gebhart/patrepeval huggingface dataset:
A non-traditional crystal-based compound screening method targeting the ATP binding site of Plasmodium falciparum GRP78 for identification of novel nucleoside analogues (2022)

Drug resistance to front-line malarial treatments represents an ongoing threat to control malaria, a vector borne infectious disease. The malarial parasite, <i>Plasmodium falciparum</i> has developed genetic variants, conferring resistance to the current standard therapeutic artemisinin and its derivatives commonly referred to as artemisinin-combination therapies (ACTs). Emergence of multi-drug resistance parasite genotypes is a warning of potential treatment failure, reaffirming the urgent and critical need to find and validate alternate drug targets to prevent the spread of disease. An attractive and novel drug target includes glucose-regulated protein 78 kDa (GRP78, or BiP), an essential molecular chaperone protein involved in the unfolded protein response that is upregulated in ACT treated <i>P. falciparum</i> parasites. We have shown that both sequence and structure are closely related to human GRP78 (hGRP78), a chaperone belonging to the HSP70 class of ATPase proteins, which is often upregulated in cellular stress responses and cancer. By screening a library of nucleoside analogues, we identified eight 'hit' compounds binding at the active site of the ATP binding domain of <i>P. falciparum</i> GRP78 using a high-throughput ligand soaking screen using x-ray crystallography. These compounds were further evaluated using protein thermal shift assays to assess target binding activity. The nucleoside analogues identified from our screen provide a starting point for the development of more potent and selective antimalarial inhibitors. In addition, we have established a well-defined, high-throughput crystal-based screening approach that can be applied to many crystallizable <i>P. falciparum</i> proteins for generating anti-<i>Plasmodium</i> specific compounds.
Strain rate sensitivity of C-alloyed, high-Mn, twinning-induced plasticity steel (2009)

The mechanical properties of twinning-induced plasticity (TWIP) steels are often assumed to be solely due to the reduction of the mean free path of glide dislocations resulting from deformation twinning. Other mechanisms may also play an essential role: Mn-C cluster formation, planar glide, pseudo-twinning, short range ordering, and dynamic strain ageing. The present contribution offers a critical analysis of the mechanical properties of high-Mn TWIP steels, especially in terms of Dynamic Strain Aging (DSA) and Static Strain Aging (SSA). The presentation offers new insights into the properties of TWIP steels which were obtained by using new experimental techniques such as in-situ strain analysis and high sensitivity infrared thermo-graphic imaging.
Brain Sigma-1 Receptor Stimulation Improves Mental Disorder and Cardiac Function in Mice With Myocardial Infarction (2013)

Mental disorder after myocardial infarction (MI) is reported by many epidemiological studies and is associated with a poor prognosis. The reduction of brain sigma-1 receptor (S1R) plays an important role in the pathogenesis of mental disorder, and we recently demonstrated that the reduction of brain S1R causes sympathoexcitation. However, the role of brain S1R in the association between MI and mental disorder, such as depression or cognitive impairment, remains unclear. To investigate this, we performed left coronary artery ligation on mice to produce an MI model (MI-mice). Compared with sham-operated controls (Sham-mice), MI-mice showed augmented sympathetic activity, decreased cardiac function, and lower S1R expression in both the hypothalamus and hippocampus. Furthermore, MI-mice displayed decreased Y-maze spontaneous alternation (a maker of spatial working memory), decreased circadian variation in locomotor activity, and increased immobility time in the tail suspension test (markers of depression-like behavior). Intracerebroventricular infusion of the S1R agonist PRE084 in MI-mice improved both mental disorder and cardiac function with lowered sympathetic activity and the recovery of the S1R expression in both the hypothalamus and hippocampus. These results indicate that brain S1R is decreased in MI-mice and that this plays an important role in the coexistence of increased heart failure via sympathoexcitation and mental disorders, such as depression or cognitive impairment.
Rectangular Full Packed Format for Cholesky's Algorithm: Factorization, Solution and Inversion (2009)

We describe a new data format for storing triangular, symmetric, and Hermitian matrices called RFPF (Rectangular Full Packed Format). The standard two dimensional arrays of Fortran and C (also known as full format) that are used to represent triangular and symmetric matrices waste nearly half of the storage space but provide high performance via the use of Level 3 BLAS. Standard packed format arrays fully utilize storage (array space) but provide low performance as there is no Level 3 packed BLAS. We combine the good features of packed and full storage using RFPF to obtain high performance via using Level 3 BLAS as RFPF is a standard full format representation. Also, RFPF requires exactly the same minimal storage as packed format. Each LAPACK full and/or packed triangular, symmetric, and Hermitian routine becomes a single new RFPF routine based on eight possible data layouts of RFPF. This new RFPF routine usually consists of two calls to the corresponding LAPACK full format routine and two calls to Level 3 BLAS routines. This means {\it no} new software is required. As examples, we present LAPACK routines for Cholesky factorization, Cholesky solution and Cholesky inverse computation in RFPF to illustrate this new work and to describe its performance on several commonly used computer platforms. Performance of LAPACK full routines using RFPF versus LAPACK full routines using standard format for both serial and SMP parallel processing is about the same while using half the storage. Performance gains are roughly one to a factor of 43 for serial and one to a factor of 97 for SMP parallel times faster using vendor LAPACK full routines with RFPF than with using vendor and/or reference packed routines.
Design space exploration of the lightweight stream cipher WG-8 for FPGAs and ASICs (2013)

WG-8 is a lightweight instance of the Welch-Gong (WG) stream cipher family, targeting for resource-constrained devices like RFID tags, smart cards, and wireless sensor nodes. Recent work has demonstrated the advantages of tower field constructions for finite field arithmetic in the AES and WG-16 ciphers. In this paper we explore three different tower field constructions for WG-8. The first tower field is tailored to FPGA cells. The second tower field uses a Type-I optimal normal basis. The third tower field exploits algebraic properties of the WG permutation and trace functions. All of the methods use a parallel LFSR to provide data rates from one to eleven bits per clock cycle. Among the three tower fields, the Type-I ONB construction offers the best trade-off in area, speed, and power consumption. However, a plain monolithic look-up table implementation with 256 entries is smaller and faster than the tower field constructions. Our analysis of the tower field options and comparisons to each other and to the monolithic look-up table will provide lessons for future work in exploring novel tower field constructions for WG and other ciphers.
Pipelined Parallel Finite Automata Evaluation (2019)

Finite automata are key compute models in modern computational theory and important building blocks for digital logic used for regular expression and protocol parsing, filtering, and control. Finite automata evaluation would seem to be a sequential operation, since we need to complete the evaluation of one state to know the next state in which to evaluate the logic. Nonetheless, parallel theory provides strategies for parallel finite automata evaluation. We show how to exploit this parallel evaluation strategy in practice on today's high capacity FPGAs, including a novel formulation for spatially pipelined evaluation. For non-deterministic finite automata (NFA) with S states, we can evaluate N inputs in a single cycle with O(N * S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) BRAMs and O(N*S <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) LUTs. This allows us, for example, to consume 64 inputs on a 16 state NFA in a single cycle on the Xilinx XZCU9EG-ffvb1156-2-i SoC FPGA, achieving 47 GB/s (377 Gb/s) single stream throughput for 8b inputs. For a 40 Gb/s network link, we can support 28 state NFAs.
Immunological characterization of a 17-kDa antigen from<i>Cryptosporidium parvum</i>recognized early by mucosal IgA antibodies (1992)

Cryptosporidium parvum antigens were characterized by immunoblot analysis of sera and intestinal secretions of BALB/c mice orally infected with 10(5) oocysts. A major band at 17 kDa under non-reduced conditions and at 18 kDa under reduced conditions was recognized by anti-C. parvum IgA and IgG in serum and intestinal secretions from day 15 post-infection. This recognition persisted throughout the experiment (day 30). Mouse-serum antibodies raised against the 17-kDa purified antigen (P17) showed no cross-reactivity with other C. parvum antigens. Immunofluorescence study revealed that this antigen is located on the sporozoite. It is suggested that this antigen could be a good candidate for studies of mucosal immune response to C. parvum and for vaccination.
Understanding Aqueous Electrolyte Stability through Combined Computational and Magnetic Resonance Spectroscopy: A Case Study on Vanadium Redox Flow Battery Electrolytes (2014)

Abstract The investigation of the vanadium electrolyte stability issue on the molecular‐level solvation structure and the dynamics has led to the successful designing of mixed acid‐based vanadium electrolytes. This new mixed‐acid based electrolyte system render approximately 70 % increase in energy density (≈40 Wh L −1 ) and approximately 80 % increase in stable temperature window (−10 to +50 °C) compared with conventional sulfuric acid‐based vanadium electrolyte. Through a comprehensive study by density functional theory and nuclear magnetic resonance spectroscopies, the improved stability is attributed to the hydrochloric acid as optimal cosolvent providing chloride anions for a ligand‐exchange process in the vanadium solvation structure. The role of the chloride counteranion in the solvation structure and dynamics of vanadium species was studied using combined magnetic resonance spectroscopy and DFT‐based theoretical methods. The solvation phenomenon of multiple vanadium species and their impact on vanadium redox flow battery electrolyte chemical stability are discussed.
Anchoring transition in a nematic liquid crystal composed of centrosymmetric molecules (1994)

A temperature-driven anchoring transition strongly influenced by ionic impurities appears in a nematic liquid crystal composed of centrosymmetric molecules. Two anchoring parameters, the tilt angle and the anchoring strength, were measured. The observed phenomena are explained as a result of a balance between the orienting tendencies of electric double layers and direct molecular interactions at the interface.
Attenuation of corneal myofibroblast development through nanoparticle-mediated soluble transforming growth factor-β type II receptor (sTGFβRII) gene transfer. (2012)

This study demonstrated that PEI-DNA nanoparticles are an attractive vector for the development of nonviral corneal gene therapy approaches and that the sTGFβRII gene delivery into keratocytes could be used to control corneal fibrosis in vivo.
328 Environmental preservation system for road tunnel (2005)

Electrostatic Precipitator (ESP) is one of the environmental preservation systems for road tunnel. ESP for road tunnel is achieved to treat high air volume with high air flow because it is installed in very limited space like a road tunnel and a tunnel ventilation station. In this paper, we describe the application of ESP for road tunnel ventilation station which is extremely limited space and has sudden widen duct. We apply CFD method to unify the air flow and measure the actual air flow.
ChemInform Abstract: The Synthesis of Chiral Fluorinated 4‐Alkyl‐4′‐[(4‐alkylphenyl)ethynyl]biphenyls. (2013)

Abstract The copper‐catalyzed coupling between aryl Grignard reagents and alkyl bromides is optimized to provide intermediates for use in the synthesis of novel cholesteric liquid crystals.
A PILOT STUDY OF INDOCYANINE GREEN CLEARANCE AS AN EARLY PREDICTOR OF GRAFT FUNCTION (1994)

Primary graft dysfunction occurs in up to 10% of liver transplant recipients and is the major reason for early mortality and retransplantation. The conventionally used markers of early graft functio—i.e., correction of acidosis, glucose requirement, consumption of potassium, serum alanine transaminase (ALT),* prothrombin time (PT), bile flow, resolution of encephalopathy and haemodynamic instability can be very misleading as they are dependent on numerous other factors. The aim of this study was to assess the use of indocyanine green clearance (ICG) as a measure of graft function. Peripheral ICG clearance was measured 18–24 hr after liver transplantation in twenty-three consecutive patients (24 transplants). Doppler ultrasonography confirmed normal hepatic arterial blood flow. Correlations between ICG clearance and other markers of graft function and outcome were sought. The mean ICG clearance was 406 mls/min (SD 137.5). A threshold value of 200 ml/min reliably predicted outcome. Significant correlations were found between ICG clearance and times to normalization of PT (P<0.02) and to the correction of acidosis (P<0.05). No correlation was found with ALT, PT, bile flow, glucose requirement, or consumption of potassium. ICG clearance measured on the day after liver transplantation accurately reflects graft function and may be used to predict graft survival and final outcome.
Novel Single-Trip Upper Completion System Saves Rig Time in Deepwater Offshore Brazil (2009)

Abstract This paper outlines the mechanism and functioning of One Trip Upper Completion System using an hydraulic tubing compesating device (HTCD), the UST (Upper-Completion Single-trip System) that enables the integration of all equipments of an upper production string in order to run in hole in one single trip. The UST with HTCD is an upper completion system that integrates safe production string running in hole and simplified hydraulic release after connecting the lower completion equipment to the upper completion system. This paper also emphasizes the difference amongst few systems from conventional dual trip upper completion until other types of tubing seals receptacles used for single trip upper completion, stating all mechanical differences and their peculiarities. This document describes field experiences of Upper-Completion Single-trip (UST) installations using Single Trip Hydraulic Tubing Compensating Device (HTCD) system and establishes a comparative analysis of rig time savings and operation differences using conventional methods compared to the UST with HTCD. Introduction In 2004 first single trip production string was installed. This first successful experience was achieved using a mechanical single trip mechanism and the main objective of this method is to reduce rig time during upper completion installation procedure. The average rig time saving since first deployment of a upper completion single trip has been 24 hours. (1) The reasons upper completion single trip technique has increased in Campos Basin are as follow:Horizontal deep water completions;Use of large bore Completions;Pressure and Temperature Gauges in the production string;Increased number of well control parameters therefore the necessity of larger number of control lines;Chemical injection mandrels and injection lines;Electric Cable and protection clamps; Upper completion string lay out has become complex and therefore deployment limitations has been the challenge. Features as horizontal lower completions; prohybitive rotation of upper completion string and the minimum tolerance between casing ID and some equipments of the production string as clamps and tubing hanger are the main application for upper completion single trip methods as the technique minimizes production string deployment and maximize rig time saving. (See Figure 1) First hydraulic actuated upper completion single trip was run in Campos Basin in Brazil in August 2005 using HTCD. Since 2005 more than 25 hydraulic actuated upper completion single trip has been run in Brazil succesfully.
71 IDENTIFICATION OF TWIST, A BHLH TRANSCRIPTION FACTOR, HIGHLY EXPRESSED IN HUMAN MEDULLOBLASTOMA AND CHARACTERIZATION OF AN IN VITRO MODEL TO EXAMINE POTENTIAL INTERACTIONS WITH SONIC HEDGEHOG SIGNALING (2005)

<h3>Background</h3> TWIST (TW), a bHLH transcription factor with an uninvestigated role in medulloblastoma (MB), has important roles in human cancer and development. Normal cerebellar granule cell precursor development requires sonic hedgehog (Shh) signaling, but mutations causing aberrant Shh signaling can give rise to MB. In vitro, TW directly regulates expression of GLI1, a Shh signaling component. Also GLI1 and TW are co-expressed in rhabdomyosarcoma, a tumor associated with aberrant Shh signaling. Thus we hypothesize that TW plays a role in MB oncogenesis by interacting with Shh signaling. To investigate we analyzed expression of TW and Shh signaling genes in MB cell lines and tumor samples and characterized in vitro Shh signaling inhibition of two MB cell lines using the Smoothened (SMO) inhibitor cyclopamine (cyclo). <h3>Methods</h3> Expression of TW and the Shh signaling pathway genes (PATCH, SMO, GLI1, GLI2 and GLI3) were quantified in 16 MB cell lines and primary tumor samples by qRT-PCR and standardized to GAPDH. TWIST expression was analyzed by immunohistochemistry (IHC) using a TW specific polyclonal antibody in selected tumor tissue samples. In DAOY and RES 256 cell lines we analyzed the concentration dependent effects of cyclo (2.5μM, 5μM, 10μM) on total cell number at 24, 48, 72, and 96 hour time points compared to media, vehicle and a related alkaloid compound, tomatadine. Further analysis of cyclo treated RES 256 was performed by flow cytometry (FC) to quantify necrotic cells, apoptotic cells, and the cell cycle phases. <h3>Results</h3> TW, PATCH, SMO, GLI2, and GLI3 were highly expressed in the majority of tumors and cell lines with GLI1 having an overall lower expression. IHC staining in tumor sections revealed high TW levels. In RES256 and DAOY, treatment with 10μM cyclo significantly reduced cell number and altered cell morphology. Based on FC data, the reduction of cell number at 10 μM cyclo was not due to increased cell necrosis or apoptosis. However, increased %G2 cells at 48 and 96 hours suggest cyclo may promote cell-cycle arrest at the G2/M checkpoint. <h3>Conclusion</h3> High levels of TW suggest a potential in the oncogenesis of MB. Inhibition of Shh signaling by cyclo, in MB, reduces cell proliferation and can provide a useful tool for future investigations of TW interactions with Shh signaling.
Memory Optimization of Data Flow Applications at the Codesign Level (2000)

International audience
Improved resolution in the acidic and basic region of 2‐DE of insect antennae proteins using hydroxyethyl disulfide (2009)

Olfaction is essential for processing chemical signals in insects, but characterizing the proteins implicated in this process has proved challenging. We optimized 2-DE gel resolution of insect proteins by using a buffer containing two reducing agents, DTT and hydroxyethyl disulfide. This buffer clearly improved resolution and decreased spot streaking and spot trains of 2-DE in comparison to DTT alone. We described for the first time that the buffer with DTT and hydroxyethyl disulfide further to reducing streaking in the basic part of the gel eliminates false spots in the acidic gel regions that appeared when only DTT was used as reducing agent.
Copper Iron Chalcogenide Semiconductor Nanocrystals in Energy and Optoelectronics Applications—State of the Art, Challenges, and Future Potential (2023)

Abstract I‐III‐VI 2 semiconductor nanocrystals have been explored in countless optoelectronics and green energy applications. While indium‐based compounds are arguably the best‐known variants of these semiconductors and have been widely studied for their photophysical properties, other I‐III‐VI 2 semiconductors are emerging as serious competitors. This review focuses on the current state of the art and recent progress made in the research and technology of one of the most promising competitors to indium‐based I‐III‐VI 2 semiconductor nanocrystals, CuFeS 2 nanocrystals. CuFeS 2 is a promising alternative to indium‐based systems, mostly because many properties are competitive and because iron is much more abundant than indium. Replacing In(III) with Fe(III) would thus significantly alleviate the issue of raw material availability. The article highlights new synthesis approaches and summarizes and discusses advanced optical properties including surface plasmon resonance and luminescence properties. Moreover, potential applications in thermoelectric, photodetection, photothermal, and photovoltaics are illustrated and discussed. Finally, future perspectives for materials development, upscaling, and application in new processes and devices, such as self‐assembly, patterning, or plasmonic catalysis, are presented as well.
A Tracing Algorithm for Short 2-Secure Probabilistic Fingerprinting Codes Strongly Protecting Innocent Users (2007)

We give a tracing algorithm for 2-secure probabilis- tic fingerprinting codes with the property that it never accuses innocent users when there are up to 2 attackers. Moreover, by using our code and tracing algorithm, innocent users are also unlikely to be accused even if either the number of attackers or attackers' abilities exceed our assumption. Our code is the first example of collusion-secure fingerprinting codes with both of these two properties. Furthermore, our code has shorter length among the preceding 2-secure codes, and possesses further properties desirable in a practical use.
Suppression of Fixational Saccades in Strabismic and Anisometropic Amblyopia (1979)

Individuals with strabismus frequently exhibit large fixational saccadic pairs (saccadic intrusions) during monocular fixation with the amblyopic eye in the light. We found two conditions in which the saccadic intrusion frequency could be markedly reduced. When instructed to ‘hold the eye steady’ in the presence of a visible target in the light, saccadic intrusions were suppressed and eye position maintained within a few degrees of the target. These results suggest that corrective drift was used by the amblyopic eye to aid in position maintenance. When instructed to ‘fixate’ in complete darkness, the intrusive pattern was replaced by a jerk nystagmus-like pattern. These results clearly demonstrate that saccadic intrusions in amblyopic eyes require the presence of a visible target for their generation, and additionally, that ‘extraretinal signals’ were involved in maintenance of eye position under this condition. Saccades could also be suppressed during the ‘hold’ command in the light by patients having amblyopia without strabismus or constant strabismus amblyopia with intermittent jerk nystagmus.