gebhart/patrepeval huggingface dataset:
Ionic Liquid‐Mediated Approach for the Synthesis of Site‐Specific Thioether Conjugates (2023)

Site-specific conjugation approaches are of great importance in drug discovery, notably for the synthesis of biochemical probes or molecular conjugates for targeted delivery. Herein, we report a mild ionic liquid (IL)-mediated thiolation technique that relies on the use of 1,3-ethyl-methyl imidazolium acetate, [C<sub>2</sub> mim][OAc] as a solvent and precursor to generate activated IL, as well as a solvent for the conjugation reaction. First, a focused library of active ILs was prepared for functionalizing/conjugating cysteine-containing small molecules and unprotected peptides. Interestingly, a bifunctional active IL could also be successfully employed as a linker for the conjugation of peptides lacking Cys. This study sets the ground for further investigation of the use of active ILs for modifying, labeling or conjugating larger and more complex therapeutic modalities such as proteins and antibodies.
Insertion Reactions of an Aminogermylene and Formation of a Single‐Source Precursor for GeTe Thin Films (2009)

Abstract Insertion reactions between a liquid germylene 1 , and either a carbodiimide or dialkyl telluride lead to the formation of the group‐14‐metal(II) guanidinate complex 2 or the stable group‐14‐metal terminal alkyl tellurolate compound 3 , respectively. The complexes 2 and 3 were structurally elucidated by multinuclear NMR and single‐crystal X‐ray crystallography. The use of 3 as a single‐source precursor (SSP) for the MOCVD of GeTe films was demonstrated. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2009)
Lidar-Radiometer Inversion Code (LIRIC) for the retrieval of vertical aerosol properties from combined lidar/radiometer data: development and distribution in EARLINET (2016)

Abstract. This paper presents a detailed description of LIRIC (LIdar-Radiometer Inversion Code) algorithm for simultaneous processing of coincident lidar and radiometric (sun photometric) observations for the retrieval of the aerosol concentration vertical profiles. As the lidar/radiometric input data we use measurements from European Aerosol Research Lidar Network (EARLINET) lidars and collocated sun-photometers of Aerosol Robotic Network (AERONET). The LIRIC data processing provides sequential inversion of the combined lidar and radiometric data. The algorithm starts with the estimations of column-integrated aerosol parameters from radiometric measurements followed by the retrieval of height dependent concentrations of fine and coarse aerosols from lidar signals using integrated column characteristics of aerosol layer as a priori constraints. The use of polarized lidar observations allows us to discriminate between spherical and non-spherical particles of the coarse aerosol mode.The LIRIC software package was implemented and tested at a number of EARLINET stations. Intercomparison of the LIRIC-based aerosol retrievals was performed for the observations by seven EARLINET lidars in Leipzig, Germany on 25 May 2009. We found close agreement between the aerosol parameters derived from different lidars that supports high robustness of the LIRIC algorithm. The sensitivity of the retrieval results to the possible reduction of the available observation data is also discussed.
Immunological fingerprint of 4CMenB recombinant antigens via protein microarray reveals key immunosignatures correlating with bactericidal activity (2020)

Serogroup B meningococcus (MenB) is a leading cause of meningitis and sepsis across the world and vaccination is the most effective way to protect against this disease. 4CMenB is a multi-component vaccine against MenB, which is now licensed for use in subjects >2 months of age in several countries. In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the three major 4CMenB antigenic components (fHbp, NHBA and NadA) in individual sera from vaccinated infants, adolescents and adults. The resulting 4CMenB protein antigen fingerprinting allowed the identification of specific human antibody repertoire correlating with the bactericidal response elicited in each subject. This work represents an example of epitope mapping of the immune response induced by a multicomponent vaccine in different age groups with the identification of protective signatures. It shows the high flexibility of this microarray based methodology in terms of high-throughput information and minimal volume of biological samples needed.
Development of a recognition algorithm for THz spectra (2013)

A new algorithm for the processing of THz absorption spectra is developed. It grants further applications of the THz radiation in the field of security control or chemical substance identification. The algorithm processes the whole spectra with small information content by means of continuous wavelet transformation (CWT).
A Form of the Metabolic Syndrome Associated with Mutations in DYRK1B (2014)

These findings indicate a role for DYRK1B in adipogenesis and glucose homeostasis and associate its altered function with an inherited form of the metabolic syndrome. (Funded by the National Institutes of Health.).
Post Recommendation System Impact on Student Participation and Performance in an Online AI Graduate Course (2022)

Embedding a post recommendation system in online course forums improves students' ability to find relevant course content. Yet, there is limited research quantifying how these interventions impact forum interactions and students' class performance. We randomly divide an on-line class in a Masters degree-seeking program into control and experimental sections. Midway through the class, for the experimental section, we introduce an information retrieval system that suggests relevant posts to students while they compose their new posts. The average number of initial posts in the discussion forum dropped by 55% for the experimental group compared to 21% in the control group. In post-hoc analysis, we classify students as having an active or passive (i.e., mostly lurking) forum participation style. Posts per student per assignment by passive participants in the experimental group decreased by 15%, while passive participants' posts in the control group increased by 200%. The number of answers given by instructors in the experimental group decreased twice as much as the control group after intervention, though the difference was not statistically significant. The reduction of posts was not associated with a decrease in academic performance (grades) for the experimental group. This line of research convinced the popular forum Piazza to implement a post recommendation system similar to that used in these experiments.
Luces Nuevas Experience Lighting Rural Bolivia: A Way to Reach SDG 7 (2021)

United Nations SDG 7 is that, by 2030, there will be an affordable, reliable and clean universal access to energy (UAE). To reach this goal, technological and social issues should be considered jointly. In this paper, the approach used by the Non-Governmental Organization “Luces Nuevas Internacional” is presented. Luces Nuevas has successfully provided basic electricity access to sparse rural communities in rural Bolivia. This paper emphasizes the methodological aspects of the approach. The key ingredient to the success is the involvement of all the stakeholders in all steps of the solution. In this way, end users feel the solution as their solution. Therefore, they are willing to use and properly maintain the devices that they buy to obtain electricity access. The case of the Tipas community shows that this approach can provide access to energy to every family that desires it. The experience shows that reaching SDG 7 requires taking into account not only the technological and economic aspects, but also the social aspects of the problem. End users involvement, from the beginning, of an electrification project is key to its success.
Mechanochemical reactions of elastomers with metals (1985)

Abstract Metal powders were incorporated into various elastomers and the mixtures were subjected to intense shearing in air or a nitrogen atmosphere. The molecular weight after shearing was still relatively high, however; greater than 100 kg/mol. The elastomer was then dissolved and centrifuged to remove the metal particles and the solution was analyzed for reaction products. A strongly ultraviolet (UV)‐absorbing species was formed by shearing a styrene–butadiene copolymer (SBR) with iron powder. The concentration increased with the concentration of iron powder in the mixture and the extent of shearing, and it was greater after shearing in a nitrogen atmosphere. These results are attributed to the direct reaction of macromolecular radicals, formed by shearing, with iron powder to yield an iron–polymer compound. Natural rubber ( cis ‐polyisoprene), which absorbed 100–200 μg of iron per gram of polymer, was about as reactive as SBR. Polybutadiene was less reactive, and an ethylene–propylene copolymer did not react with or solubilize a significant amount of iron. Zinc was, in general, solubilized to a somewhat lesser degree than iron, whereas aluminum powder appeared to undergo virtually no reaction with sheared elastomers. The maximum extent of reaction (solubilization) was of the order of one metal atom per final polymer molecule, which was consistent with the proposed mechanism. Moreover, an analogous reaction took place between simple organic radicals and iron particles in suspension.
Sialylneolacto-N-tetraose c (LSTc)-bearing Liposomal Decoys Capture Influenza A Virus (2013)

Influenza is a severe disease in humans and animals with few effective therapies available. All strains of influenza virus are prone to developing drug resistance due to the high mutation rate in the viral genome. A therapeutic agent that targets a highly conserved region of the virus could bypass resistance and also be effective against multiple strains of influenza. Influenza uses many individually weak ligand binding interactions for a high avidity multivalent attachment to sialic acid-bearing cells. Polymerized sialic acid analogs can form multivalent interactions with influenza but are not ideal therapeutics due to solubility and toxicity issues. We used liposomes as a novel means for delivery of the glycan sialylneolacto-N-tetraose c (LSTc). LSTc-bearing decoy liposomes form multivalent, polymer-like interactions with influenza virus. Decoy liposomes competitively bind influenza virus in hemagglutination inhibition assays and inhibit infection of target cells in a dose-dependent manner. Inhibition is specific for influenza virus, as inhibition of Sendai virus and respiratory syncytial virus is not observed. In contrast, monovalent LSTc does not bind influenza virus or inhibit infectivity. LSTc decoy liposomes prevent the spread of influenza virus during multiple rounds of replication in vitro and extend survival of mice challenged with a lethal dose of virus. LSTc decoy liposomes co-localize with fluorescently tagged influenza virus, whereas control liposomes do not. Considering the conservation of the hemagglutinin binding pocket and the ability of decoy liposomes to form high avidity interactions with influenza hemagglutinin, our decoy liposomes have potential as a new therapeutic agent against emerging influenza strains.
A backscatter-based method for treatment targeting in the application of High Intensity Focused Ultrasound (2008)

High Intensity Focused Ultrasound (HIFU) has been investigated as a non-invasive ablation method for morbid tissue in various diseases. It is of great importance to know where the focus would be in HIFU treatment planning to ensure that only the desired tissue is ablated while sparing normal tissue. We investigated a method for HIFU targeting based on the change in radiofrequency (RF) signals at pre-ablative HIFU intensity levels. In ex vivo experiment, HIFU was applied to chicken tissue at low intensity levels for 5 seconds, during which no tissue damage was observed. RF data were collected during this period and the amplitude change was analyzed. High intensity was then applied to induce lesion in tissue and hyperecho in B-mode images. Focus estimated from RF data was compared with that obtained from hyperechoic region. Results showed that RF amplitude of the focal region increased immediately after the start of HIFU exposure, even at pre-ablative intensity levels. The difference between focus locations based on RF data and B-mode images was 1.92 plusmn 1.02 mm (mean plusmn standard deviation). No statistically significant difference was found between focus coordinates in the axial and lateral dimensions (axial: p = 0.50 and lateral: p = 0.07). The increasing rate in RF amplitude was shown to be a signature of HIFU focus and could be used for HIFU treatment planning.
Deep-dive analysis of the data analytics workload in CloudSuite (2014)

Exponential growth of digital data has introduced massively-parallel systems, special orchestration layers, and new scale-out applications. While recent works suggest characteristics of scale-out workloads are different from those of traditional ones, their root causes are not understood. Such understanding is extremely important to improve efficiency; even a 1% performance gain for a core can have a large impact on the datacenter as a whole. This paper studies the characteristics of a Big Data Analytics (BDA) workload on a modern cloud server. It is intentionally focused on a single workload-platform in order to enable deep-dive analysis that aims to understand the root causes of the CPU bottlenecks which this paper identify. We choose the Data Analytics benchmark from CloudSuite [1] as a representative of a growing family of important applications. This paper describes a customization of a comprehensive threefold analysis method. The method consists of a System level, where sensitivity to system parameters is examined, as well as Application and Architectural levels; where bottlenecks are attributed back to the application and runtime codes, respectively. The paper also adopts a proof-by-optimization approach to prove bottlenecks' validity. Overall, 65% net speedup is measured with significant power reduction. The paper reveals that BDA workloads suffer from overheads related to managing the data rather than accessing the data. For example, Hash index lookup is found to be a key performance limiter. Inefficiencies leading to such unexpected behavior are demonstrated, including JVM selection and heavily unoptimized application code, both of which have a big impact. Suboptimal microarchitecture areas are demonstrated too, in addition to programming styles that limit exploitation of upcoming JVM and CPU parallelization features.
Growth of vertically aligned carbon nanofibers by low-pressure inductively coupled plasma-enhanced chemical vapor deposition (2003)

Vertically aligned carbon nanofibers (VACNFs) have been grown using a low-pressure, plasma-enhanced, chemical vapor deposition process. The nanofibers are grown from a nickel catalyst that can be patterned to form arrays of individual, isolated VACNFs. The fibers are grown at pressures below 100 mTorr, using an inductively coupled plasma source with a radio-frequency bias on the sample substrate to allow for independent control of the ion energies. Plasma conditions are related to growth results by comparing optical emission from the plasma to the physical structure of the nanofibers. We find that the ratio of etching species in the plasma to depositing species is critical to the final shape of the carbon structures that are formed.
Identification and Characterization of Mutations in Ha-Ras That Selectively Decrease Binding to cRaf-1 (1997)

The oncoprotein Ras transforms cells by binding to one or more effector proteins. Effector proteins have been identified by their ability to bind to Ras in the GTP but not GDP form, and by their requirement for the Ras effector domain for binding. The best understood Ras effectors are serine/threonine kinases of the Raf family, but other candidate Ras effectors, including a Ral guanine nucleotide dissociation stimulator and phosphatidylinositol 3-kinase (PI3 kinase) have also been identified. To investigate the mechanism of binding of cRaf-1 to Ras, and to investigate the roles of other candidate Ras effectors in transformation, we have isolated and characterized mutants of activated Ras with decreased binding to cRaf-1 relative to other candidate effectors. Examination of these mutants indicates that surface-exposed residues of Ras outside the minimal effector domain interact differentially with cRaf-1 and other Ras-binding proteins, and that fibroblast transformation correlates with cRaf-1 binding and mitogen-activated protein (MAP) kinase activation. Furthermore, activation of PI3 kinase can occur in the absence of significant MAP kinase activation, suggesting that PI3 kinase activation is a primary effect of Ras.
Inhibition of Plasmodium Liver Infection by Ivermectin (2016)

Avermectins are powerful endectocides with an established potential to reduce the incidence of vector-borne diseases. Here, we show that several avermectins inhibit the hepatic stage of Plasmodium infection in vitro Notably, ivermectin potently inhibits liver infection in vivo by impairing parasite development inside hepatocytes. This impairment has a clear impact on the ensuing blood stage parasitemia, reducing disease severity and enhancing host survival. Ivermectin has been proposed as a tool to control malaria transmission because of its effects on the mosquito vector. Our study extends the effect of ivermectin to the early stages of mammalian host infection and supports the inclusion of this multipurpose drug in malaria control strategies.
A compact architecture for dialogue management based on scripts and meta-outputs (2000)

We describe an architecture for spoken dialogue interfaces to semi-autonomous systems that transforms speech signals through successive representations of linguistic, dialogue, and domain knowledge. Each step produces an output, and a meta-output describing the transformation, with an executable program in a simple scripting language as the final result. The output/meta-output distinction permits perspicuous treatment of diverse tasks such as resolving pronouns, correcting user misconceptions, and optimizing scripts.
Ultrahigh Surface Area Nanoporous Silica Particles via an Aero-Sol−Gel Process (2004)

We describe a new salt-assisted aero-sol-gel approach to produce spherical nanosized mesoporous silica particles. As an alternative to expensive templating mediums in prior works, salt (NaCl) was employed as a templating medium because it is thermally stable, recyclable, and easily leached. Furthermore, we demonstrate the ability to carry out traditional sol-gel chemistry within an aerosol droplet. The role of salt in sol-gel chemistry and aerosol processing was investigated as a function of hydrolysis time. It was verified that salt accelerates the kinetics of silica gelation, and simultaneously becomes an excellent templating medium to support nano-sized pores inside silica structures in the aerosol processing route. The presence of salt results in a roughly ten-fold increasing in the pore specific surface area and pore volume, subsequent to leaching of the salt matrix. The surface area and pore volume of the as-produced nanoporous silica particles was found to increase with increasing sol-gel hydrolysis time.
Inter Spike Interval and Stochasticity Engineering of Floating Gate Technology-based Neurons for Spiking Neural Network Hardware (2022)

An analytical model has been developed for a stochastic spiking neuron with the floating gate (FG) technology. The electron injection statistics have been applied to the leaky-integrate-and-fire (LIF) neuron model for the first time and inter spike interval (ISI) stochasticity has been quantified. The model has demonstrated low voltage operations below 2V and the ability to fine-tune ISI mean values by 6 orders of magnitude and the degree of ISI stochasticity ranging from 0% to 60%. With the strong interests in the stochastic neurons in spiking neural network (SNN), the ISI stochasticity and tunability of the FG-based neuron have potential to realize efficient and robust spiking neural network hardware.
Repository Guidance for Researchers - TAG A/D (2017)

TBD, potentially Implementing a tool to provide guidance for researchers to find appropriate repositories for their data and other digital research products.
Association Between Sex Hormone Levels and Gut Microbiota Composition and Diversity—A Systematic Review (2022)

The findings gathered highlight an association between sex hormones and the gut microbiota composition/diversity and may contribute to the sex-based variations observed in disease pathogenesis. Factors such as age and medical conditions are implicated in the associations observed and should be accounted for in future studies. As the understanding of the complex symbiotic relationship between humans and their gut microbiota increases, microbiota modulation could be an attractive option for the prevention and treatment of gastrointestinal disorders.
Inside Cover: Ribonucleoside 3′‐Phosphates as Pro‐Moieties for an Orally Administered Drug (ChemMedChem 8/2012) (2012)

The inside cover picture depicts a new strategy for the sustained release of orally administered drugs. The strategy avails the ability of a systemic enzyme, human pancreatic ribonuclease, to catalyze the cleavage of a ribonucleoside 3′-phosphate prodrug. Efficacy against Bacteroides fragilis is demonstrated with metronidazole as the released drug. For more details, see the Communication by Ronald T. Raines et al. on p. 1361 ff.
Changes in the expression of IL‐6‐Mediated MicroRNAs in the dorsal root ganglion under neuropathic pain in mice (2016)

A multiplex analysis for profiling the expression of candidate microRNAs (miRNAs), which are small noncoding RNAs that function as key post-transcriptional regulators, may lead to a better understanding of the complex machinery of neuropathic pain. In the present study, we performed a miRNA array analysis using tissues of the dorsal root ganglion (DRG), a primary site for pain processing, obtained from mice with partial sciatic nerve ligation. Among 1135 total miRNAs, 26 miRNAs showed up-regulation (more than 2-fold change) and only 4 miRNAs showed down-regulation (less than 0.5-fold change) in the DRG of nerve-ligated mice. In a RT-qPCR assay, the levels of miR-21, miR-431, and miR-511-3p were significantly increased on the ipsilateral side of the DRG from 3 to 7 days after sciatic nerve ligation. These elevations were almost absent in IL-6 knockout mice. Furthermore, the expression level of miR-21, but not those of miR-431 or miR511-3p, was significantly increased in exosomes extracted from blood of nerve-ligated mice. These findings suggest that the increased expression of IL-6-regulated miR-21, miR-431, and miR-511-3p in the DRG and increased exosomal miR-21 extracted from blood after sciatic nerve ligation may play at least a partial role in neuropathic pain. Synapse 70:317-324, 2016. © 2016 Wiley Periodicals, Inc.