gebhart/patrepeval huggingface dataset:
Introduction of neutralizing immunogenicity index to the rational design of MERS coronavirus subunit vaccines (2016)

Viral subunit vaccines often contain immunodominant non-neutralizing epitopes that divert host immune responses. These epitopes should be eliminated in vaccine design, but there is no reliable method for evaluating an epitope's capacity to elicit neutralizing immune responses. Here we introduce a new concept 'neutralizing immunogenicity index' (NII) to evaluate an epitope's neutralizing immunogenicity. To determine the NII, we mask the epitope with a glycan probe and then assess the epitope's contribution to the vaccine's overall neutralizing immunogenicity. As proof-of-concept, we measure the NII for different epitopes on an immunogen comprised of the receptor-binding domain from MERS coronavirus (MERS-CoV). Further, we design a variant form of this vaccine by masking an epitope that has a negative NII score. This engineered vaccine demonstrates significantly enhanced efficacy in protecting transgenic mice from lethal MERS-CoV challenge. Our study may guide the rational design of highly effective subunit vaccines to combat MERS-CoV and other life-threatening viruses.
Identification of key proteins and pathways in cadmium tolerance of Lactobacillus plantarum strains by proteomic analysis (2017)

Our previous study confirmed the protective potential of Lactobacillus plantarum (L. plantarum) strains in alleviation of cadmium (Cd) toxicity in vivo and demonstrated that the observed protection largely depended on the tolerance of the strains to Cd-induced stress. It was also observed that there were significant intra-species differences in Cd tolerance of L. plantarum strains. In this study, we investigated the mechanism of Cd induced stress response of L. plantarum strains using the isobaric tags for relative and absolute quantitation (iTRAQ) based comparative proteomics. L. plantarum CCFM8610 (strongly resistant to Cd) and L. plantarum CCFM191 (sensitive to Cd) were selected as target strains, and their proteomic profiles in the presence and absence of Cd exposure were compared. We propose that the underlying mechanism of the exceptional Cd tolerance of CCFM8610 may be attributed to the following: (a) a specific energy-conservation survival mode; (b) mild induction of its cellular defense and repair system;
Base Editing: Chemistry on the Genome (2018)

Genome editing methods have commonly relied on the initial introduction of double-stranded DNA breaks (DSBs), resulting in stochastic insertions, deletions, and translocations at the target genomic locus. To achieve gene correction, these methods typically require the introduction of exogenous DNA repair templates and low-efficiency homologous recombination processes. Here I describe the development of base editing, a new approach to genome editing that enables the direct, irreversible conversion of one target DNA base into another in a programmable manner, without requiring double-stranded DNA backbone cleavage or a donor template. Base editors employ single-stranded DNA-specific deaminase enzymes tethered to a catalytically impaired Cas9 protein (dCas9) to directly chemically convert thymines to uracils or adenines to inosines in the genome. These chemoselective genomic modifications efficiently and cleanly result in permanent C•G to T•A or T•A to C•G correction in living cells and organisms. C•G to T•A base editing overview. DNA with a target C (red) at a locus specified by a guide RNA (green) is bound by dCas9 (blue), which mediates local DNA strand separation. Cytidine deamination by a tethered APOBEC1 enzyme (red) converts the single-stranded target C→U. The resulting G:U heteroduplex can be permanently converted to an A:T base pair following DNA replication or DNA repair. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Molecular complexation of curcumin with Eudragit� EPO to enhance the aqueous solubility, stability and bioavailability of curcumin (2016)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
High-Speed Photorefractive Response Capability in Triphenylamine Polymer-Based Composites (2012)

We present here the poly(4-diphenylamino)styrene (PDAS)-based photorefractive composites with a high-speed response time. PDAS was synthesized as a photoconductive polymer and photorefractive polymeric composite (PPC) films by using triphenylamine (TPA) (or ethylcarbazole, ECZ), 4-homopiperidino-2-fluorobenzylidene malononitrile (FDCST), and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) were investigated. The photorefractive quantities of the PDAS-based PPCs were determined by a degenerate four-wave mixing (DFWM) technique. Additionally, the holographic images were recorded through an appropriate PDAS-based PPC. Those holographic images clearly reconstruct the original motion with high-speed quality. The present approach provides a promising candidate for the future application of dynamic holographic displays.
Conduction mechanism in low-resistivity <i>n</i>-type ZnSe prepared by organometallic chemical vapor deposition (1982)

n-type ZnSe layers with a room-temperature resistivity of less than 0.05 Ω cm and mobilities of ∼400 cm2/(V sec) have been grown on (100) GaAs by organometallic chemical vapor deposition (OM-CVD), using triethylaluminum as a dopant. No further treatment after the layer growth is necessary in order to achieve the high electrical conductivity. An analysis of the low-temperature electrical transport data and of the photoluminescence data, however, suggests that the physical properties of the layers differ from those of ZnSe prepared by other methods. Charge transport occurs via impurity-band conduction in the more heavily doped layers and via thermally activated hopping in the more lightly doped layers rather than via thermally activated extrinsic conductivity. The degree of compensation of donors is larger than 0.5. The exact nature of the compensating centers in the material prepared by OM-CVD is uncertain at this point, although the photoluminescence data suggest the presence of Al-VZn complexes.
Negative Refraction and Left-Handed Electromagnetism in Microwave Photonic Crystals (2004)

We demonstrate the negative refraction of microwaves in a metallic photonic crystal prism. The spectral response of the photonic crystal prism, which manifests both positive and negative refraction, is in complete agreement with band-structure calculations and numerical simulations. The validity of Snell's law with a negative refractive index is confirmed experimentally and theoretically. The negative refraction observed corresponds to left-handed electromagnetism that arises due to the dispersion characteristics of waves in a periodic medium. This mechanism for negative refraction is different from that in metamaterials.
Regioregular, Head-to-Tail Coupled Poly(3-alkylthiophenes) Made Easy by the GRIM Method:  Investigation of the Reaction and the Origin of Regioselectivity (2001)

An investigation of the new synthetic method to synthesize regioregular, head-to-tail coupled poly(3-alkylthiophenes) using magnesium−halogen exchange (Grignard metathesis) called the GRIM method is described. Treatment of 2,5-dibromo-3-alkylthiophenes with a variety of alkyl and vinyl Grignard reagents resulted in two metalated, regiochemical isomers, namely, 2-bromo-3-alkyl-5-bromomagnesiothiophene and 2-bromomagnesio-3-alkyl-5-bromothiophene in an 85:15 ratio. This ratio appears to be independent of reaction time, temperature, and Grignard reagent employed. Introduction of a catalytic amount of Ni(dppp)Cl2 to this isomeric mixture afforded poly(3-alkylthiophene) that contained greater than 95% HT−HT couplings (typically 98% HT couplings were seen). The high degree of regioregularity found in the polymer can be explained by a combination of kinetic and thermodynamic effects arising from steric and electronic effects found in the catalytic reaction. A series of reaction investigations led to a general explanation of the origin of regioregularity in polythiophene polymerization reactions. These reactions included kinetic studies and competition experiments.
Optimizing Energy Efficiency Over Energy-Harvesting LTE Cellular Networks (2017)

We consider the problem of downlink scheduling in an LTE network powered by energy harvesting devices. We formulate optimization problems that seek to optimize popular energy efficiency metrics subject to mandatory LTE network constraints along with energy harvesting causality constraints. We identify a key sub-problem pertaining to maximizing the weighted sum rate that is common for all optimization problems that we consider, and is also of independent interest. We show that the latter sub-problem can be reformulated as a constrained submodular set function maximization problem which enables us to design a constant-factor approximation algorithm for maximizing the weighted sum rate. We leverage this algorithm to design approximation algorithms (with provable performance guarantees) for maximizing all considered energy efficiency metrics over an energy harvesting LTE downlink. Our proposed algorithms are simple to implement and offer superior performance.
Enhancing the performances of traditional electron cyclotron resonance ion sources with multiple-discrete-frequency microwave radiation (1998)

The performances of electron cyclotron resonance (ECR) ion sources, in terms of high-charge-state yields and intensities within a particular charge state, can be enhanced by increasing the physical sizes of the ECR zones in relation to the sizes of their plasma volumes. The creation of a large ECR plasma “volume” permits coupling of more power into the plasma, resulting in the heating of a much larger electron population to higher energies, the effect of which is to produce higher charge-state distributions and higher intensities within a particular charge state than possible in present forms of the ECR source. The ECR plasma “volumes” of traditional B-minimum ECR sources can be increased by injecting broadband microwave radiation (multiple-discrete-frequency, variable frequency, or broad-band-width frequency microwave radiation) derived from standard klystron, gyrotron, or traveling-wave-tube (TWT) technologies (frequency domain). To demonstrate that the frequency domain technique can be used to enhance the performance of a traditional B-minimum ECR ion source, comparative studies were made to assess the relative performances of the Oak Ridge National Laboratory Caprice ECR ion source, in terms of multiply charged ion-beam generation capabilities, when excited with high-power, single-frequency, or multiple-discrete-frequency microwave radiation, derived from standard klystron and/or TWT technologies. These studies demonstrate that the charge-state populations for Ar q+ and Xeq+ move toward higher values when excited with two and three discrete-frequency, microwave power compared to those observed when single-frequency microwave power is used. For example, the most probable charge state for Xe is increased by one charge-state unit while the beam intensities for charge states higher than the most probable are increased by factors of ∼3 compared to those observed for single-frequency plasma excitation. The results of these measurements along with details on the modifications to the injection system required to couple the microwave radiation into the plasma volume of the Caprice source will be presented in this report.
Enhanced production of L-sorbose from D-sorbitol by improving the mRNA abundance of sorbitol dehydrogenase in Gluconobacter oxydansWSH-003 (2014)

The artificial poly(A/T) tails could significantly enhance the mRNA abundance of the sldhAB. Immobilized G. oxydans-sldhAB6 cells could further enlarge the positive effect caused by enhanced mRNA abundance of the sldhAB.
Poster (2011)

Large reservoir simulation is computationally challenging. High resolution reservoir models provide necessary realism in heterogeneous reservoirs. Large number of simulations of such models is necessary in reducing uncertainties in reservoir characterizations and creating efficient field development plans. To meet such challenges, Saudi Aramco, the world's leading oil producing company, developed a parallel reservoir simulator, POWERS [1], and built a computing center currently hosting computing power of over 300 teraflops [2]. Both reservoir simulator and computing center are world leaders in the oil industry. In this paper we review some of most innovative HPC works in the oil industry. We review computational characteristics of the POWERS simulator and benchmark results for computations of large reservoir simulation models throughout the past few years. We also share studies to enhance POWERS in various aspects such as GPU usage to solve critical computing blocks, MPI tuning, and reducing the eco footprint of the simulator.
Fabrication of a metallic glass/solder laminate composite (1994)

Metallic glass (or amorphous metal) foils have physical and mechanical properties that make them well suited for many engineering applications. A technique has been developed to assemble a laminate composite material containing metallic glass ribbon which can then be fabricated into several simple bulk geometries (patent pending). The composite consists of layers of metallic glass foil held together by a 2{emdash}5 {mu}m (0.0001{emdash}0.0002 in.) thick layer of solder. This project had several facets: (1) a determination of the solderability of metallic glass ribbons; (2) the fabrication of a suitable solder alloy; and (3) development of a process to manufacture the laminate. Selection of the appropriate solder alloy was based upon the need for adequate strength and the melting properties. An apparatus was constructed to build the laminate by winding the metallic glass alloy in a bath of the modified Pb-In solder. The laminate was found to be extremely strong, both in the form of the full coil as well as in the machined configuration. The metallic glass is very resilient, owing to its amorphous structure. In summary, a process was developed to fabricate a laminate composite comprised of metallic glass foil layers bonded together with a thin film of solder.more » The development sequence included studies which determined the wettability of metallic glass ribbon by solders using conventional fluxes; the fabrication of new solder alloys to meet the wetting and strength constraints required of the laminate; and finally the construction of the assembly equipment and the manufacture of prototype composites.« less
Design for testability for path delay faults in sequential circuits (1993)

We experimentally study the reasons for low coverage of path delay faults in several sequential benchmark circuits. Causes for undetected faults are classified into three categories: (A) Combinationally nonactivated paths, (B) Sequentially nonactivated paths, and (C) Unobservable fault effect. The type A faults can only be made detectable by modifying or resynthesizing the combinational logic as has been discussed by others. We find that almost 80% of sequentially untested faults are in category B. Most are not activated because the two successive states necessary to create a transition and to propagate it through the path cannot be produced in the sequential circuit. We study the partial scan technique in which flipflops are scanned to break cycles and show that a substantial increase in the coverage of path delay faults is possible.
The expression of adipogenic genes is decreased in obesity and diabetes mellitus (2000)

Obesity is strongly correlated with type 2 diabetes mellitus, a common disorder of glucose and lipid metabolism. Although adipocytes are critical in obesity, their role in diabetes has only recently been appreciated. We conducted studies by using DNA microarrays to identify differences in gene expression in adipose tissue from lean, obese, and obese-diabetic mice. The expression level of over 11,000 transcripts was analyzed, and 214 transcripts showed significant differences between lean and obese mice. Surprisingly, the expression of genes normally associated with adipocyte differentiation were down-regulated in obesity. Not all obese individuals will become diabetic; many remain normoglycemic despite profound obesity. Understanding the transition to obesity with concomitant diabetes will provide important clues to the pathogenesis of type 2 diabetes. Therefore, we examined the levels of gene expression in adipose tissue from five groups of obese mice with varying degrees of hyperglycemia, and we identified 88 genes whose expression strongly correlated with diabetes severity. This group included many genes that are known to be involved in signal transduction and energy metabolism as well as genes not previously examined in the context of diabetes. Our data show that a decrease in expression of genes normally involved in adipogenesis is associated with obesity, and we further identify genes important for subsequent development of type 2 diabetes mellitus.
Towards the selection of patients requiring ICD implantation by automatic classification from Holter monitoring indices (2014)

The purpose of this study is to optimize the selection of prophylactic cardioverter defibrillator implantation candidates. Currently, the main criterion for implantation is a low Left Ventricular Ejection Fraction (LVEF) whose specificity is relatively poor. We designed two classifiers aimed to predict, from long term ECG recordings (Holter), whether a low-LVEF patient is likely or not to undergo ventricular arrhythmia in the next six months. One classifier is a single hidden layer neural network whose variables are the most relevant features extracted from Holter recordings, and the other classifier has a structure that capitalizes on the physiological decomposition of the arrhythmogenic factors into three disjoint groups: the myocardial substrate, the triggers and the autonomic nervous system (ANS). In this ad hoc network, the features were assigned to each group; one neural network classifier per group was designed and its complexity was optimized. The outputs of the classifiers were fed to a single neuron that provided the required probability estimate. The latter was thresholded for final discrimination A dataset composed of 186 pre-implantation 30-mn Holter recordings of patients equipped with an implantable cardioverter defibrillator (ICD) in primary prevention was used in order to design and test this classifier. 44 out of 186 patients underwent at least one treated ventricular arrhythmia during the six-month follow-up period. Performances of the designed classifier were evaluated using a cross-test strategy that consists in splitting the database into several combinations of a training set and a test set. The average arrhythmia prediction performances of the ad-hoc classifier are NPV = 77% $\pm$ 13% and PPV = 31% $\pm$ 19% (Negative Predictive Value $\pm$ std, Positive Predictive Value $\pm$ std). According to our study, improving prophylactic ICD-implantation candidate selection by automatic classification from ECG features may be possible, but the availability of a sizable dataset appears to be essential to decrease the number of False Negatives.
Development of Multifunctional Histone Deacetylase 6 Degraders with Potent Antimyeloma Activity (2019)

Histone deacetylase 6 (HDAC6) primarily catalyzes the removal of acetyl group from the side chain of acetylated lysine residues in cytoplasmic proteins such as α-tubulin and HSP90. HDAC6 is involved in multiple disease-relevant pathways. Based on the proteolysis targeting chimera strategy, we previously developed the first HDAC6 degrader by tethering a pan-HDAC inhibitor with cereblon (CRBN) E3 ubiquitin ligase ligand. We herein report our new generation of multifunctional HDAC6 degraders by tethering selective HDAC6 inhibitor Nexturastat A with CRBN ligand that can synergize with HDAC6 degradation for the antiproliferation of multiple myeloma (MM). This new class of degraders exhibited improved potency and selectivity for the degradation of HDAC6. After the optimization of the linker length and linking positions, we discovered potent HDAC6 degraders with nanomolar DC<sub>50</sub> and promising antiproliferation activity in multiple myeloma (MM) cells.
Automated subset identification and characterization pipeline for multidimensional flow and mass cytometry data clustering and visualization (2019)

When examining datasets of any dimensionality, researchers frequently aim to identify individual subsets (clusters) of objects within the dataset. The ubiquity of multidimensional data has motivated the replacement of user-guided clustering with fully automated clustering. The fully automated methods are designed to make clustering more accurate, standardized and faster. However, the adoption of these methods is still limited by the lack of intuitive visualization and cluster matching methods that would allow users to readily interpret fully automatically generated clusters. To address these issues, we developed a fully automated subset identification and characterization (SIC) pipeline providing robust cluster matching and data visualization tools for high-dimensional flow/mass cytometry (and other) data. This pipeline automatically (and intuitively) generates two-dimensional representations of high-dimensional datasets that are safe from the curse of dimensionality. This new approach allows more robust and reproducible data analysis,+ facilitating the development of new gold standard practices across laboratories and institutions.
Identification of an <i>S</i>‐locus glycoprotein allele introgressed from <i>B. napus</i> ssp. <i>rapifera</i> to <i>B. napus</i> ssp. <i>oleifera</i> (1992)

Self-incompatible Brassica napus ssp. oleifera lines were generated by introgressing the S-locus from the self-incompatible B. napus ssp. rapifera Z line into the self-compatible cultivars, Topas and Regent, resulting in T2 and R2, respectively. Screening of a cDNA library made from R2 stigma RNA produced several candidate SLG (S-locus glycoprotein) cDNAs. One of the cDNAs, A14, was found to be represented in only the R2, T2 and Z lines. In addition, the corresponding A14 gene was demonstrated to segregate with the T2 self-incompatibility phenotype in an F2 population derived from a cross between T2 and Topas, and to exhibit high mRNA levels in the stigmas prior to anthesis. Sequence analysis of the A14 cDNA revealed close homology to B. oleracea SLG alleles associated with a Class I high activity self-incompatibility phenotype.
Diaryliodonium salts as thermal initiators of cationic polymerization (1983)

Abstract Diaryliodonium salts (I) undergo efficient thermal decomposition in the presence of copper (II) compounds. Such systems can be employed as a novel class of latent thermal initiators for cationic polymerization. An investigation of the mechanism of the reaction demonstrated that the copper (II) compound is first reduced to the corresponding copper (I) compound, which subsequently reduces the diaryliodonium salt. The cationic polymerization of some typical monomers using these new initiators was carried out to demonstrate the scope of their utility.