gebhart/patrepeval huggingface dataset:
Aspartic acid 320 is required for optimal activity of rat pancreatic cholesterol esterase. (1993)

The acidic amino acid residue required for the catalytic activity of rat pancreatic cholesterol esterase has been identified in this study by sequence comparison with other serine esterases and by site-directed mutagenesis experiments. The sequence comparison studies identified 3 acidic residues in homologous domains between cholesterol esterase, acetylcholinesterase, cholinesterase, and Geotrichum candida lipase that may potentially be the catalytic acidic residue in these proteins. The role of Glu78, Asp79, and Asp320 in the catalytic activity of rat cholesterol esterase was then addressed by mutagenesis and expression of the cDNA. Results showed that replacement of Glu78 or Asp79 with alanine has no effect on the ability of the cholesterol esterase to hydrolyze the artificial water-soluble substrate p-nitrophenyl butyrate. In contrast, the Asp320-->Ala320 substitution abolished the enzyme activity of the cholesterol esterase. The specific requirement of Asp320 for optimal enzyme activity was demonstrated by substitution of the aspartic acid with glutamic acid, thus retaining the charge unit at this position. The Asp320-->Glu320 substitution resulted in an enzyme that displayed normal interaction with bile salt. However, catalytic activity of this mutagenized protein was reduced by approximately 50%. These results strongly suggested that aspartic acid 320 is an important component of the catalytic triad of pancreatic cholesterol esterase. The specific requirement of aspartic acid, instead of glutamic acid, for optimal activity is different from that of other members of the serine esterase gene family.
Capacitation Induces Cyclic Adenosine 3′,5′-Monophosphate-Dependent, but Apoptosis-Unrelated, Exposure of Aminophospholipids at the Apical Head Plasma Membrane of Boar Sperm Cells1 (2002)

The capacitating agent bicarbonate/CO(2) has been shown to induce profound changes in the architecture and dynamics within the sperm's plasma membrane lipid bilayer via a cAMP-dependent protein phosphorylation signaling pathway. Here we have investigated the effect of bicarbonate on surface exposure of endogenous aminophospholipids in boar spermatozoa, detecting phosphatidylserine (PS) with fluorescein-conjugated annexin V and phosphatidylethanolamine (PE) with fluorescein-conjugated streptavidin/biotinylated Ro-09-0198. Flow cytometric analyses revealed that incubation with 15 mM bicarbonate induced 30%-70% of live acrosome-intact cells to expose PE very rapidly; this exposure was closely related to a decrease in lipid packing order as detected by enhanced binding of merocyanine 540. PS exposure was detectable in the same proportion of cells, though its expression was slower. Confocal microscopy revealed that exposure of aminophospholipids in intact cells was restricted to the anterior acrosomal region of the head plasma membrane. Aminophospholipid exposure, merocyanine stainability, and a subsequent migration of cholesterol to the apical region of the head plasma membrane, were all under the control of the cAMP-dependent protein phosphorylation pathway. The close coupling of decreased lipid packing order with exposure of PE led us to conclude that bicarbonate was inducing phospholipid scrambling (i.e., collapse of asymmetric transverse distribution), and that the scrambling was a prerequisite for cholesterol relocation. There was no evidence whatever that the bicarbonate-induced scrambling was an apoptotic process. It was not accompanied by major loss of viability or by DNA degeneration or by loss of mitochondrial function, and it could not be blocked by the broad-specificity caspase inhibitors zVAD-fmk and BocD-fmk. In the absence of bicarbonate, scrambling could not be induced by the apoptotic agents UV, staurosporine, or cycloheximide. Bicarbonate-induced phospholipid scrambling thus appears to be an important and early physiological event in the capacitation process.
A Stable Lipid-Induced Aggregate of α-Synuclein (2010)

The Parkinson's disease-related protein alpha-Synuclein (alphaS) is a 140 residue intrinsically disordered protein. Its membrane-binding properties are thought to be relevant for its physiological or pathologic activity. Here, the interaction of alphaS with POPG [1-Palmitoyl-2-Oleoyl-sn-Glycero-3-(Phosphorac-(1-glycerol))] small unilamellar vesicles (SUVs) is investigated by spin-label EPR using double electron-electron resonance (DEER). Intermolecular distances between four single mutants reveal that well-defined aggregates are formed. The data suggest a coexistence of two dimer structures with main interactions in the helix 2, encompassing residues 50-100. Previously, the horseshoe conformation was detected by intramolecular restraints obtained by DEER on alphaS double mutants (Drescher et al. J. Am. Chem. Soc. 2008, 130, 7796). The present study suggests that interdigitation of two monomers in the aggregate fills the void between the two helices of each of the monomers thus providing a rationale for the horseshoe structure. This aggregate is lipid induced and affects the structure of the POPG SUVs, which become leaky and diminish in size upon contact with alphaS suggesting a possible origin of conflicting results in the recent literature (Jao et al. Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (50), 19666; Georgieva et al. J. Am. Chem. Soc. 2008, 130 (39), 12856; Bortolus et al. J. Am. Chem. Soc. 2008, 130, 6690).
The G534E polymorphism of the gene encoding the factor VII–activating protease is associated with cardiovascular risk due to increased neointima formation (2006)

The G534E polymorphism (Marburg I [MI]) of factor VII-activating protease (FSAP) is associated with carotid stenosis and cardiovascular disease. We have previously demonstrated that FSAP is present in atherosclerotic plaques and it is a potent inhibitor of vascular smooth muscle proliferation and migration in vitro. The effect of wild-type (WT)- and MI-FSAP on neointima formation in the mouse femoral artery after wire-induced injury was investigated. Local application of WT-FSAP led to a 70% reduction in the neointima formation, and this effect was dependent on the protease activity of FSAP. MI-FSAP did not inhibit neointima formation in vivo. This is due to a reduced proteolytic activity of MI-FSAP, compared to WT-FSAP, toward platelet-derived growth factor BB, a key mediator of neointima development. The inability of MI-FSAP to inhibit vascular smooth muscle accumulation explains the observed linkage between the MI-polymorphism and increased cardiovascular risk. Hence, FSAP has a protective function in the vasculature, and analysis of MI polymorphism is likely to be clinically relevant in restenosis.
Lokale antimikrobielle Aknebehandlung eine Alternative für die systemische Antibiotikatherapie (1980)

Die saprophytären Keime im Talgdrüseninfundibulum spielen sowohl bei der Entstehung von Comedonen als auch von entzündlichen Akneefloreszenzen eine Rolle. Langjährige Erfahrungen haben gezeigt, daß eine Hemmung dieser Keime zuverlässig zu therapeutischen Erfolgen führt. Nach neuen Erkenntnissen scheint es jedoch nicht ausreichend für einen therapeutischen Erfolg zu sein, wenn nur die Propionibakterien, nicht aber die Micrococcaceae beeinflußt werden. Bestimmungen der minimalen Hemmkonzentration zeigen, daß eine Reihe von Antibiotika für eine derartige Behandlung in Frage kommen. Bei Desinfizientien liegt die minimale Hemmkonzentration zwar in der Regel höher, eine therapeutische Ausnützbarkeit scheint jedoch ebenfalls diskutabel. Neben der in vitro-Wirkung ist sowohl bei der systemischen als auch bei der topischen antimikrobiellen Therapie wesentlich, daß der Wirkstoff in ausreichender Menge in das Infundibulum gelangt. Der Ersatz der langbewährten systemischen Antibiotikatherapie durch eine topische antimikrobielle Therapie erscheint aus verschiedenen Gründen als wünschenswert. Hauptgrund ist, daß eine Resistenzbildung pathogener Keime in inneren Organen bislang nicht ausgeschlossen werden kann. Bei Auswahl geeigneter Grundlagen kann heute in der Regel mit der topischen Antibiotikatherapie ein gleichwertiger Erfolg wie mit der systemischen Therapie erzielt werden. Dies läßt sich durch klinische Untersuchungen, durch biochemische Analysen der Hautoberflächenlipide und durch bakteriologische Untersuchungen in gleicher Weise belegen. Es wird über entsprechende Untersuchungen berichtet. Außerdem werden in der Praxis bewährte Rezepturen angegeben. Local Antimicrobial Treatment of Acne – An Alternative to Systemical Antibiotic Therapy The saprophytic germs in sebaceous gland infundibulum play a role, both in the formation of comedones and acne efflorescences. Long experience has shown that the inhibition of these germs lead to reliable therapeutical success. Recent studies have shown that inadequate therapeutical success is achieved if only the propioni bacteria but not the micrococcaceae are affected. The determination of minimum inhibitor concentration has shown that a series of antibiotics can be used for such treatment. With desinfectants, the minimum inhibitor concentration is generally higher, yet their therapeutic application appears feasible. Apart from the in vitro action, it is essential in systemic as well as topical antimicrobial therapy that the active principle reaches the infundibulum in adequate amounts. A substitution of customary antibiotica therapy by topical antimicrobial therapy is desirable for several reasons. The main reason is that the resistance of pathogenic germs in the internal organs can not be ruled out. Using suitable bases, the topical antibiotica therapy can be carried out with the same degree of success as the systemic therapy. This is evidenced by clinical investigations, biochemical analysis of skin surface lipids and by bacteriological studies. Several prescriptions are recommended.
An efficient A* stack decoder algorithm for continuous speech recognition with a stochastic language model (1992)

The stack decoder is an attractive algorithm for controlling the acoustic and language model matching in a continuous speech recognizer. The author previously described a near-optimal admissible Viterbi A* search algorithm for use with non-crossword acoustic models and no-grammar language models (1991). This algorithm is extended to include unigram language models, and a modified version of the algorithm which includes the full (forward) decoder, cross-word acoustic models and longer-span language models is described. The resultant algorithm is not admissible, but has been demonstrated to have a low probability of search error and to be very efficient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Human adenine phosphoribosyltransferase. Immunochemical quantitation and protein blot analysis of mutant forms of the enzyme. (1982)

We have studied the catalytic, immunochemical, and electrophoretic properties of adenine phosphoribosyltransferase in hemolysates from 30 patients with a deficiency of this enzyme in six unrelated families. We have found that: 1) the level of adenine phosphoribosyltransferase enzyme activity and immunoreactive protein in the four homozygous deficient patients was less than 1% of control values; 2) adenine phosphoribosyltransferase enzyme activity was uniformly decreased to approximately 25% of normal in all 26 heterozygotes studied while the level of adenine phosphoribosyltransferase immunoreactive protein was consistent within each kindred but ranged in value from 22% to 112% of control; and 3) protein blot analysis revealed a single isoelectric form of the adenine phosphoribosyltransferase subunit in hemolysate from normal controls and from every heterozygote except for patient M.R. who exhibited both a normal and a more acidic adenine phosphoribosyltransferase subunit species. These studies provide the first evidence for the existence of a variety of different mutations in the structural gene for adenine phosphoribosyltransferase in patients exhibiting a deficiency of enzyme activity. We further conclude from our data that: 1) the variant enzymes are more labile in vivo and/or catalytically nonfunctional, and 2) heterozygotes express only 25% of normal enzyme activity because the normal and variant enzyme subunits form a hybrid dimer which is either more labile or less catalytically active than the normal adenine phosphoribosyltransferase dimer.
The use of selection experiments for detecting quantitative trait loci (1997)

Gene frequency changes following selection may reveal the existence of gene effects on the trait selected. Loci for the selected quantitative trait (SQTL) may thus be detected. Additionally, one can estimate the average effect (alpha) of a marker allele associated with an SQTL from the allele frequency change (delta q) due to selection of given intensity (i). In a sample of unrelated individuals, it is optimal to select the upper and lower 27% for generating delta q in order to estimate alpha. For a given number of individuals genotyped, this estimator is 0.25i2 times more efficient than the classical estimator of alpha, based on the regression of the trait on the genotype at the marker locus. The method is extended to selection criteria using information from relatives, showing that combined selection considerably increases the efficiency of estimation for traits of low heritability. The method has been applied to the detection of SQTL in a selection experiment in which the trait selected was pig litter size averaged over the first four parities, with i = 3. Results for four genes are provided, one of which yielded a highly significant effect. The conditions required for valid application of the method are discussed, including selection experiments over several generations. Additional advantages of the method can be anticipated from determining gene frequencies on pooled samples of blood or DNA.
Long Distance PCR (2004)

The polymerase chain reaction (PCR) is a common tool of molecular biology and is utilized in the field of medical diagnostics to identify genetic disorders and the causative agents of human infections. PCR is also used for typing microorganisms, thus playing an important role in both epidemiology and phylogenetics. The PCR method is a starting point that when used together with cloning is influential in the sequencing of novel genes and genomes.
Two-dimensional angular optical scattering for the characterization of airborne microparticles (1998)

Two-dimensional angular optical scattering (TAOS) is recorded for several particle shapes and configurations. A lens is used to collect a large solid angle of the light and transform the angular profile into a planar distribution according to the Abbé sine condition. Qualitative agreement is found between experiment and theory for the TAOS from spheroids having the same aspect ratio but different sizes. A distinctive irregular island structure is observed in the TAOS from clusters of Bacillus subtilis spores and polystyrene latex spheres. The density per solid angle of these islands is found to increase with cluster diameter.
Constraint filtered-x and filtered-u least-mean-square algorithms for the active control of noise in ducts (1994)

In the active control of noise in ducts, it is common practice to locate an error microphone far from the control source to avoid the near-field effects by evanescent waves. Such a distance between the control source and the error microphone makes a certain level of time delay inevitable and, hence, may yield undesirable effects on the convergence properties of control algorithms such as filtered-x and filtered-u least-mean-square (LMS). This paper discusses the dependence of the convergence rate on the acoustic error path in these popular algorithms and introduces new algorithms ‘‘constraint filtered-x and constraint filtered-u LMS,’’ which increase the convergence region regardless of the time delay in the acoustic error path. In the algorithms, coefficients of the controller are adapted using modified residuals that are defined in such a way that the control process become stationary. Performances of the new LMS algorithms are presented in comparison with those by the conventional algorithms based on computer simulations.
Suppression of ringing in the tuned input circuit of a SQUID detector used in low-field NMR measurements (2009)

In low-field NMR measurements, we employ a high temperature superconducting quantum interference device (SQUID) as a detector with an inductively coupled liquid-nitrogen-cooled LC tuned input circuit. However, ringing across the LC circuit appears after the sudden switch-off of the prepolarizing magnetic field. This ringing leads to instability of the SQUID readout and prevents the acquisition of short-relaxation-time signals. We developed and tested two simple and effective FET-based Q switch circuits with adjustable parameters which suppress the ringing. Each of these Q switches makes it possible to record free induction decay signals with a Larmor frequency of 1.2 kHz and an effective relaxation time constant of 30 ms. A gradually changing current caused by the release of charges stored in the p–n junction of the FET, which delays the Q value recovery of the LC circuit, can only be observed by the SQUID because of its frequency-independent sensitivity.
Bis[bis‐(4‐alkoxyphenyl)amino] Derivatives of Dithienylethene, Bithiophene, Dithienothiophene and Dithienopyrrole: Palladium‐Catalysed Synthesis and Highly Delocalised Radical Cations (2007)

Five diamines with thiophene-based bridges--(E)-1,2-bis{5-[bis(4-butoxyphenyl)amino]-2-thienyl}ethylene (1), 5,5'-bis[bis(4-methoxyphenyl)amino]-2,2'-bithiophene (2), 2,6-bis[bis(4-butoxyphenyl)amino]dithieno[3,2-b:2',3'-d]thiophene (3), N-(4-tert-butylphenyl)-2,6-bis[bis(4-methoxyphenyl)amino]dithieno[3,2-b:2',3'-d]pyrrole (4 a) and N-tert-butyl-2,6-bis[bis(4-methoxyphenyl)amino]dithieno[3,2-b:2',3'-d]pyrrole (4 b)--have been synthesised. The syntheses make use of the palladium(0)-catalysed coupling of brominated thiophene species with diarylamines, in some cases accelerated by microwave irradiation. The molecules all undergo facile oxidation, 4 b being the most readily oxidised at about -0.4 V versus ferrocenium/ferrocene, and solutions of the corresponding radical cations were generated by addition of tris(4-bromophenyl)aminium hexachloroantimonate to the neutral species. The near-IR spectra of the radical cations show absorptions characteristic of symmetrical delocalised species (that is, class III mixed-valence species); analysis of these absorptions in the framework of Hush theory indicates strong coupling between the two amine redox centres, stronger than that observed in species with phenylene-based bridging groups of comparable length. The strong coupling can be attributed to high-lying orbitals of the thiophene-based bridging units. ESR spectroscopy indicates that the coupling constant to the amino nitrogen atoms is somewhat reduced relative to that in a stilbene-bridged analogue. The neutral species and the corresponding radical cations have been studied with the aid of density functional theory and time-dependent density functional theory. The DFT-calculated ESR parameters are in good agreement with experiment, while calculated spin densities suggest increased bridge character to the oxidation in these species relative to that in comparable species with phenylene-based bridges.
A request/response protocol for ISO remote operations (2002)

The authors describe the request/response protocol (RRP) which provides protocol support for ISO remote operations. RRP requires no separate protocol data unit (PDU) transfer to establish or release an association. Data transfer is efficient in terms of network utilization, unnecessary retransmissions and acknowledgements. RRP assumes an unsequenced, unreliable, and error prone datagram service. RRP segments and concatenates data too large to be transmitted by the underlying network. It uses selective retransmission to help deal with receiver overrun. RRP optionally monitors client reachability, and monitors server reachability while the client has an outstanding request. RRP is especially efficient for server applications requiring a large number of short-lived connections which transfer small amounts of data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microbial Flora in NSAID-Induced Intestinal Damage: A Role for Antibiotics? (2006)

Upper gastrointestinal (GI) complications are well-recognized adverse events associated with non-steroidal anti-inflammatory drug (NSAID) use. However, NSAID-induced damage to the distal GI tract is also common and more frequent than previously recognized. These untoward effects include increased mucosal permeability, mucosal inflammation, anemia and occult blood loss, malabsorption, protein loss, ileal dysfunction, diarrhea, mucosal ulceration, strictures due to diaphragm disease as well as active bleeding and perforation. Studies with selective COX-2 inhibitors have shown that, in the short term, these agents do not increase mucosal permeability and display a reduced by 50% incidence of serious lower GI side effects compared to traditional NSAIDs. However, the long-term use of this therapeutic strategy is limited by the increased risk of serious cardiovascular events, especially in patients with multiple risk factors. Several studies have suggested that intraluminal bacteria play a significant role in the pathogenesis of small-bowel damage induced by NSAIDs and that enterobacterial translocation into the mucosa represents the first step that sets in motion a series of events leading to gross lesion formation. Experimental and clinical investigations indicate that in the short term, antibacterial agents either reduce or abolish NSAID enteropathy. However, potential adverse effects of systemic antimicrobials and the possible occurrence of drug resistance have so far precluded this interesting approach. The availability of poorly absorbed and effective antibiotics, like rifaximin, may represent an attractive alternative to prevent or limit NSAID-associated intestinal damage.
A secure credit card protocol over NFC (2016)

NFC ("Near Field Communication") is a short-range wireless communication channel. The current NFC credit card protocol allows a contactless credit card to communicate wirelessly with a Point-of-Sale in order to perform a purchase. This protocol is vulnerable to four common attacks: eavesdropping, skimming, relay attacks, and compromised Points-of-Sale. The attacker's objective is twofold: stealing sensitive information, and performing unauthorized. We use stepwise refinement to design a secure NFC credit card protocol which defends against all four of these attacks. The resulting protocol does not use heavyweight cryptographic operations, instead using only inexpensive primitives such as pre-computed hashes, indexing, and XOR operations. Moreover, it explores the lower-bound of computation required on the card to mount an effective defense against these four classes of attacks. As such, the energy and computational requirements of the credit card in our protocol are kept to a minimum.