gebhart/patrepeval huggingface dataset:
Synthesis and applications of an aldehyde-containing analog of SCH-23390 (1990)

SCH-23390 is a high-affinity antagonist selective for D1 dopamine receptors (Ki = 2.5 nM). It does not contain a functional group that can be conveniently coupled to commercially available resins for affinity chromatography or to prepare photolabels for photoaffinity labeling of receptors. To construct an affinity resin for purification of dopamine D1 receptors, an aldehyde analogue of SCH-23390, (+/-)-7-chloro-8-hydroxy-1-(4'-formylphenyl)-3-methyl-2,3,4,5-tetrahydro -1H- 3-benzazepine (ASCH), was synthesized. 8-Methoxy-1-(4'-bromophenyl)-SCH-23390 was lithiated, formylated, and O-demethylated to form the aldehyde. NMR and IR analyses were performed to characterize the product. Assays were performed with the radioligand [125I]SCH-23982 to define the biological activity of the aldehyde. ASCH displaced [125I]SCH-23982 binding from caudate membranes with a Ki value of 7.1 nM. ASCH has been coupled through the aldehyde group on the phenyl ring to diaminodipropylamine-agarose for affinity chromatography. After solubilization of caudate membranes in 1% digitonin, the affinity resin retained binding sites for [125I]SCH-23982 that were eluted with 10 mM SCH-23390. The aldehyde was also covalently coupled to biotin hydrazide for fluorescence labeling of dopamine D1 receptors. The biotin-conjugated aldehyde of SCH-23390 displaced [125I]SCH-23982 binding from caudate membranes with a Ki value of 9.3 nM.
GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations (2012)

In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.
Review of different fault detection methods and their impact on pre‐emptive VSC‐HVDC dc protection performance (2017)

Multi‐terminal voltage‐sourced converters (VSC) high‐voltage direct current (HVDC) transmission system is expected to play a vital role in future power systems. Compared with ac power transmission, dc transmission is more vulnerable to faults due to low dc‐side impedances and sensitive power electronics in the converters. Dc protection issues must be tackled before any multi‐terminal VSC‐HVDC grid can be built. The multi‐terminal VSC‐HVDC system is studied in detail using switching models for two‐level converters, detailed equivalent models for the modular multi‐level converters, detailed hybrid circuit breaker switching models and frequency‐dependent phase models for dc cables. Using such high‐fidelity system models, a systematic study of HVDC fault protection methodologies in more detail than previous studies is conducted. This is the first comprehensive study that includes pre‐emptive circuit breaker operation. The results presented in this study underline the benefits of such a detailed treatment of the breaker, and of considering it as part of a fast power electronics system rather than isolated dc equipment. The study identifies the best existing fault detection method and tests it extensively. In order to further improve post‐fault system recovery response, which is a key but often neglected part of previous studies, a novel bump‐less transfer control has been implemented in the converters.
Peanut rhizobia under salt stress: role of trehalose accumulation in strain ATCC 51466 (1995)

Strain ATCC 51466, a motile peanut Rhizobium sp., showed patterns of utilization of diverse carbon sources characteristic of fast growers. Bacteria had periplasmic neutral glucans with molecular weight close to 3000. When the extracellular concentration of NaCl was raised to 400 mM, the lag phase of the culture was prolonged about threefold and the generation time was increased almost twice. The changes in growth behavior of salt-stressed bacteria were accompanied by the full suppression of periplasmic oligoglucans and the accumulation of cellular trehalose. Almost identical changes in cell-associated oligoglucans were observed after exposing peanut Rhizobium sp. strain ATCC 10317 to hypersalinity. When the osmotic pressure of the medium was augmented by the addition of either 200 mM mannitol or 16% (w/v) polyethylene glycol, cells of strain ATCC 51466 contained decreased levels of oligoglucans and accumulated trehalose. On the other hand, the content of cellular trehalose increased throughout logarithmic and stationary phases of growth of strain ATCC 51466 in a medium supplemented with 400 mM NaCl. When bacterial cultures were shifted from hypersaline to basal media, oligoglucans were the only oligosaccharides detected. The addition of 10 mM proline to bacteria grown under hypersalinity led to a 50% decrease in the level of trehalose and to the accumulation of oligoglucans. The addition of 10 mM glycine betaine to bacteria grown under hypersalinity also produced accumulation of oligoglucans, but the level of trehalose did not decrease. The results presented here are consistent with a role for trehalose as a compatible solute in peanut Rhizobium ATCC 51466, and they suggest that exogenously added proline may act as a compatible solute in preference to trehalose.Key words: periplasmic glucans, trehalose, peanut Rhizobium, osmotic stress.
Mapping of rRNA genes with integrable plasmids in Bacillus subtilis (1986)

Integrable plasmids pGR102 and pWR103 containing ribosomal sequences from within the transcriptional units for 16S and 23S were used to transform Bacillus subtilis. To date, these plasmids integrated into 7 of 10 known rrn operons. Two such events occurred at unassigned operons, revealing a close linkage of the CAT gene of the plasmid to pha-1 situated between dal-1 and purB33 for rrnE and to thiA78 situated between glyB133 and re-12 for rrnD. All seven integration events that led to the loss of unique ribosomal BclI fragments can now be assigned to known rrn operons.
Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan (2016)

Many human diets contain arabinoxylan, and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets.
Functional characterization of NPM1–TYK2 fusion oncogene (2022)

Gene fusions are known to drive many human cancers. Therefore, the functional characterization of newly discovered fusions is critical to understanding the oncobiology of these tumors and to enable therapeutic development. NPM1-TYK2 is a novel fusion identified in CD30 + lymphoproliferative disorders, and here we present the functional evaluation of this fusion gene as an oncogene. The chimeric protein consists of the amino-terminus of nucleophosmin 1 (NPM1) and the carboxyl-terminus of tyrosine kinase 2 (TYK2), including the kinase domain. Using in vitro lymphoid cell transformation assays and in vivo tumorigenic xenograft models we present direct evidence that the fusion gene is an oncogene. NPM1 fusion partner provides the critical homodimerization needed for the fusion kinase constitutive activation and downstream signaling that are responsible for cell transformation. As a result, our studies identify NPM1-TYK2 as a novel fusion oncogene and suggest that inhibition of fusion homodimerization could be a precision therapeutic approach in cutaneous T-cell lymphoma patients expressing this chimera.
Apoptotic cell-mediated suppression of streptococcal cell wall-induced arthritis is associated with alteration of macrophage function and local regulatory T-cell increase: a potential cell-based therapy? (2009)

Our data indicate that apoptotic cells modulate macrophage function and result in Treg generation/increase. This may be involved in inhibition of inflammation and amelioration of arthritis. This highlights and confirms previous studies showing that in vivo generation of Tregs using apoptotic cell injection may be a useful tool to prevent and treat inflammatory autoimmune responses.
The crystal structure of apo‐pseudoazurin from <i>Alcaligenes faecalis</i> S‐6 (1995)

The 3D structure of the apo-pseudoazurin (copper free pseudoazurin) from Alcaligenes faecalis strain S-6 is determined and refined at pH 6.7 using X-ray diffraction data to 1.85 A resolution. The final crystallographic R-factor is 0.164. Comparing the structures of apo-pseudoazurin and the native (Cu2+) protein, we observed limited differences ranging between 0.1-0.4 A at the vicinity of the copper site, at the loops connecting the secondary structural elements, at certain beta-strands and at the amino and carboxy termini of the protein.
Feline Coronavirus Participation in Diarrhea of Cats. (1999)

Fecal samples were examined for viruses participated in gastrointestinal disorders of cats, especially focusing on feline coronavirus (FCoV) by a reverse transcriptase-polymerase chain reaction assay. It was found that a primary viral pathogen was feline panleukopenia parvovirus (FPLV; 28.5% of the positive rate) and the secondary was FCoV (10.7%). Commonly reported clinical signs of cats of which feces were FCoV-positive were vomiting, diarrhea and dehydration with an exception of one serious case with concurrent FPLV infection.
Email fraud detection by identifying email sender (2017)

Tackling irrelevant emails have become part of every email user's activity. Emails that seem valid are received in the inbox and sometimes relevant emails are directed to spam. Another aspect of the problem is that, due to very high number of incoming emails, it is very difficult to identify the required ones easily. In this process, user wastes so much of their time, energy and efforts by sifting through irrelevant emails in which they have no interest. Sometimes users also get frustrated getting such junk emails frequently. Features like Ngram, Lemmatization, creating personalized vocabulary, and observation of patterns are used in the paper. Text Mining algorithms like Ngram and Lesk will be used to find the frequency of words like positive words, negative words and most frequent words. A WordNet library is used to find relevant words in the text. Unigram, Bigram and Trigram algorithms are incorporated to learn the writing behavior of the users by creating a user vocabulary, which contains particular words and its frequency in the incoming emails. Test emails can be used to evaluate the performance of the system. The system can start working as a fraud detection system which identifies the real sender.
GNSS Spoof Detection Based on Pseudoranges from Multiple Receivers (2015)

Spoofing is the common term used for describing the intentional broadcasting of false radio frequency signals intended to disrupt and mislead systems that depend on accurate position, navigation, and timing information provided by Global Navigation Satellite Systems (GNSS). Spoofing is an increasingly recognized threat garnering increased interest from researchers and users, both military and civilian. This paper presents a GNSS spoof detection algorithm that exploits the geometric distribution of a horizontal array of GNSS receiver antennae and the geometric configuration of visible navigation satellites. Using a Neyman-Pearson hypothesis testing formulation, a spatial correlation test is developed that can accurately and dependably detect a GNSS spoofing event. This paper develops the generalized likelihood ratio test using standard statistical models of the GNSS range measurements and maximum likelihood estimates of the unknown variables. An analysis is presented showing the performance effects of the number of receivers used, internal receiver clock bias estimation, unknown antenna array orientation, and temporal and spatial locations of the detector. Simulations were conducted using a GNSS simulator and receiver combination to further substantiate theoretical claims. Furthermore, comparisons to similar prior work using position solutions shows a marked improvement in performance.
A novel human autoantigen, endothelial cell growth factor, is a target of T and B cell responses in patients with Lyme disease (2012)

T and B cell responses to ECGF occur in a subset of patients with Lyme disease, particularly in those with antibiotic-refractory arthritis, providing the first direct evidence of autoimmune T and B cell responses in this illness.
Polyphenols: Extraction Methods, Antioxidative Action, Bioavailability and Anticarcinogenic Effects (2016)

Being secondary plant metabolites, polyphenols represent a large and diverse group of substances abundantly present in a majority of fruits, herbs and vegetables. The current contribution is focused on their bioavailability, antioxidative and anticarcinogenic properties. An overview of extraction methods is also given, with supercritical fluid extraction highlighted as a promising eco-friendly alternative providing exceptional separation and protection from degradation of unstable polyphenols. The protective role of polyphenols against reactive oxygen and nitrogen species, UV light, plant pathogens, parasites and predators results in several beneficial biological activities giving rise to prophylaxis or possibly even to a cure for several prevailing human diseases, especially various cancer types. Omnipresence, specificity of the response and the absence of or low toxicity are crucial advantages of polyphenols as anticancer agents. The main problem represents their low bioavailability and rapid metabolism. One of the promising solutions lies in nanoformulation of polyphenols that prevents their degradation and thus enables significantly higher concentrations to reach the target cells. Another, more practiced, solution is the use of mixtures of various polyphenols that bring synergistic effects, resulting in lowering of the required therapeutic dose and in multitargeted action. The combination of polyphenols with existing drugs and therapies also shows promising results and significantly reduces their toxicity.
A 40-Gb/s Self-Clocked Bidirectional Serial/Parallel Converter for Asynchronous Label Swapping (2007)

A novel scheme for self-clocked bidirectional serial/parallel conversion is proposed with an optically clocked transistor array (OCTA). As a result of its internal clock generation, serial-to-parallel (SP) and parallel-to-serial (PS) conversion capability, the OCTA alone realizes a single-chip low-power interface between input-output high-speed asynchronous burst optical packets and complimentary metal-oxide-semiconductor electronics, thus enabling a compact low-power solution for label swapping of optical packets. An eight-channel OCTA demonstrates self-clocked SP and PS conversion at 40 Gb/s
Validation of Volume-Pressure Recording Tail-Cuff Blood Pressure Measurements (2008)

We conclude that the VPR tail-cuff method provides accurate blood pressure measurements over the physiological range of blood pressure in mice.
VLSI implementation of pulse density modulated neural network structure (2003)

An efficient implementation of a Hopfield-type, fully connected neural-network architecture is presented. It is based on a pulse-density-modulation technique implemented using switched-capacitor structures. The synaptic weights are programmable, and thus the area of one synapse and the entire network depends on the resolution of the weight. Advantages of the design are simple synapse structure and thus small area, expandability, and modularity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The E8 subfragment of laminin promotes locomotion of myoblasts over extracellular matrix. (1989)

The locomotion of murine myoblasts over the extracellular matrix components laminin and fibronectin was analyzed using quantitative videomicroscopy, and the organization of the cytoskeleton was observed in parallel immunofluorescence studies. Cells plated on the laminin-nidogen complex locomoted twice as fast as on laminin alone. The main form of translocation on laminin was a jerky cycle of prolonged lamellipod extension followed by rapid (approximately 200- less than 500 microh h-1) movement of the cell body into the extended lamellipod. The locomotion-stimulating activity of laminin resides in the elastase digestion fragment E8, part of the laminin long arm, while the E1-4 fragment containing the three short arms is inactive. Myoblasts moved poorly over fibronectin irrespective of whether high, intermediate, or low coating concentrations were used (approximately 5,000- approximately 10 fmol cm-2). In contrast, the locomotory responses both to laminin and to E8 peaked sharply at coating concentrations approximately 20-50 fmol cm-2 and decreased at higher concentrations. This response corresponds to that expected for a haptotactic stimulant. When cells locomoted over a mixed substrate of laminin and fibronectin, the fibronectin effects appeared to predominate. The cytoskeleton has been implicated in many cellular motile processes. Within 6 h on fibronectin many cells expressed vinculin-containing focal contacts, elaborated stress fibers and had periodically organized alpha actinin, whereas on laminin, most cells showed diffuse vinculin and alpha actinin and a fine meshlike actin cytoskeleton. We conclude that the poor locomotion of cells over fibronectin is because of the cytoskeletal stabilization it induces.
Experimental Resilience Assessment of an Open-Source Driving Agent (2018)

Autonomous vehicles (AV) depend on the sensors like RADAR and camera for the perception of the environment, path planning, and control. With the increasing autonomy and interactions with the complex environment, there have been growing concerns regarding the safety and reliability of AVs. This paper presents a Systems-Theoretic Process Analysis (STPA) based fault injection framework to assess the resilience of an open-source driving agent, called openpilot, under different environmental conditions and faults affecting sensor data. To increase the coverage of unsafe scenarios during testing, we use a strategic software fault-injection approach where the triggers for injecting the faults are derived from the unsafe scenarios identified during the high-level hazard analysis of the system. The experimental results show that the proposed strategic fault injection approach increases the hazard coverage compared to random fault injection and, thus, can help with more effective simulation of safety-critical faults and testing of AVs. In addition, the paper provides insights on the performance of openpilot safety mechanisms and its ability in timely detection and recovery from faulty inputs.
Palladium‐Phosphinous Acid‐Catalyzed Sonogashira Cross‐Coupling Reactions in Water. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Non-Metabolic Membrane Tubulation and Permeability Induced by Bioactive Peptides (2007)

We showed that the degree of membrane permeabilization with amphipathic peptides is dependent on both peptide size and hydrophobic nature of the residues. We propose a model for peptide-induced membrane perturbations that explains the differences in peptide membrane activities and suggests the existence of a facilitated "physical endocytosis," which represents a new pathway for peptide cellular internalization.
Power-Scaling Output-Compensated Three-Stage OTAs for Wide Load Range Applications (2020)

With the aggressive scaling of transistor dimensions, intrinsic device gains are dropping but the need for high-gain amplifiers still exists, resulting in a great interest in multistage amplifiers. Most existing amplifier topologies rely on Miller capacitors which achieve stability at the expense of reduced speed. In this paper, a new state feedback compensation strategy with gain enhancement using partial positive feedback is proposed whereby a multistage amplifier can be made output-compensated, thereby requiring no Miller capacitance while being able to drive a wide range of load capacitances. After a thorough theoretical analysis, a topology prototype is fabricated in a standard 130 nm CMOS technology and is able to drive loads from 90 nF-50 nF (~ 555×) using three discrete modes. The amplifier's power and bandwidth are scalable depending on the expected capacitive load range, with a maximum power consumption of 185 μW from a 1 V supply. Comparison with state-of-the-art amplifiers shows superior small-signal performance and competitive large-signal performance while driving a significantly larger range of capacitive loads.
Gibberellin Biosynthesis and the Regulation of Plant Development (2006)

Gibberellins (GAs) form a large family of plant growth substances with distinct functions during the whole life cycle of higher plants. The rate of GA biosynthesis and catabolism determines how the GA hormone pool occurs in plants in a tissue and developmentally regulated manner. With the availability of genes coding for GA biosynthetic enzymes, our understanding has improved dramatically of how GA plant hormones regulate and integrate a wide range of growth and developmental processes. This review focuses on two plant systems, pumpkin and Arabidopsis, which have added significantly to our understanding of GA biosynthesis and its regulation. In addition, we present models for regulation of GA biosynthesis in transgenic plants, and discuss their suitability for altering plant growth and development.