gebhart/patrepeval huggingface dataset:
Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation (2020)

DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative <b>13e</b> showed potent activity against <i>Escherichia coli</i> DNA gyrase with an IC<sub>50</sub> value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.
An in vivo model of the human CD1 antigen presenting system (42.24) (2009)

Abstract CD1 molecules are a family of antigen presenting molecules that present lipids and glycolipids for recognition by specialized T cells. The CD1 system has been implicated in microbial infections, autoimmune and allergic disorders, and immunological control of tumors. However, our understanding of its role in human disease remains limited because animal models that resemble the human CD1 system are lacking. Here we report that a severely immune deficient mouse engrafted with human fetal tissues and hematopoietic stem cells develops an intact human CD1 antigen presenting system. Human CD1a, b, c, and d isoforms are highly expressed in the thymic organoid that develops in the engrafted mice, and histological analysis indicates the presence of CD1a+ APCs. Moreover, CD1+ APCs are expressed in peripheral tissues including the spleen and liver, and are capable of presenting bacterial glycolipids to human T cells specific for CD1a, b, or c. Staining with CD1d tetramers detected comparable percentages of human CD1d-restricted T cells in engrafted mice and human blood, and CD1d-restricted T cells isolated from the mice expressed a characteristic Vα24+/Vβ11+ TCR and recognized the glycolipid antigen α-GalCer. These results demonstrate the functional reconstitution of the human CD1 system in a mouse model.
Local Non-Rigid Structure-From-Motion From Diffeomorphic Mappings (2020)

We propose a new formulation to non-rigid structure-from-motion that only requires the deforming surface to preserve its differential structure. This is a much weaker assumption than the traditional ones of isometry or conformality. We show that it is nevertheless sufficient to establish local correspondences between the surface in two different images and therefore to perform point-wise reconstruction using only first-order derivatives. To this end, we formulate differential constraints and solve them algebraically using the theory of resultants. We will demonstrate that our approach is more widely applicable, more stable in noisy and sparse imaging conditions and much faster than earlier ones, while delivering similar accuracy. The code is available at https://github.com/cvlab-epfl/diff-nrsfm/.
Effect of Light/Dark Cycles on Expression of Nitrate Assimilatory Genes in Maize Shoots and Roots (1991)

The level of nitrate reductase (NR) and nitrite reductase (NiR) varied in both shoot and root tissue from nitrate-fed Zea mays L. grown under a 16-hour light/8-hour dark regime over a 10-day period postgermination, with peak activity occurring in days 5 to 6. To study the effect of different light regimes on NR and NiR enzyme activity and mRNA levels, 6-day-old plants were grown in the presence of continuous KNO(3) (10 millimolar). Both shoot NRA and mRNA varied considerably, peaking 4 to 8 hours into the light period. Upon transferring plants to continuous light, the amplitude of the peaks increased, and the peaks moved closer together. In continuous darkness, no NR mRNA or NR enzyme activity could be detected by 8 hours and 12 hours, respectively. In either a light/dark or continuous light regime, root NRA and mRNA did not vary substantially. However, when plants were placed in continuous darkness, both declined steadily in the roots, although some remained after 48 hours. Although there was no obvious cycling of NiR enzyme activity in shoot tissue, changes in mRNA mimicked those seen for NR mRNA. The expression of NR and NiR genes is affected by the light regime adopted, but light does not have a direct effect on the expression of these genes.
Conjugated linoleic acids and conjugated vegetable oils: From nutraceutical to bio‐polymer (2013)

Recent interest from academia, nutritionists, the chemical as well as the feed and food industry in conjugated linoleic acids (CLAs) and conjugated vegetable oils has grown spectacularly. CLA isomers, either in their natural or synthetic forms, have not only been associated with diverse health and physiological effects, but they are also interesting renewable compounds in the production of industrial products such as paints, glues, and polymers, due to their very reactive conjugated double bond system. Due to the depletion of the world crude oil reserves and the increasing trend to use renewable feedstock in the chemical industry, it is to be expected that the use of conjugated fatty acids and oils will continue to grow in the near future. As high amounts of CLAs and conjugated vegetable oils will be needed and natural resources are limited, efficient production processes are urgently needed. An efficient process for the production of CLA from methyl linoleate, using the Wilkinson catalyst, is described by Behr et al. in this issue of European Journal of Lipid Science and Technology .
Engineering design for a photovoltaic central station power plant using tracking concentrator photovoltaic arrays (1982)

A preliminary engineering design has been developed for a photovoltaic central station power plant that utilizes tracking concentrator photovoltaic (PV) arrays. This effort is part of a continuing research program funded by The Aerospace Corporation with the objective of defining and developing specifications for the subsystems and interfaces associated with the design of a photovoltaic power plant. In previous work in this program a power plant design using flat plate photovoltaic technology was developed. The principles developed in the earlier work have now been applied to a design that uses tracking concentrator photovoltaic arrays( ). The approach taken was to use electric utility design practices wherever possible and to provide sufficient definition of equipment to permit subsequent preparation of engineering cost estimates. The study has produced single-line electrical diagrams, site layout drawings, and functional diagrams for a station nominally rated at 200MW.
Xetal-II: A 107 GOPS, 600 mW Massively Parallel Processor for Video Scene Analysis (2008)

Xetal-II is a single-instruction multiple-data (SIMD) processor with 320 processing elements. It delivers a peak performance of 107 GOPS on 16-bit data while dissipating 600 mW. A 10 Mbit on-chip memory is provided which can store up to four VGA frames, allowing efficient implementation of frame-iterative algorithms. A massively parallel interconnect provides an internal bandwidth of more than 1.3 Tbit/s to sustain the peak performance. The IC is realized in 90 nm CMOS and takes up 74 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Cytotoxic and alpha amylase-inhibitory metabolites from Tagetes minuta: In vitro evaluation and docking studies (2023)

Purpose: To investigate the cytotoxic and alpha-amylase inhibitory (AAI) potential of methanol (MeOH) extract of T. minuta and its isolated metabolites. &#x0D; Methods: Phytochemical investigation of MeOH extract of the aerial parts of T. minuta was accomplished using SiO2 and Rp-18 column chromatography (CC). The structures of the isolated metabolites were determined and verified based on various data, in addition to comparison with literature data. The metabolites were assessed for cytotoxic potential against HepG2, MCF-7, and HCT116 cell lines utilizing sulphur rhodamine B (SRB) assay. The in vitro AAI potential of the metabolites were also assayed, and the findings were confirmed using results from molecular docking studies. &#x0D; Results: One thiophene (compound 1), one coumarin (compound 2), and three phenolic compounds (compounds 3-5) were isolated and characterized. Compound 1 exhibited a marked cytotoxic effect (IC50 values: 2.7 – 7.3 μM) on HepG2, MCF-7, and HCT116 cell lines, relative to doxorubicin (IC50 values: 0.18 - 0.60 μM), whereas compound 2 had a moderate cytotoxic effect on MCF-7 (IC50 17.7 μM). Besides, compounds 4 and 5 produced potent AAI effects, with IC50 values of 12.3 and 9.2 μM, respectively, and 91.8 and 94.7 % inhibition, respectively), when compared to acarbose (94.7 % inhibition and IC50 of 7.1 μM). Interestingly, the in vitro AAI and in silico results were in agreement with each other. Compounds 5 and 4 had more negative docking scores (-13.655 and -12.135 kcal/mol, respectively) than the native inhibitors, myricetin (-12.155 kcal/mol) and acarbose (-15.105 kcal/mol). &#x0D; Conclusion: These results suggest that T. minuta is a valuable source of anti-diabetic and cytotoxic metabolites. However, there is a need to validate these results through additional in vivo and in vitro investigations.
IR spectroscopic investigation of internal silanol groups in different zeolites with pentasil structure (2021)

Various isomorphically substituted high-silica zeolites, including ZSM-5, beta, ferrisilicates, gallosilicates and borosilicates, were investigated by diffuse reflectance IR spectroscopy. The narrow band at 3735 cm–1 and the broad band at 3500 cm–1 were assigned to internal silanol groups. These defect sites in the as-synthesized Na-forms of zeolites arise during the template decomposition.
3000-V 4.3-$\hbox{m}\Omega \cdot \hbox{cm}^{2}$ InAlN/GaN MOSHEMTs With AlGaN Back Barrier (2012)

This letter reports the fabrication of InAlN/GaN high-electron mobility transistors (HEMTs) with a three-terminal off-state breakdown voltage (BV) of 3000 V and a low specific on-resistance of 4.25 mΩ·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . To reduce the drain-to-source leakage current in these devices, an AlGaN back barrier has been used. The gate leakage current in these devices is in the ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-10</sup> A/mm range owing to the use of a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gate dielectric. This current level is more than six orders of magnitude lower than in Schottky-barrier HEMTs. The combination of an AlGaN back barrier, the high charge sheet density of InAlN/GaN HEMTs, and the low leakage due to the gate-dielectric layer allows for a figure-of-merit BV <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> / <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON,SP</sub> of ~2.1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ·Ω <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ·cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> .
Atomic-scale nanofacet structure in semipolar $(20\bar{2}\bar{1})$ and $(20\bar{2}1)$ InGaN single quantum wells (2014)

Atomic-scale nanofacets were observed in semipolar and InGaN quantum wells (QWs)/GaN quantum barriers interfaces. Transmission electron microscopy studies showed that these nanofacets were mainly composed of , and planes, which led to significant fluctuations in QW thickness. Atom probe tomography studies were carried out to visualize the nanofacet structure. The In composition in the InxGa1−xN alloys followed a binominal distribution despite the formation of the nanofacet structure. One-dimensional (1D) Schrödinger–Poisson drift-diffusion simulation showed that these nanofacets and associated QW thickness fluctuations will lead to a large wavelength shift and a broadened spectral linewidth for semipolar QWs.
Turning Astrocytes from the Rostral Migratory Stream into Neurons: A Role for the Olfactory Sensory Organ (2008)

Neurogenesis persists within a few restricted areas of the adult mammalian brain, giving rise to neurons that functionally integrate into preexisting circuits. One of these areas, the subventricular zone (SVZ), was believed, until recently, to be the unique source providing the adult olfactory bulb (OB) with newborn neurons. Because of the fact that neuroblasts derived in the SVZ migrate through the rostral migratory stream (RMS) en route to the OB, the existence of candidate neural stem cells within the RMS was long overlooked. Here, we confirm and considerably extend recent evidence for the existence of adult neural stem cells within the RMS, and go on to investigate their proliferative regulation. Specifically targeting RMS-astrocytes with lentiviral vectors encoding GFP, we demonstrate that glial cells in the RMS differentiate into both OB granule and periglomerular interneurons. In addition, ultrastructural analysis unambiguously reveals the astrocytic nature of stem cells in the adult RMS, and patch-clamp recordings demonstrate the functional integration of RMS-derived interneurons into OB circuitry. Proliferative regulation was investigated via two contrasting manipulations: exposure to an odor-enriched environment that enhances candidate stem cell proliferation in both the RMS and SVZ, and chemical lesion of the main olfactory epithelium that increases cell proliferation in the RMS only. New neurons in the adult OB can therefore arise from different neurogenic areas that can be separately regulated.
Closed-Tube SNP Genotyping Without Labeled Probes (2007)

Two methods for closed-tube single nucleotide polymorphism (SNP) genotyping without labeled probes have become available: unlabeled probe and amplicon melting. Unlabeled probe and amplicon melting assays were compared using 5 SNPs: human platelet antigens 1, 2, 5, and 15 and a C>T variant located 13910 base pairs (bp) upstream of the lactase gene. LCGreen Plus (Idaho Technology, Salt Lake City, UT) was used as the saturating DNA dye. Unlabeled probe data were readily interpretable and accurate for all amplicon lengths tested. Five targets that ranged in size from 42 to 72 bp were well resolved by amplicon melting on the LightScanner (Idaho Technology) or LightTyper (Roche, Indianapolis, IN) with no errors in genotyping. However, when larger amplicons (206 bp) were used and analyzed on lower resolution instruments (LightTyper and I-Cycler, Bio-Rad, Hercules, CA), the accuracy of amplicon genotyping was only 73% to 77%. When 2 temperature standards were used to bracket the amplicon of interest, the accuracy of amplicon genotyping of SNPs was increased to 100% (LightTyper) and 88% (I-Cycler).
Supplementary File 3 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma (2023)

&lt;p&gt;Summary of somatic and de novo germline events.&lt;/p&gt;
Extracellular Cyclic GMP Modulates Membrane Expression of The GluA1 and GluA2 Subunits of AMPA Receptor in Cerebellum: Molecular Mechanisms Involved (2017)

There is increasing evidence that extracellular cGMP modulates glutamatergic neurotransmission and some forms of learning. However, the underlying mechanisms remain unknown. We proposed the hypotheses that extracellular cGMP may regulate membrane expression of AMPA receptors. To do this extracellular cGMP should act on a membrane protein and activate signal transduction pathways modulating phosphorylation of the GluA1 and/or GluA2 subunits. It has been shown that extracellular cGMP modulates glycine receptors. The aims of this work were to assess: 1) whether extracellular cGMP modulates membrane expression of GluA1 and GluA2 subunits of AMPA receptors in cerebellum in vivo; 2) whether this is mediated by glycine receptors; 3) the role of GluA1 and GluA2 phosphorylation and 4) identify steps of the intracellular pathways involved. We show that extracellular cGMP modulates membrane expression of GluA1 and GluA2 in cerebellum in vivo and unveil the mechanisms involved. Extracellular cGMP reduced glycine receptor activation, modulating cAMP, protein kinases and phosphatases, and GluA1 and GluA2 phosphorylation, resulting in increased GluA1 and reduced GluA2 membrane expression. Extracellular cGMP therefore modulates membrane expression of AMPA receptors and glutamatergic neurotransmission. The steps identified may be therapeutic targets to improve neurotransmission and neurological function in pathological situations with abnormal glutamatergic neurotransmission.
Charge transport in nanocrystal wires created by direct electron beam writing (2010)

The authors report the fabrication and electrical characterisation of nanowires created via direct electron beam writing in films of passivated gold nanocrystals. Charge transport measurements yield room temperature resistances in the range 105–108 Ω. Variable temperature measurements yield two distinct sets of characteristics: activated conduction (high resistance) consistent with weakly coupled metal nanocrystals separated by alkyl–thiol tunnel barriers and quasi-localised behaviour (low resistance) consistent with stronger coupling between granular metallic islands in a carbonaceous matrix. The data indicate that electron beam writing is a promising method for local manipulation of inter-nanocrystal coupling in nanocrystal arrays.
Conservation of Genetic Alterations in Recurrent Melanoma Supports the Melanoma Stem Cell Hypothesis (2008)

It is generally accepted that human cancers derive from a mutated single cell. However, the genetic steps characterizing various stages of progression remain unclear. Studying a unique case of metastatic melanoma, we observed that cell lines derived from metachronous metastases arising over a decade retained a central core of genetic stability in spite of divergent phenotypes. In the present study, we expanded our previous observations comparing these autologous cell lines of clonal derivation with allogeneic ones and correlated array comparative genomic hybridization (aCGH) with gene expression profiling to determine their relative contribution to the dynamics of disease progression. aCGH and gene expression profiling were performed on autologous cell lines and allogeneic melanoma cell lines originating from other patients. A striking correlation existed between total extent of genetic imbalances, global transcriptional patterns, and cellular phenotypes. They did not follow a strict temporal progression but stemmed independently at various time points from a central core of genetic stability best explained according to the cancer stem cell hypothesis. Although their contribution was intertwined, genomic imbalances detectable by aCGH contributed only 25% of the transcriptional traits determining autologous tumor distinctiveness. Our study provides important insights about the dynamics of cancer progression and supports the development of targeted anticancer therapies aimed against stable genetic factors that are maintained throughout the end stage of disease.
Linear and nonlinear performance of 42.7-Gb/s single-polarization RZ-DQPSK format (2006)

We experimentally examine the performance of a single-polarization 42.7-Gb/s return-to-zero differential quadrature phase-shift keying optical signal. We evaluate the penalties arising from chromatic dispersion, polarization-mode dispersion, narrowband optical filtering, and nonlinear transmission over standard single-mode fiber.
Conserved genetic signatures between mouse and human DC subsets (2011)

Hierarchical with complete linkage clustering was performed on the indicated DC populations isolated from mouse and human.<b>Copyright information:</b>Taken from "Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling"http://genomebiology.com/2008/9/1/R17Genome Biology 2008;9(1):R17-R17.Published online 24 Jan 2008PMCID:PMC2395256.
The effect of immature adult-born dentate granule cells on hyponeophagial behavior is related to their roles in learning and memory (2015)

The neurogenesis hypothesis of depression is based on the correlation between the rate of adult hippocampal neurogenesis and the affective status of rodents. However, studies investigating the role of neurogenesis in the causation of mood regulation have reported inconsistent results. Here, we explored whether the affective state can be affected differentially by adult-born neurons with distinctive physiological characteristics at different maturation stages. We revealed that reducing the immature newborn neuron population had no effect on anxiety- or depression-like behaviors in an array of tests; however, it enhanced hyponeophagia in a novelty suppressed feeding test, but only when the novel environment was drastically different from the home cage. We further demonstrated that reducing the immature newborn neuron population led to delayed habituation to a novel environment and impaired contextual learning. Hence, rather than being directly involved in mood regulation, our studies raise the possibility that adult neurogenesis may influence hyponeophagia through its role in mnemonic processing.
OPAQUE: An Asymmetric PAKE Protocol Secure Against Pre-Computation Attacks. (2018)

Password-Authenticated Key Exchange (PAKE) protocols allow two parties that only share a password to establish a shared key in a way that is immune to offline attacks. Asymmetric PAKE (aPAKE) strengthens this notion for the more common client-server setting where the server stores a mapping of the password and security is required even upon server compromise, that is, the only allowed attack in this case is an (inevitable) offline exhaustive dictionary attack against individual user passwords. Unfortunately, most suggested aPAKE protocols (that dispense with the use of servers’ public keys) allow for pre-computation attacks that lead to the instantaneous compromise of user passwords upon server compromise, thus forgoing much of the intended aPAKE security. Indeed, these protocols use – in essential ways – deterministic password mappings or use random “salt” transmitted in the clear from servers to users, and thus are vulnerable to pre-computation attacks.
OrganoSoxhlet: circular fractionation to produce pulp for textiles using CO2 as acid source (2021)

Organosolv pulping performed in a high-pressure Soxhlet extractor using carbon dioxide as a mild and recyclable acid is described.
Extended Precision in Video-Bandwidth Analog-to-Digital Converters Using Optical Techniques (1984)

Analog-to-digital converters (ADCs) are widely used to translate sensor measurements into the digital language of computing, information processing, and control systems. There is presently considerable interest in high-precision (8-10 bit) conversion at rates of 10-20 Msamples/sec for use in digital transmission and recording of television signals. 1 However, for some applications (e.g., in radar signal processing) even higher precision at video sampling rates is desired for enhanced dynamic range. It has proven very difficult to achieve precision beyond 10 bits at these rates using conventional silicon integrated circuit technology.