gebhart/patrepeval huggingface dataset:
Interaction traces mining for efficient system responses generation (2013)

Software service emulation is an emerging technique for creat-ing realistic executable models of server-side behaviour. It is particularly useful in quality assurance and DevOps, replicating production-like conditions for large-scale enterprise software sys-tems. Existing approaches can automatically build client-server and server-server interaction models of complex software systems directly from analysis of service interaction trace data. However, when these interaction traces become large, searching an entire trace library to generate a run-time responses can become very slow. In this paper we describe a new technique that utilises data mining, specifically clustering algorithms, to pre-process large amounts of recorded interaction trace data. With the obtained clusters we facilitate efficient yet well-formed runtime response generation in our Enterprise System emulation environment. We evaluate our approach using two common application-layer pro-tocols: LDAP and SOAP. Our experimental results show that by utilising clustering techniques in the pre-processing step, the response generation time can be reduced by 99 % on average com-pared with existing approaches.
MutLα and Proliferating Cell Nuclear Antigen Share Binding Sites on MutSβ (2010)

MutSbeta (MSH2-MSH3) mediates repair of insertion-deletion heterologies but also triggers triplet repeat expansions that cause neurological diseases. Like other DNA metabolic activities, MutSbeta interacts with proliferating cell nuclear antigen (PCNA) via a conserved motif (QXX(L/I)XXFF). We demonstrate that MutSbeta-PCNA complex formation occurs with an affinity of approximately 0.1 microM and a preferred stoichiometry of 1:1. However, up to 20% of complexes are multivalent under conditions where MutSbeta is in molar excess over PCNA. Conformational studies indicate that the two proteins associate in an end-to-end fashion in solution. Surprisingly, mutation of the PCNA-binding motif of MutSbeta not only abolishes PCNA binding, but unlike MutSalpha, also dramatically attenuates MutSbeta-MutLalpha interaction, MutLalpha endonuclease activation, and bidirectional mismatch repair. As predicted by these findings, PCNA competes with MutLalpha for binding to MutSbeta, an effect that is blocked by the cell cycle regulator p21(CIP1). We propose that MutSbeta-MutLalpha interaction is mediated in part by residues ((L/I)SRFF) embedded within the MSH3 PCNA-binding motif. To our knowledge this is the first case where residues important for PCNA binding also mediate interaction with a second protein. These findings also indicate that MutSbeta- and MutSalpha-initiated repair events differ in fundamental ways.
Boyer J.-C, Amsterdam la plus petite des grandes métropoles (2000)

Chaline Claude. Boyer J.-C, Amsterdam la plus petite des grandes métropoles. In: Annales de Géographie, t. 109, n°616, 2000. p. 655.
Factors Controlling the Substrate Specificity of Peroxidases:  Kinetics and Thermodynamics of the Reaction of Horseradish Peroxidase Compound I with Phenols and Indole-3-acetic Acids (1997)

The rates of oxidation of reducing substrates by heme peroxidases have previously been thought to be controlled only by their ease of oxidation. In the present study, we have compared the kinetics and thermodynamics of the oxidation of indole-3-acetic acid and derivatives and of phenols by horseradish peroxidase. Different dependencies of the reaction rates on the thermodynamic driving force reveal substrate specificity controlled by the enzyme−substrate complexes dissociation constants (Michaelis−Menten constants) and by the reorganization energies of electron-transfer within those complexes.
YME1L controls the accumulation of respiratory chain subunits and is required for apoptotic resistance, cristae morphogenesis, and cell proliferation (2012)

Mitochondrial ATPases associated with diverse cellular activities (AAA) proteases are involved in the quality control and processing of inner-membrane proteins. Here we investigate the cellular activities of YME1L, the human orthologue of the Yme1 subunit of the yeast i‑AAA complex, using stable short hairpin RNA knockdown and expression experiments. Human YME1L is shown to be an integral membrane protein that exposes its carboxy-terminus to the intermembrane space and exists in several complexes of 600–1100 kDa. The stable knockdown of YME1L in human embryonic kidney 293 cells led to impaired cell proliferation and apoptotic resistance, altered cristae morphology, diminished rotenone-sensitive respiration, and increased susceptibility to mitochondrial membrane protein carbonylation. Depletion of YME1L led to excessive accumulation of nonassembled respiratory chain subunits (Ndufb6, ND1, and Cox4) in the inner membrane. This was due to a lack of YME1L proteolytic activity, since the excessive accumulation of subunits was reversed by overexpression of wild-type YME1L but not a proteolytically inactive YME1L variant. Similarly, the expression of wild-type YME1L restored the lamellar cristae morphology of YME1L-deficient mitochondria. Our results demonstrate the importance of mitochondrial inner-membrane proteostasis to both mitochondrial and cellular function and integrity and reveal a novel role for YME1L in the proteolytic regulation of respiratory chain biogenesis.
Fluorine NMR reporter for phosphate anions (2013)

A fluorine-labelled zinc(II)-dipicolylamine coordination complex reports the presence of phosphate anions in aqueous solution, especially pyrophosphate and ADP, and is used to monitor the enzymatic hydrolysis of ATP.
Cerebral Cortical Gray Matter Overgrowth and Functional Variation of the Serotonin Transporter Gene in Autism (2007)

The SLC6A4 promoter polymorphism 5-HTTLPR influences cerebral cortical gray matter volumes in young male children with autism.
A hierarchical fractal net for pattern classification (2002)

Hierarchical nets having sparse and localized connectivity with fractal connections within layers have been studied. The performance of the proposed net in classification problems has been compared to that of a fully connected multilayer perceptron and a randomly connected sparse net with an artificially generated fractal data set and a real data set derived from sonar signals for underwater target recognition. A simple version of the backpropagation algorithm has been used to train all the nets. The fractal net seems to be far better than the randomly connected sparse net in fractal pattern recognition. For the second data set the fractally connected net performs well compared to the fully connected net as fractal dimension is increased above 0.75. Moreover the fractal net seems to possess more generalization capability compared to the fully connected net in recognizing patterns other than training patterns.
Beneficial effect of nonmagnetic Y on magnetic properties due to the enhancement of exchange coupling in nanocomposite (Nd,Y)2Fe14B/α–Fe magnets (2002)

We have studied the nanocomposite magnets with nominal compositions of Nd8−xYxFe88B4 (x=0–4.0) by mechanical milling techniques and subsequent heat treatment. We find that there exists the beneficial effect of nonmagnetic Y substitution for magnetic Nd on magnetic properties in nanocomposite magnets. The extension of the exchange coupling length, due to a decrease of the anisotropy of the hard-magnetic phase, results in that more soft-magnetic grains participate well in the exchange coupling, improving the magnetic properties of the nanocomposite magnets.
Direct Modification of a Gold Electrode with Aminophenyl Groups by Electrochemical Reduction of in Situ Generated Aminophenyl Monodiazonium Cations (2006)

Aminophenyl groups were electrochemically grafted at the surface of a gold electrode by reduction of in situ generated aminophenyl monodiazonium cations. The in situ aminophenyl monodiazonium cations were generated by reaction of 1 equiv of p-phenylenediamine with 1 equiv of sodium nitrite in 0.5 M HCl, and their formation was confirmed by gas chromatography−mass spectrometry. The presence of aminophenyl groups at the surface of the gold electrode was demonstrated by electrochemistry and infrared and X-ray photoelectron spectroscopies. The formation of an inhomogeneous multilayered film was also evidenced by atomic force microscopy. Furthermore, grafted aminophenyl groups present at the gold electrode surface reacted with trifluoroacetic acid anhydride in dry tetrahydrofuran with a reaction yield of about 75% for the trifluoroacetylation of the amine groups.
Maternal identity in preterm birth (2000)

The development of maternal identity appears to be considerably delayed in the event of preterm birth. Women with high risk pregnancies may be afforded some protection by means of adaptation prior to birth. Tactile contact appears to make the experience more real for women who are attempting to make the transition to motherhood. Even in a group of moderate risk preterm infants, the psychological challenges facing mothers experiencing neonatal intensive care are considerable. Conflicting responsibilities and time pressures contribute significantly to the stressful experience of mothers in NICU.
Characterization of Streptococcus gordonii (S. sanguis) PK488 adhesin-mediated coaggregation with Actinomyces naeslundii PK606 (1990)

Intergeneric coaggregation of Streptococcus gordonii (S. sanguis) PK488 and Actinomyces naeslundii PK606 was studied by using coaggregation-defective (Cog-) mutants of both strains. A streptococcal protein of 38 kilodaltons was identified with anti-S. gordonii serum absorbed with Cog- cells of the streptococcus. Absorbed immunoglobulin G specifically blocked coaggregation of the streptococcus-actinomyces pair but did not affect the coaggregation of the streptococcus with other coaggregation partners. The 38-kilodalton protein was found in the supernatant of mild sonicated cell suspensions and was extracted from whole cells with sodium barbital or with 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS). An immunoreactive protein of the same size was found in sonicated cell supernatants of several other oral streptococci that also coaggregated with A. naeslundii PK606. Inhibition of S. gordonii PK488-A. naeslundii PK606 coaggregation was not observed with any of 16 different sugars tested. We propose that a functionally similar adhesin that mediates coaggregations with A. naeslundii PK606 is expressed by several species of the genus Streptococcus.
Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function (2017)

Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
ChemInform Abstract: AZASULFONIUM SALTS, INTERMEDIATES IN A GENERAL PROCEDURE FOR THE ALKYLATION OF AROMATIC AMINES (1974)

Die Aniline (I) werden mit Ca-hypochlorit zu den Chloranilinen (II) und weiter mit Dimethylsulfid (III) zu den Azasulfoniumsalzen (IV) umgesetzt, die mit Na-methanolat über die entsprechenden Azasulfoniumylide und deren Sommelet-Hauser-Umlagerung in die Alkylmercaptoalkylderivate (V) übergehen.
Isolation and Characterization of EMS16, a C-Lectin Type Protein from <i>Echis multisquamatus</i> Venom, a Potent and Selective Inhibitor of the α2β1 Integrin (2000)

We have isolated and characterized EMS16, a potent and selective inhibitor of the alpha2beta1 integrin, from Echis multisquamatus venom. It belongs to the family of C-lectin type of proteins (CLPs), and its amino acid sequence is homologous with other members of this protein family occurring in snake venoms. EMS16 (M(r) approximately 33K) is a heterodimer composed of two distinct subunits linked by S-S bonds. K562 cells transfected with alpha2 integrin selectively adhere to immobilized EMS16, but not to two other snake venom-derived CLPs, echicetin and alboaggregin B. EMS16 inhibits adhesion of alpha2beta1-expressing cells to immobilized collagen I at picomolar concentrations, and the platelet/collagen I interaction in solution at nanomolar concentrations. EMS16 inhibits binding of isolated, recombinant I domain of alpha2 integrin to collagen in an ELISA assay, but not the interaction of isolated I domain of alpha1 integrin with collagen IV. Studies with monoclonal antibodies suggested that EMS16 binds to the alpha2 subunit of the integrin. EMS16 inhibits collagen-induced platelet aggregation, but has no effect on aggregation induced by other agonists such as ADP, thromboxane analogue (U46619), TRAP, or convulxin. EMS16 also inhibits collagen-induced, but not convulxin-induced, platelet cytosolic Ca(2+) mobilization. In addition, EMS16 inhibits HUVEC migration in collagen I gel. In conclusion, we report a new, potent viper venom-derived inhibitor of alpha2beta1 integrin, which does not belong to the disintegrin family.
Hormone Regulation of Glucose Metabolism in the Genetically Obese-Diabetic Mouse (<i>db</i>/<i>db</i>): Glucose Metabolism in the Perfused Hindquarters of Lean and Obese Mice (1981)

Glucose metabolism and insulin sensitivity in the skeletal muscle of genetically obese-diabetic mice (db/db) 5-6 wk of age (an early stage of the diabetes-obesityc syndrome) were examined using an in situ perfused hindquarter preparation. Rates of glucose uptake, 14CO2 production from (U-14C) glucose, and lactate production from glucose were all lower in muscles from dbldb mice than those from their lean littermates. Lactate production in muscle perfused without exogenous glucose was similar in both lean and obese mouse hindquarters. Likewise, epinephrine, which activated phosphorylase equally in both lean and obese mouse muscle, also elevated the tissue glucose-6-phosphate level and lactate production from endogenous source(s) to a similar degree in the two preparations. However, epinephrine was less effective In stimulating glucose uptake in the db/db mouse preparation. Glucose uptake was lower in the obese mouse hindquarter at all insulin concentrations tested (0-1000 μU/ml). The half-maximally effective dose of insulin (50 μU/ml) remained unaltered, however, indicating a decrease in insulin responsiveness rather than sensitivity. Both basal and insulin (1 mU/ml)-stimulated (3H)-D-allose uptake In the dbldb mouse hindquarter were below normal. No difference in assayed hexokinase activity was observed. Muscle pyruvate dehydrogenase and glycogen synthase activities were elevated by insulin (1 mU/ml) to a similar extent in both lean and obese mice. These findings suggest that at an early phase of development when obesity, hyperglycemia, and hyperinsulinemia are moderate, a defect in glucose transport plays a major role in the “insulin resistance” of the skeletal muscles of dbldb mice.
Effects of Timber Density on Northern Bobwhite Autumn Abundance (2017)

Mature pine (Pinus spp.) ecosystems maintained with frequent prescribed fire are the primary habitat of northern bobwhites (Colinus virginianus) in the Red Hills region of northern Florida and southern Georgia. Timber volume is thought to be negatively related to bobwhite abundance; however, this relationship has not been quantified. We related mean basal area of mature trees (>15cm dbh) to autumn covey call count indices at 23 locations on 6 study areas with varying timber volume, but similar bobwhite management practices, 2002 - 2004. Bobwhite abundance was inversely related to timber volume (r = -0.61, P = 0.002). Adjusted covey counts averaged 11.3 coveys below, and 6.4 coveys above, 9.2 m2/ha (40 ft^2/ac) of basal area (F1,21 = 19.4, P < 0.001). Where maintaining high densities of bobwhites is a priority, we recommend pine basal areas be < 10 m^2/ha. However, our data also suggested that bobwhites can be maintained at a bobwhite/0.4 ha at basal areas up to 14 m2/ha assuming sound management is applied.
Nanometer-Scale Arrangement of Human Serum Albumin by Adsorption on Defect Arrays Created with a Finely Focused Ion Beam (1998)

Well-ordered arrays of pits were prepared on gallium arsenide and silicon wafers using a finely focused ion beam (FFIB). The defect pits on gallium arsenide, examined with tapping mode scanning force microscopy (TM-SFM), had a rim diameter of 60 nm and were spaced 185 nm apart. TM-SFM images showed that human serum albumin (HSA) adsorption was highly specific to the inner portion of the rims of the pits on gallium arsenide, while there was no specific adsorption to the rims of pits on silica. This study demonstrates that a controlled spatial distribution of adsorbed proteins can be achieved on a nanometer scale and that the choice of material is of importance. Moreover, surface features such as pits and lines produced by FFIB can serve as a guide to easily reposition the TM-SFM probe tip at a specific location on the surface to within a few nanometers after temporary removal of the sample from the microscope.
Protocols for dry <scp>DNA</scp> storage and shipment at room temperature (2013)

The globalization of DNA barcoding will require core analytical facilities to develop cost-effective, efficient protocols for the shipment and archival storage of DNA extracts and PCR products. We evaluated three dry-state DNA stabilization systems: commercial Biomatrica(®) DNAstable(®) plates, home-made trehalose and polyvinyl alcohol (PVA) plates on 96-well panels of insect DNA stored at 56 °C and at room temperature. Controls included unprotected samples that were stored dry at room temperature and at 56 °C, and diluted samples held at 4 °C and at -20 °C. PCR and selective sequencing were performed over a 4-year interval to test the condition of DNA extracts. Biomatrica(®) provided better protection of DNA at 56 °C and at room temperature than trehalose and PVA, especially for diluted samples. PVA was the second best protectant after Biomatrica(®) at room temperature, whereas trehalose was the second best protectant at 56 °C. In spite of lower PCR success, the DNA stored at -20 °C yielded longer sequence reads and stronger signal, indicating that temperature is a crucial factor for DNA quality which has to be considered especially for long-term storage. Although it is premature to advocate a transition to DNA storage at room temperature, dry storage provides an additional layer of security for frozen samples, protecting them from degradation in the event of freezer failure. All three forms of DNA preservation enable shipment of dry DNA and PCR products between barcoding facilities.
Cell volume regulation in human neutrophils: 2-(aminomethyl)phenols as Cl- channel inhibitors (1993)

When subjected to hypotonic stress, human peripheral neutrophils initially swell due to rapid water entry and thereafter recover toward the normal cell size (approximately 330 microns 3). Neutrophils do not behave as perfect osmometers: when resuspended in half-isotonic medium (150 mosM), they swell by only approximately 40% rather than doubling in size as predicted for ideal behavior. As with lymphocytes, restoration to the normal cell size involves the net loss of K+ and Cl- from the cytosol through independent conductance pathways. Volume regulation is sensitive to 0.4-1 mM of quinine, UK-5099, 3,5-diiodosalicylate (DISA), MK-473 (an indanyloxyacetate derivative), and to MK-447 [a 2-(aminomethyl)phenol]. From correlation of drug effects on the time course of cell volume recovery and the associated volume-activated 86Rb+ and 36Cl- fluxes, it was evident that quinine blocked only K+ channels, whereas MK-447 acted as a selective inhibitor of Cl- channels. In contrast, UK-5099, DISA, and MK-473 were nonspecific in that the compounds displayed comparable suppressive effects on all three parameters. Structure-activity relationships in the MK-447 series revealed the critical elements of the molecule responsible for drug potency. In particular, the importance of the neighboring ionizable 1-hydroxyl and 2-aminomethyl groups and the formation of secondary ring structures for biological activity is emphasized. The most potent derivative thus far identified, termed analogue A [inhibitor constant (Ki) approximately 16 microM], had a potency approximately sixfold greater than that of the parent compound (Ki approximately 90 microM). These findings define the mechanism of action of a relatively new class of agents that behave as inhibitors of swelling-activated Cl- channels in these cells.
Antimicrobial, Antimalarial, and Antileishmanial Activities of Mono‐ and Bis‐quaternary Pyridinium Compounds (2010)

Pyridinium-based oxime compounds have been utilized worldwide as antidotes following exposure to anticholinesterase agents. In the event of combined chemical and biological incident, it is of vital importance to know the ability of antidotes to provide additional protection against biological threats. This paper reports results of in vitro antimicrobial and antiprotozoal activities of a series of quaternary pyridinium oximes against a number of lower pathogenicity BSL-1 and 2 agents. In general, our compound panel had little to no antimicrobial action except for thiophene- and benzothiophene-substituted monoquaternary pyridinium compounds 21 and 24 that showed moderate antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus with IC(50) values ranging from 12.2 to 17.7 μg/mL. Compounds 21 and 24 also exhibited antileishmanial activity against Leishmania donovani with IC(50) values of 19 and 18 μg/mL, respectively. Another monoquaternary pyridinium compound with a bromobutyl side chain 17 showed antimalarial activity against both a chloroquine sensitive and resistant strains of Plasmodium falciparum with IC(50) values of 3.7 and 4.0 μg/mL, respectively. None of the bisquaternary pyridinium compounds showed antimicrobial or antiprotozoal activity. None of the compounds showed cytotoxic effects toward mammalian kidney fibroblasts. Results of this study indicate that the pyridinium compounds, some of which are already in use as antidotes, do not have significant antimicrobial and antiprotozoal activities and cannot be relied upon for additional protection in the event of combined chemical-biological incident.