activity is induced during postnatal muscle maturation, suggesting a role of nerve and/or muscle activity. Indeed, denervation of gastrocnemius in newborn mice prevented the activation of the promoter in this muscle, despite the nerve-independent formation of 2B fibers. Although the nerve was necessary for pM onset during development, denervating the gastrocnemius in adults had only mild effects on pM activity. By contrast, a transgene including the pM proximal regulatory sequences that are sufficient to reproduce the 2B fiber-specific expression of the endogenous promoter was shown to be highly sensitive to both neonatal and adult denervation. Transgenes containing muscle-specific pM proximal promoter elements were used to delineate the regulatory elements involved in this response to innervation and changes in the contractile activity pattern. Nerve- and activity-dependent elements could be localized in the 130-base pair-long proximal promoter region of the human aldolase A gene.
New passive perfusion PTCA catheter (1990)

Percutaneous coronary angioplasty with a new passive perfusion balloon catheter was compared to a standard angioplasty balloon catheter during prolonged balloon inflations in miniature swine. Inflations with the passive perfusion balloon were alternated with a standard balloon with the initial balloon chosen randomly in 24 coronary arteries. End-points for terminating the balloon inflation were the appearance of 2 mm of ST segment deviation from baseline on the electrocardiogram, the occurrence of ventricular fibrillation, or 30 min of balloon inflation. During balloon inflation contrast injections were performed through the guiding catheter and flow distal to the balloon was graded 0-3 using the TIMI scale. The average (+/- SD) inflation time for the standard balloon was 3.1 +/- 2.2 minutes and for the perfusion balloon was 27.2 +/- 4.8 min (P less than 0.001). Electrocardiographic evidence of 2 mm of ST segment deviation from baseline was seen during 11/13 inflations with the standard balloon and in 3/11 balloon inflations with the perfusion balloon. Ventricular fibrillation occurred during 2/13 of the standard balloon inflations and in none during passive balloon inflations. Distal contrast flow during passive balloon inflations averaged 2.7 +/- 0.5 (TIMI scale 0-3) and was absent during inflations with the standard balloon. The perfusion balloon allowed prolonged inflations with excellent distal flow when compared to the standard balloon.(ABSTRACT TRUNCATED AT 250 WORDS)
A Multiple Regression-Enhanced Convolution Estimator for the Density of a Response Variable in the Presence of Auxiliary Information (2021)

In this paper we propose a convolution estimator for estimating the density of a response variable that employs an underlying multiple regression framework to enhance the accuracy of the estimates through the incorporation of auxiliary information. Suppose we have a sample of $N$ observations of a response variable and an associated set of covariates, along with an additional auxiliary sample featuring $M$ observations of the covariates only. We prove that the mean square error of the multiple regression-enhanced estimator converges as $O(N^{-1})$, and additionally, for a large fixed $N$, the mean square error converges as $O(M^{-4/5})$ before eventually tailing off as a saturation point is reached. Thus, while the incorporation of auxiliary covariate information isn't quite as effective as incorporating more complete case information, it nevertheless allows for significant improvements in accuracy. In contrast to convolution estimators based on the Nadaraya-Watson estimator for a nonlinear regression model, the convolution estimator proposed herein utilizes the ordinary least squares estimator for a multiple linear regression model. While this type of underlying estimator is not suited to strongly nonlinear data, its strength lies in the fact that it allows the multiple regression-enhanced convolution estimator to provide better performance on data that is generally linear or well fit by low order polynomials, since the ordinary least squares estimator estimator does not suffer from the curse of dimensionality and does not require one to choose hyperparameters. The estimator proposed in this paper is particularly useful estimating the density of a response variable that is challenging to measure, while being in possession of a large amount of auxiliary information. In fact, an application of this type from the field of ophthalmology motivated our work in this paper.
Phytotherapeutic activity of curcumol: Isolation, GC–MS identification, and assessing potentials against acute and subchronic hyperglycemia, tactile allodynia, and hyperalgesia (2015)

Curcumol, a natural metabolite with a good safety-profile, showed results comparable with tramadol in reversing diabetes-induced tactile allodynia and hyperalgesia.
Redox-Controlled Size-Selective Fabrication of Nanostructured Transition Metal Colloids (1999)

Nanostructured transition metal clusters and colloids have various potential applications, their properties depending on the particle size, which ranges from 1 to 10 nm. Here is described a new way to prepare transition metal colloids size-selectively by simply varying the redox properties of a particular class of reductants, i.e. by varying the carboxylate anion according to the pKa value of the corresponding carboxylic acid. The method is applied here to a large range of systems and requires no complicated separation or purification procedures.
High-density InAs/GaAs1−xSbx quantum-dot structures grown by molecular beam epitaxy for use in intermediate band solar cells (2016)

InAs quantum-dot structures were grown using a GaAs1−xSbx matrix on a GaAs(001) substrate. The use of GaAs1−xSbx for the buffer and cap layers effectively suppressed coalescence between dots and significantly increased the dot density. The highest density (∼3.5 × 1011/cm2) was obtained for a nominal 3.0 monolayer deposition of InAs with an Sb composition of x = 13–14% in the GaAs1−xSbx matrix. When the Sb composition was increased to 18%, the resulting large photoluminescent red shift (∼90 meV) indicated the release of compressive strain inside the quantum dots. For x &amp;gt; 13%, we observed a significant decrease in photoluminescence intensity and an increase in the carrier lifetime (≥4.0 ns). This is attributed to the type-II band alignment between the quantum dots and matrix material.
Molecular Engineering of Side Chain Liquid Crystalline Polymers by Living Polymerizations (1998)

The prelims comprise: Introduction ‘Living’ Polymerizations used to Synthesize Side Chain Liquid Crystalline Polymers Structure/Property Correlations Determined using ‘Living’ Polymerizations Chain Copolymerizations Other Factors Controlling the Thermotropic Behavior of SCLCPs as Studied using Living Polymerizations: Induction of Smectic Layering using Immiscible Components The Future
Accelerated Monte Carlo for Kullback-Leibler divergence between Gaussian mixture models (2008)

Kullback Leibler (KL) divergence is widely used as a measure of dissimilarity between two probability distributions; however, the required integral is not tractable for gaussian mixture models (GMMs), and naive Monte-Carlo sampling methods can be expensive. Our work aims to improve the estimation of KL divergence for GMMs by sampling methods. We show how to accelerate Monte-Carlo sampling using variational approximations of the KL divergence. To this end we employ two different methodologies, control variates, and importance sampling. With control variates we use sampling to estimate the difference between the variational approximation and the the unknown KL divergence. With importance sampling, we estimate the KL divergence directly, using a sampling distribution derived from the variational approximation. We show that with these techniques we can achieve improvements in accuracy equivalent to using a factor of 30 times more samples.
On the Performance of Polynomial-time CLIQUE Algorithms on Very Large Graphs (1994)

Abstract The performance of a randomized version of the subgraph-exclusion algorithm (called Ramsey) for CLIQUE by Boppana and Halld\''{o}rsson is studied on very large graphs. We compare the performance of this algorithm with the performance of two common heuristic algorithms, the greedy heuristic and a version of simulated annealing. These algorithms are tested on graphs with up to 10,000 vertices on a workstation and graphs as large as 70,000 vertices on a Connection Machine. Our implementations establish the ability to run clique approximation algorithms on very large graphs. We test our implementations on a variety of different graphs. Our conclusions indicate that on randomly generated graphs minor changes to the distribution can cause dramatic changes in the performance of the heuristic algorithms. The Ramsey algorithm, while not as good as the others for the most common distributions, seems more robust and provides a more even overall performance. In general, and especially on deterministically generated graphs, a combination of simulated annealing with either the Ramsey algorithm or the greedy heuristic seems to perform best. This combined algorithm works particularly well on large Keller and Hamming graphs and has a competitive overall performance on the DIMACS benchmark graphs.
The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5 (2022)

Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.
OPTICS OF THE FERMILAB ELECTRON COOLER (2004)

Antiproton electron cooling is a key part of the Run II upgrade plan at Fermilab [1]. A unique parameter of this project is its energy (the relativistic factor is 9.5), which is much higher than for conventional coolers, and requires original solutions for the electron optics.
A compact size 12-Port Combiner/Splitter (2013)

A compact size 12-Port Power Combiner/Splitter is designed and fabricated for 2.45 GHz operation. The combiner provides measured isolation between its ports of at least 22.5 dB and an amplitude imbalance of less than 1 dB. The combiner is fabricated on an FR-4 substrate with 0.8 mm thickness. The total size of the board is 78 × 61 × 0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The phase imbalance due to the internal IC phase imbalance was minimized by more than 30% via careful PCB design and phase compensation.
3094 Production of Engineered Cardiac Tissue for Disease Modeling (2019)

OBJECTIVES/SPECIFIC AIMS: Cardiovascular diseases (CVD) is the leading cause of death worldwide in both men and women due to lack of cardiac regeneration after disease or damaged is caused. There are many challenges to studying CVD since native cardiomyocytes cannot be cultured in vitro. With the advancements in biomaterial and pluripotent stem cells research, scientists are now able to produce engineered cardiac tissue models in vitro that mimic the native myocardium. This study shows our methods for producing engineered cardiac tissue with potential applications in cardiac regeneration, disease modeling, and scalable production. METHODS/STUDY POPULATION: In this study, human induced pluripotent stem cells (hiPSCs) were combined with two different photocrosslinkable hybrid biomaterials, poly (ethylene)- glycol fibrinogen (PF) and gelatin methacrylate (GelMa), in various tissue geometries to form 3D human engineered cardiac tissues (3D-hECTs). To study tissue growth and contraction, image and video analysis was performed at specific timepoints. To analyze differentiation efficiency and cell population, flow cytometry was performed using cardiac markers. To evaluate gene expression, qPCR was performed using pluripotency and cardiac specific primers. RESULTS/ANTICIPATED RESULTS: Direct cardiac differentiation of encapsulated hiPSCs resulted in synchronously contracting 3D-hECTs in both biomaterials and all tissue geometries. Spontaneous contractions started on Day 7 and increased in velocity, frequency, and synchronicity over time. 3D-hECTs had high cell viability with &gt; 70% of cells positive for cardiac markers. Engineered tissues showed appropriate temporal changes in gene expression over time with pluripotency gene expression decreasing and cardiac gene expression increasing. DISCUSSION/SIGNIFICANCE OF IMPACT: This study shows the potential for direct differentiation of encapsulated hiPSCs to produce physiologically relevant engineered cardiac tissues. Resulting 3D-hECTS showed features of mature myocardium with appropriate cardiomyocyte populations, mechanical motion, and gene expression. Using this platform, we are able to produce engineered cardiac tissue in a variety of biomaterials and tissue geometries to study new therapeutics, mechanism of disease, and scalable tissue culture.
Enhancing Zeolite Performance by Catalyst Shaping in a Mesoscale Continuous‐Flow Diels–Alder Process (2018)

In contrast to most lab-scale batch procedures, a continuous-flow implementation requires a thorough consideration of the solid catalyst design. In a previous study, irregular zeolite pellets were applied in a miniaturized continuous-flow reactor for the Diels-Alder reaction in the construction of norbornene scaffolds. After having faced the challenges of continuous operation, the aim of this study is to exploit catalyst structuring. To this end, microspheres with high uniformity and various sphere diameters were synthesized according to the vibrational droplet coagulation method. The influence of the use of these novel zeolite shapes in a mesoscale continuous-flow Diels-Alder process of cyclopentadiene and methyl acrylate is discussed. An impressive enhancement of catalyst lifetime is demonstrated, as even after a doubled process time of 14 h, the microspheres still exceeded the conversion after 7 h when using zeolite pellets by 30 %. A dual reason is found for this beneficial impact of catalyst shaping. The significant improvement in catalyst longevity can be attributed to the interplay of the chemical composition and the porosity structure of the microspheres.
A search for Higgs boson pair production in the bbtautau final state in proton-proton collisions at sqrt(s) = 8 TeV (2017)

Results are presented from a search for production of Higgs boson pairs (HH) where one boson decays to a pair of b quarks and the other to a tau lepton pair. This work is based on proton-proton collision data collected by the CMS experiment at sqrt(s) = 8 TeV, corresponding to an integrated luminosity of 18.3 inverse femtobarns. Resonant and non-resonant modes of HH production have been probed and no significant excess relative to the background-only hypotheses has been found in either mode. Upper limits on cross sections of the two HH production modes have been set. The results have been combined with previously published searches at sqrt(s) = 8 TeV, in decay modes to two photons and two b quarks, as well as to four b quarks, which also show no evidence for a signal. Limits from the combination have been set on resonant HH production by an unknown particle X in the mass range m[X] = 300 GeV to m[X] = 1000 GeV. For resonant production of spin 0 (spin 2) particles, the observed 95% CL upper limit is 1.13 pb (1.09 pb) at m[X] = 300 GeV and to 21 fb (18 fb) at m[X] = 1000 GeV. For non-resonant HH production, a limit of 43 times the rate predicted by the standard model has been set.
A decreased capacity of hepatic growth hormone (GH) receptors and failure of thyrotrophin-releasing hormone to stimulate the peripheral conversion of thyroxine into triiodothyronine in sex-linked dwarf broiler hens (1989)

The effect of two different doses of thyrotrophic releasing hormone (TRH) upon the plasma levels of growth (GH) and thyroid hormones in both sex-linked dwarf (dw) and normal (Dw) broiler hens was determined. In normal hens, 1.5 and 24 microg TRH/kg increased the GH plasma concentrations after 15 min. Plasma concentrations of T3 increased significantly 1 h after TRH injection, whereas T4 concentration decreased after 2 following injection of 24 microg/kg TRH. In dwarf hens both doses of TRH increased the plasma concentrations of GH and the GH response lasted longer. However, TRH was ineffective in raising T3 and T4 levels. Saline-injected dwarf birds showed no differences in plasma T4 and T3 levels in comparison with normal hens. A smaller number of hepatic cGH receptors was found in dwarf hens, whereas the affinity of the hepatic GH receptor was not influenced by the genotype. It is concluded that the sex-linked dwarf broiler hen is unable to respond to a TRH-induced GH stimulus probably because of a deficiency in hepatic GH receptors resulting in a failure to stimulate the T4 to T3 converting activity.
[Degradation of Pentachlorophenol by Fulvic Acid in a Municipal Solid Waste Landfill]. (2018)

The structural composition and functional group changes in fulvic acid (FA) at various landfills were studied using ultraviolet and infrared spectroscopy. The electron transfer ability of FA and its ability to degrade pentachlorophenol (PCP) were also studied considering the various landfills. The results showed that the use of MR-1 as an electron donor and the simultaneous addition of fulvic acid in different stages as an electron shuttle can significantly increase the degradation rate of PCP, leading it beyond 80%. Due to the different redox properties of fulvic acid at the different landfill stages, the degradation of PCP has different reduction conversion abilities. Landfill fulvic acid is able to reduce and transform PCP because of its electron transfer ability. These functions are all conducive to promoting PCP reductive dechlorination.
Pituitary Disease in MEN Type 1 (MEN1): Data from the France-Belgium MEN1 Multicenter Study (2002)

To date, data on pituitary adenomas in MEN type 1 (MEN1) still have to be evaluated. We analyzed the data of a large series of 324 MEN1 patients from a French and Belgian multicenter study. Data on pituitary disease were compared with those from 110 non-MEN1 patients with pituitary adenomas, matched for age, year of diagnosis, and follow-up period. Genetic analysis of the MEN1 gene was performed in 197 of the MEN1 patients. In our MEN1 series, pituitary disease occurred in 136 of 324 (42%), less frequently than hyperparathyroidism (95%, P < 0.001) and endocrine enteropancreatic tumors (54%, P < 0.01). Mean age of onset of pituitary tumors was 38.0+/-15.3 yr (range, 12-83 yr). Pituitary disease was associated with hyperparathyroidism in 90% of cases, with enteropancreatic tumors in 47%, with adrenal tumors in 16%, and with thoracic neuroendocrine tumors in 4%. Pituitary disease was the initial lesion of MEN1 in 17% of all MEN1 patients. MEN1 pituitary adenomas were significantly more frequent in women than in men (50% vs. 31%, P < 0.001). Among the 136 pituitary adenomas, there were 85 prolactinomas and 12 GH-secreting, 6 ACTH-secreting, 13 cosecreting, and 20 nonsecreting tumors. Eighty-five percent of MEN1-related pituitary lesions were macroadenomas (vs. 42% in non-MEN1 patients, P < 0.001), including 32% of invasive cases. Among secreting adenomas, hormonal hypersecretion was normalized, after treatment, in only 42% (vs. 90% in non-MEN1 patients, P < 0.001), with a median follow-up of 11.4 yr. No correlation was found between the type of MEN1 germ-line mutation and the presence or absence of pituitary adenoma. Our study, based on a large group of MEN1 patients, shows that pituitary adenomas occur in 42% of the cases and are characterized by a larger size and a more aggressive presentation than without MEN1.