gebhart/patrepeval huggingface dataset:
Biochemical and Mutational Analyses of AcuA, the Acetyltransferase Enzyme That Controls the Activity of the Acetyl Coenzyme A Synthetase (AcsA) in <i>Bacillus subtilis</i> (2008)

The acuABC genes of Bacillus subtilis comprise a putative posttranslational modification system. The AcuA protein is a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily, the AcuC protein is a class I histone deacetylase, and the role of the AcuB protein is not known. AcuA controls the activity of acetyl coenzyme A synthetase (AcsA; EC 6.2.1.1) in this bacterium by acetylating residue Lys549. Here we report the kinetic analysis of wild-type and variant AcuA proteins. We contrived a genetic scheme for the identification of AcuA residues critical for activity. Changes at residues H177 and G187 completely inactivated AcuA and led to its rapid turnover. Changes at residues R42 and T169 were less severe. In vitro assay conditions were optimized, and an effective means of inactivating the enzyme was found. The basic kinetic parameters of wild-type and variant AcuA proteins were obtained and compared to those of eukaryotic GNATs. Insights into how the isolated mutations may exert their deleterious effect were investigated by using the crystal structure of an AcuA homolog.
CheckMate: Automated Synthesis of Hardware Exploits and Security Litmus Tests (2018)

Recent research has uncovered a broad class of security vulnerabilities in which confidential data is leaked through programmer-observable microarchitectural state. In this paper, we present CheckMate, a rigorous approach and automated tool for determining if a microarchitecture is susceptible to specified classes of security exploits, and for synthesizing proof-of-concept exploit code when it is. Our approach adopts "microarchitecturally happens-before" (μhb) graphs which prior work designed to capture the subtle orderings and interleavings of hardware execution events when programs run on a microarchitecture. CheckMate extends μhb graphs to facilitate modeling of security exploit scenarios and hardware execution patterns indicative of classes of exploits. Furthermore, it leverages relational model finding techniques to enable automated exploit program synthesis from microarchitecture and exploit pattern specifications. As a case study, we use CheckMate to evaluate the susceptibility of a speculative out-of-order processor to Flush+Reload cache side-channel attacks. The automatically synthesized results are programs representative of Meltdown and Spectre attacks. We then evaluate the same processor on its susceptibility to a different timing side-channel attack: Prime+Probe. Here, CheckMate synthesized new exploits that are similar to Meltdown and Spectre in that they leverage speculative execution, but unique in that they exploit distinct microarchitectural behaviors-speculative cache line invalidations rather than speculative cache pollution-to form a side-channel. Most importantly, our results validate the CheckMate approach to formal hardware security verification and the ability of the CheckMate tool to detect real-world vulnerabilities.
Thermo- and pH-Responsive Biodegradable Poly(α-<i>N</i>-substituted γ-glutamine)s (2003)

New double stimuli-responsive poly(alpha-N-substituted gamma-glutamine) has been developed, which was synthesized by the reaction of poly(gamma-glutamic acid) with amino alcohols. Appropriate combinations of the amino alcohols provided the biodegradable poly(amino acid) exhibiting a sharp lower critical solution temperature (LCST) in water. Furthermore, the phase transition temperature was highly sensitive to pH changes.
Arrhythmic Pulses Detection Using Lempel-Ziv Complexity Analysis (2006)

Computerized pulse analysis based on traditional Chinese medicine (TCM) is relatively new in the field of automatic physiological signal analysis and diagnosis. Considerable researches have been done on the automatic classification of pulse patterns according to their features of position and shape, but because arrhythmic pulses are difficult to identify, until now none has been done to automatically identify pulses by their rhythms. This paper proposes a novel approach to the detection of arrhythmic pulses using the Lempel-Ziv complexity analysis. Four parameters, one lemma, and two rules, which are the results of heuristic approach, are presented. This approach is applied on 140 clinic pulses for detecting seven pulse patterns, not only achieving a recognition accuracy of 97.1% as assessed by experts in TCM, but also correctly extracting the periodical unit of the intermittent pulse.
Enhancing hydrogen production of microalgae by redirecting electrons from photosystem I to hydrogenase (2014)

The solar light-dependent hydrogen production by the [FeFe] hydrogenase HYDA1 is increased by knowledge-based modification of its native electron donor.
ChemInform Abstract: Synthesis and Class III Antiarrhythmic Activity of (Phenylbut‐2‐enyl)ammonium Salts. Effect of Conformation on Activity. (1987)

Abstract The anilines (I) are converted to the diazonium compounds (II) which are coupled with butadiene (III) to give the isomeric olefines (IV) and (V).
TROUBLE ON OILED WATERS: Lessons from the<i>Exxon Valdez</i>Oil Spill (1996)

▪ Abstract The Exxon Valdez oil spill was the largest in US maritime history. We review post-spill research and set it in its legal context. The Exxon Corporation, obviously responsible for the spill, focused on restoration, whereas the Trustees, a coalition of state and federal entities, focused on damage and its assessment. Despite billions of dollars expended, little new understanding was gained about the recovery dynamics of a high latitude marine ecosystem subject to an anthropogenic pulse perturbation. We discuss a variety of case studies that highlight the limitations to and shortcomings of the research effort. Given that more spills are inevitable, we recommend that future studies address spatial patterns in the intertidal, and focus on the abundances of long-lived species and on organisms that preserve a chronological record of growth. Oil spills, while tragic, represent opportunities to gain insight into the dynamics of marine ecosystems and should not be wasted.
Nanomaterials as Assisted Matrix of Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Analysis of Small Molecules (2017)

Matrix-assisted laser desorption/ionization (MALDI), a soft ionization method, coupling with time-of-flight mass spectrometry (TOF MS) has become an indispensible tool for analyzing macromolecules, such as peptides, proteins, nucleic acids and polymers. However, the application of MALDI for the analysis of small molecules (<700 Da) has become the great challenge because of the interference from the conventional matrix in low mass region. To overcome this drawback, more attention has been paid to explore interference-free methods in the past decade. The technique of applying nanomaterials as matrix of laser desorption/ionization (LDI), also called nanomaterial-assisted laser desorption/ionization (nanomaterial-assisted LDI), has attracted considerable attention in the analysis of low-molecular weight compounds in TOF MS. This review mainly summarized the applications of different types of nanomaterials including carbon-based, metal-based and metal-organic frameworks as assisted matrices for LDI in the analysis of small biological molecules, environmental pollutants and other low-molecular weight compounds.
The Stability Constants of Ethylenediaminetetraacetato, Trimethylenediaminetetraacetato and Propylenediaminetetraacetato Complexes of Some Divalent Metal Ions (1965)

Abstract Two methods are presented for the determination of the stability constants of ethylenediaminetetraacetato, trimethylenediaminetetraacetato and propylenediaminetetraacetato complexes of some divalent metal ions. One is a new method which is based on the polarographic measurement of the concentration of an uncomplexed ligand in a solution containing two kinds of ligands and an appropriate metal ion. The other is a modification of the method described in the previous paper. From the results obtained by these methods and those obtained previously, the individual stability constants have been calculated. The values of the logarithmic stability constants of complexes at 25°C and ionic strength 0.2 are: Mn 13.64, Co 15.71, Ni 18.12, Cu 18.46, Zn 15.94, Cd 15.98 and Pb 17.76 for ethylenediaminetetraacetato complexes; Mn &lt;10.8, Co 14.48, Ni 17.29, Cu 18.04, Zn 14.26, Cd 12.69 and Pb 13.04 for trimethylenediaminetetraacetato complexes, and Mn 14.85, Co 17.07, Ni 19.42, Cu 19.64, Zn 17.14, Cd 17.43 and Pb 18.69 for propylenediaminetetraacetato complexes.
Bishop, Elizabeth: Das lyrische Werk (2020)

Elizabeth Bishop verstand sich früh als Schriftstellerin und veröffentlichte schon als Collegestudentin Kurzgeschichten und Gedichte in landesweit erscheinenden Magazinen. Vermittelt durch Marianne Moore erschienen 1935 drei ihrer Gedichte in einer Anthologie, die junge Dichter vorstellte. Zwei der Gedichte zeigen ihr an der englischen Lyrik des 17. und 19. Jh.s geschultes Formbewusstsein, das dritte jedoch, „The Map“ (Die Landkarte), deutet auf zentrale Charakteristika ihres späteren Schaffens voraus und leitet dann auch programmatisch ihren ersten Gedichtband North & South, 1946 (Nord & Süd), ein. Die Karte – und im weiteren Sinne die Geographie – als ein Leitthema in Bishops Werk lädt in den Gedichten zu präzisen Beschreibungen ein und verankert diese im Konkreten und Sichtbaren. Doch das scheinbar Fixierte gerät in Bewegung, sobald nach den Beziehungen zwischen den Zeichen, zwischen Zeichen und Bezeichnetem, wie auch zwischen den Zeichen, seinen Schöpfern und Interpreten und der Realität gefragt wird. In Bishops Gedichten wird Geographie somit persönlich, historisch, moralisch und ästhetisch gedeutet.
Epidemiological Correlates of Virulence Genotype and Phylogenetic Background among<i>Escherichia coli</i>Blood Isolates from Adults with Diverse‐Source Bacteremia (2002)

Associations of virulence genotype and phylogenetic background with epidemiological factors (primary source of bacteremia, host compromise status, and hospital versus community origin) were assessed among 182 Escherichia coli blood isolates from adults with diverse-source bacteremia in comparison with fecal controls from the E. coli Reference collection. A continuum of virulence was found, from urinary and pulmonary source bacteremia isolates (high virulence), through "other" or unknown source bacteremia isolates (intermediate virulence), to fecal isolates (low virulence), with a corresponding graded phylogenetic distribution from predominantly group B2 to predominantly groups A and B1. Associations of bacterial traits with clinical factors varied considerably, depending on subgroup and statistical method. However, certain putative virulence genes (including several "nontraditional" markers, such as pathogenicity island-associated malX) repeatedly emerged as significant epidemiological predictors, which provided evidence of their possible relevance in host-pathogen interactions and hence as potential targets for preventive interventions against extraintestinal infections due to E. coli.
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks. (2018)

An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our framework can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.
A novel parallel deadlock detection algorithm and architecture (2001)

A novel deadlock detection algorithm and its hardware implementation are presented in this paper. The hardware deadlock detection algorithm has a run time complexity of O/sub hw/(min(m,n)), where m and n are the number of processors and resources, respectively. Previous algorithms based on a resource allocation graph have O/sub sw/(m/spl times/n) run time complexity for the worst case. We simulate a realistic example in which the hardware deadlock detection unit is applied, and demonstrate that the hardware implementation of the novel deadlock detection algorithm reduces deadlock detection time by 99.5%. Furthermore, in a realistic example, total execution time is reduced by 68.9%.
HERPES SIMPLEX VIRUS INFECTION AND APOPTOSIS (2004)

Consequences of human herpes simplex virus (HSV) infection include the induction of apoptosis and the concomitant synthesis of proteins which act to block this process from killing the infected cell. Recent data has clarified our current understanding of the mechanisms of induction and prevention of apoptosis by HSV. These findings emphasize the fact that modulation of apoptosis by HSV during infection is a multicomponent phenomenon. We review recent evidence showing how this important human pathogen modulates the fundamental cell death process.
Grasp sensing for human-computer interaction (2010)

The way we grasp an object depends on several factors, e.g. the intended goal or the hand's anatomy. Therefore, a grasp can convey meaningful information about its context. Inferring these factors from a grasp allows us to enhance interaction with grasp-sensitive objects. This paper highlights an grasp as an important source of meaningful context for human-computer interaction and gives an overview of prior work from other disciplines. This paper offers a basis and framework for further research and discussion by proposing a descriptive model of meaning in grasps. The GRASP model combines five factors that determine how an object is grasped: goal, relationship between user and object, anatomy, setting, and properties of the object. The model is validated both from an epistemological perspective and by applying it to scenarios from related work.
Production of alkyl ester as biodiesel from fractionated lard and restaurant grease (2002)

Abstract Methyl or ethyl esters were produced from lard and restaurant grease by lipase‐ or base‐catalyzed reactions. Before esterifying, some renewable substrates (lard and restaurant grease) should be manipulated through acetone fractionation or on a chromatography column packed with an adsorbent to obtain maximal reaction rate. Because lipase activity was hindered by excess amounts (more than 1 mol) of methanol, each 1 M methanol was added sequentially after 24 h of reaction. Through a three‐step reaction, 74% conversion to tallow‐methyl ester was obtained. However, a porous substance, such as silica gel, improved the conversion when more than 1 M methanol was used as reaction substrate. When a 1∶3 (fractionated lard/methanol, mole ratio) substrate was used, the conversion rates (i.e., extent of conversion) were 2.7 (24 h) and 2.8% (48 h). However, with 10% silica gel in the reaction mixture, the conversion rates increased to 25 and 58%, respectively. Regenerated restaurant grease (FFA removed through column chromatography) was further converted to esters by alkali‐catalyzed methanolysis. After 24 h of reaction, 96% conversion was obtained, while only 25% conversion was observed from crude grease. Alkyl esters produced in this study could be used for fuels, potentially as biodiesel.
New Challenges for Intervertebral Disc Treatment Using Regenerative Medicine (2009)

The development of tissue engineering therapies for the intervertebral disc is challenging due to ambiguities of disease and pain mechanisms in patients, and lack of consensus on preclinical models for safety and efficacy testing. Although the issues associated with model selection for studying orthopedic diseases or treatments have been discussed often, the multifaceted challenges associated with developing intervertebral disc tissue engineering therapies require special discussion. This review covers topics relevant to the clinical translation of tissue-engineered technologies: (1) the unmet clinical need, (2) appropriate models for safety and efficacy testing, (3) the need for standardized model systems, and (4) the translational pathways leading to a clinical trial. For preclinical evaluation of new therapies, we recommend establishing biologic plausibility of efficacy and safety using models of increasing complexity, starting with cell culture, small animals (rats and rabbits), and then large animals (goat and minipig) that more closely mimic nutritional, biomechanical, and surgical realities of human application. The use of standardized and reproducible experimental procedures and outcome measures is critical for judging relative efficacy. Finally, success will hinge on carefully designed clinical trials with well-defined patient selection criteria, gold-standard controls, and objective outcome metrics to assess performance in the early postoperative period.
EFFECTS OF SOME PHOSPHATIDYL COMPOUNDS ON BOAR SPERMATOZOA FOLLOWING COLD SHOCK OR SLOW COOLING (1975)

A.R.C Unit of Reproductive Physiology and Biochemistry, 307 Huntingdon Road, Cambridge CB3 0JQ (Received 9th October 1974) Rapid cooling of the spermatozoa of most mammalian species leads to irreversible decrease in motility and metabolism (Milovanov, 1934; Chang & Walton, 1940), leakage of intracellular proteins and enzymes (Mann & Lutwak-Mann, 1955), increase in the proportion of differentially stained cells (Easley, Mayer & Bogart, 1942) and changes in cellular cation concentrations (Blackshaw & Salisbury, 1957). These effects could all result from changes in permeability which suggests that the cell membrane is the principal target of injury. The visible disruption of membranes, particularly in the acrosomal region (Hancock, 1952), supports this hypothesis. Phospholipids are of major importance in membrane structure and ram, bull and boar spermatozoa are known to release phospholipid into the surrounding medium on cold shock and freezing (Darin-Bennett, Poulos & White, 1973). Various compounds, most notably milk and egg yolk,
Effect of Parathyroid Hormone on Gastrin and Somatostatin Release from the Gastric Antrum (1981)

The release of immunoreactive gastrin and somatostatin form the gastric antrum was studied in anesthetized pigs after parathyroid hormone (PTH) infusion into the antral circulation. PTH (40 units/20 min) was infused into the right gastro-epiploic artery. Blood was sampled from the right gastro-epiploic vein (antral venous blood) and from the superior vena cava (mixed venous blood). The basal gastrin concentration in antral venous blood was 17 times higher than that in mixed venous blood (1220 + 367 versus 71 +25 pmol/1, mean +SE). The somatostatin concentrations in antral and mixed venous blood were 127 +20 and 82 +23 pg/ml (mean +SE), respectively. After PTH infusion the gastrin level both in antral and mixed venous blood increased significantly without inducing systemic hypercalcemia. PTH infusion did not significantly influence the somatostatin level either in antral venous blood or in mixed venous blood. The findings demonstrate that PTH can induce gastrin release from the gastric antrum without concomitant systemic hypercalcemia and that this release of gastrin is not accompanied by a change in the somatostatin level in antral venous blood.
Synthesis and some pharmacological properties of the 23-peptide 15-lysine-secretin-(5-27). Special role of the residue in position 15 in biological activity of the vasoactive intestinal polypeptide (1978)

The 23-peptide 15-lysine-secretin-(5-27) [S(5-27)] was synthesized on an insoluble support. The residue in position 15 of secretin, aspartic acid, was replaced by lysine, which occupies that position in the vasoactive intestinal polypeptide (VIP), a member of the secretin family. The resulting analogue showed increased VIP-like activity on smooth muscle preparations and unaltered secretin-like activity on pancreatic juice secretion in the rat. The affinity of the new analogue was high-affinity secretin receptors in acinar cells from guinea pig pancreas was less than that of S(5-27) but was higher than that of S(5-27) for high-affinity VIP receptors in the same cells.
Dextran Hydrogels Containing Poly(<i>N</i>‐isopropylacrylamide) as Grafts and Cross‐Linkers Exhibiting Enzymatic Regulation in a Specific Temperature Range (2004)

Abstract Summary: Specific temperature‐responsive biodegradable hydrogels were synthesized and characterized in terms of their regulation of enzymatic accessibility based on the physical properties of the temperature‐responsive polymers. The hydrogels consist of glycidyl methacrylate‐modified dextran grafted with the poly( N ‐isopropylacrylamide) (PNIPAAm) homopolymer, and cross‐linked by co‐polymerization with NIPAAm and N , N ‐dimethylacrylamide (DMAAm). The coil‐globule change in the grafted poly(NIPAAm) chains and only a slight dehydration of the poly(NIPAAm‐co‐DMAAm) cross‐linkers are effective in controlling the enzymatic degradation over a specific temperature range. The thermo‐responses of the graft chains (steric hindrance) and the crosslinkers (slight deswelling of the hydrogel networks) control the enzymatic degradation of the hydrogel. image The thermo‐responses of the graft chains (steric hindrance) and the crosslinkers (slight deswelling of the hydrogel networks) control the enzymatic degradation of the hydrogel.
Antioxidant, Pro-Oxidant and Other Biological Activities of Sesquiterpenes (2014)

Sesquiterpenes, 15-carbon compounds formed from 3 isoprenoid units, are secondary metabolites produced mainly in higher plants but also in fungi and invertebrates. Sesquiterpenes occur in human food, but they are principally taken as components of many folk medicines and dietary supplements. Moreover, sesquiterpenes could become a rich reservoir of candidate compounds for drug discovery as several sesquiterpenes and their derivatives possess interesting biological activities. Recent efforts in the research and development of new drugs derived from natural products have led to the identification of a variety of sesquiterpenes that possess promising anti-inflammatory, antiparasitic and anti-carcinogenic activities. On the other hand, some sesquiterpenes can cause serious toxicity and other adverse effects. Therefore, more and more attention has been paid to the investigation of the mechanisms of biological activities of sesquiterpenes in vitro as well as in vivo. The data collected in this review show that many of sesquiterpenes biological activities are based on antioxidant or pro-oxidant actions of sesquiterpenes. Structure, concentration, metabolism as well as type of cells determine if sesquiterpene acts as anti-oxidant or pro-oxidant. Therefore, detailed research of sesquiterpenes is very important for evaluation of their efficacy and for their safe use.