gebhart/patrepeval huggingface dataset:
Mapping of the Active Sites of Transglutaminases (1973)

Abstract Calcium-activated guinea pig liver transglutaminase catalyzes the incorporation of amines at the carboxamide group of several aliphatic amides. Initial velocity findings with n-valeramide and methylamine as substrates are consistent with a modified double displacement mechanism for this reaction. This mechanism has already been demonstrated for amine incorporation at the γ-carboxamide group of peptide-bound glutamine (Folk, J. E. (1969) J. Biol. Chem. 244, 3707). Inhibition patterns for aliphatic amides suggest that binding of these compounds occurs at the site in the enzyme to which the carboxamide side chain of peptide-bound glutamine residues attaches. All of the straight-chain amides tested proved to be substrates with the exception of formamide. Branched-chain amides in which there is a methyl group in the α or β position of the methylene side chain are not substrates; those with methyl groups on the γ-carbon of the side chain are. These observations and their consideration lead to the suggestion that peptide-bound glutamine attaches to the enzyme with its β and γ methylene groups situated in a hydrophobic binding region and with its carboxamide group directed toward the active site —SH group of the enzyme. The dimensions of this site preclude the productive binding of peptide-bound asparagine. An active site pocket of fixed dimensions into which the carboxamide group and methylene side chain of substrate must be injected and from which product must be extruded is not consistent with the substrate specificity of the enzyme or with the ready dissociation of many products. This, taken together with present observations, favors an hypothesis of an essential substrate-induced conformational change in the active site of the enzyme that precedes or accompanies enzyme acylation.
Immunohistochemical and Mutational Analysis of c-kit in Gastrointestinal Neuroendocrine Cell Carcinoma (2006)

The frequency of c-kit expression in gastrointestinal NEC was similar to that previously reported for pulmonary NEC. These findings suggest that c-kit inhibitor may be effective against some gastrointestinal NECs.
Dual-wavelength demultiplexing InGaAsP/InP photodiode (1979)

Most of the work on lightwave systems has concentrated on coupling a single source to a fiber and, hence, transmission of a singlewavelength band. The information capacity of these systems could be increased, however, by combining signals from sources emitting at different wavelengths, i.e., wavelength-division multiplexing.1 This approach, however, will require demultiplexing the different wavelength channels at the receiver. In this talk we describe a new photodiode structure capable of both detecting and demultiplexing two wavelength bands simultaneously.
Stability versus Neuronal Specialization for STDP: Long-Tail Weight Distributions Solve the Dilemma (2011)

Spike-timing-dependent plasticity (STDP) modifies the weight (or strength) of synaptic connections between neurons and is considered to be crucial for generating network structure. It has been observed in physiology that, in addition to spike timing, the weight update also depends on the current value of the weight. The functional implications of this feature are still largely unclear. Additive STDP gives rise to strong competition among synapses, but due to the absence of weight dependence, it requires hard boundaries to secure the stability of weight dynamics. Multiplicative STDP with linear weight dependence for depression ensures stability, but it lacks sufficiently strong competition required to obtain a clear synaptic specialization. A solution to this stability-versus-function dilemma can be found with an intermediate parametrization between additive and multiplicative STDP. Here we propose a novel solution to the dilemma, named log-STDP, whose key feature is a sublinear weight dependence for depression. Due to its specific weight dependence, this new model can produce significantly broad weight distributions with no hard upper bound, similar to those recently observed in experiments. Log-STDP induces graded competition between synapses, such that synapses receiving stronger input correlations are pushed further in the tail of (very) large weights. Strong weights are functionally important to enhance the neuronal response to synchronous spike volleys. Depending on the input configuration, multiple groups of correlated synaptic inputs exhibit either winner-share-all or winner-take-all behavior. When the configuration of input correlations changes, individual synapses quickly and robustly readapt to represent the new configuration. We also demonstrate the advantages of log-STDP for generating a stable structure of strong weights in a recurrently connected network. These properties of log-STDP are compared with those of previous models. Through long-tail weight distributions, log-STDP achieves both stable dynamics for and robust competition of synapses, which are crucial for spike-based information processing.
Signal Detection Theory (2008)

Signal detection theory is a principled explanation for decision making under noisy conditions. All real decisions are made under a certain degree of uncertainty determined by extrinsic environmental conditions and intrinsic neural and cognitive processes. A typical situation of concern to the theory is the simple forced choice, a type of binary classifier system. In this situation, a subject must
Flexibilized Gelatin Film-Based Artificial Skin Model: I. Preparation and Properties of the Films (1992)

A method was developed to prepare a simple, flexibilized gelatin film-based artificial skin model. The films are tough, adhere to open wounds spontaneously, are permeable to body fluids, and can release incorporated bioactive compounds over 4-5 days.
Characterization of novel natural killer (NK)–cell and γδ T-cell lines established from primary lesions of nasal T/NK-cell lymphomas associated with the Epstein-Barr virus (2001)

Studies on nasal T/natural killer (NK)-cell lymphoma have been hampered by its tendency to cause necrosis. Thus, the establishment of cell lines of this neoplasm would seem to be valuable. This study attempted to establish cell lines from primary lesions of this tumor, and successfully obtained 2 novel Epstein-Barr virus (EBV)-positive cell lines, SNK-6 and SNT-8, by means of high-dose recombinant interleukin 2. Flow cytometry showed that SNK-6 had an NK-cell phenotype, CD3- CD4- CD8- CD19- CD56+ T-cell receptor (TCR) alpha/beta- TCR gamma/delta-, whereas SNT-8 was CD3+ CD4- CD8- CD19- CD56+ TCR alpha/beta- TCR gamma/delta+. These were consistent with immunophenotypes of their original tumors, and the cell lines had monoclonal EBV clones identical to ones in their original tumors. Thus, the cell lines developed from cells forming the primary lesions. Genotypic analysis showed that SNK-6 had unrearranged TCR and immunoglobulin heavy-chain genes, supporting the conclusion that SNK-6 was of NK-cell lineage. On the other hand, SNT-8 had rearranged TCR beta-, gamma-, and delta-chain genes, and together with its phenotype, SNT-8 proved to be a gammadelta T-cell line. This is the first report of the establishment of cell lines from primary lesions of nasal T/NK cell lymphomas, and the results demonstrated that there are at least 2 lineages, NK- and gammadelta T-cell, in this neoplasm. Moreover, it has been suggested that nasal T/NK cell lymphomas of these lineages may belong to the same clinicopathologic entity because both types of cases shared common clinical and histopathologic features.
[Patients' information in percutaneous core breast biopsy]. (2005)

Information takes a large part of patient's perceptions of the procedure. If the information is adapted, patients tolerate the procedure well. We point out indications and explain the different types of procedure. For infraclinical masses, sonographically guided automated core needle biopsy removes samples. Sonographically guided vacuum-assisted large-core biopsy is only used for diagnosis generally on second purpose for masses. Stereotaxic vacuum-assisted large-core biopsy is used for microcalcifications (needle 8 or 11 gauge). Haematoma and bleeding are rare (< 4%), but care is necessary to avoid complications. Information is executed before the procedure and a booklet is giving to the women. This information has to be adapted because lot of informations could increase patient's anxiety if they don't want more informations and "not enough information" could also increase anxiety if they want more informations. The practitioner, by hearing, his formation and his experience, is able to adapt informations.
Ethylene mass flow measurements with an automatic CO_2 laser long-path absorption system (1982)

A computer controlled CO(2) laser long-path absorption system has been used in a field experiment to measure the total emission of ethylene from a petrochemical factory. The ethylene concentration was measured along eight measurement paths at different elevations. Simultaneously meteorological data were collected. From these data we have calculated the mass flow from the factory. The result of the calculations agree well with the value estimated at the factory using conventional methods.
Determination of volume fractions and ligand layer thickness of polymer/CdSe quantum dot blend films by effective medium approximations (2011)

Abstract We investigate hybrid organic/inorganic films using different polymers and CdSe quantum dots (QD) and nanorods (NR) with hexanoic acid (HA)‐treated hexadecylamine (HDA) or pyridine as the capping ligands. The volume ratios of the polymer:nanoparticle (NP) blends are studied by spectroscopic ellipsometry and transmission intensity data. Effective medium approximation based on the results of the pristine films is applied. With this routine, the polymer/NP volume ratio of the blend can be identified. In combination with the mass ratio of the components, the mass density of the NP including the inorganic crystalline core and the organic ligand layer is obtained. A geometrical model for QD and NR allows for the estimation of the ligand layer thickness. We find pyridine and HDA after HA treatment to be 0.9 and 0.6 nm on the QD surface, respectively. By contrast, the effective thickness of the organic ligand is 3.0 nm on the investigated NR. In both cases, the organic layer is thicker than a monolayer of the expected pyridine due to the presence of extant synthesis ligands as a result of incomplete ligand exchange. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 000: 000–000, 2011
Slip Angles and Longitudinal Slip Measurement of the Cooperative Redundant Steering/Drive System (2006)

Wheeled vehicles (especially those working on steep slopes) have the inherent problems regarding tractability, stability, manoeuvrability and safety. The objective of this paper is to apply "X-by-wire" technology to rectify the inherent problems while at the same time minimise fuel consumption and damage to the ground traversed. The key feature of this work is that both of the two basic methods of steering a vehicle are used so that they both tend to produce the same centre of curvature for the path of the vehicle. This deliberate, cooperative redundancy means that the inevitable failure of one steering system is prevented by both steering systems acting in unison. In order to achieve this objective a measuring methodology has to be first devised for the slip angles and the longitudinal slip, which is the topic of this paper. This is an important step for the application of the required correction
Band Resonant Tunneling in DNA Molecules (2001)

The charge migration process in DNA is subject to a lively debate among researchers at the moment. We have performed calculations on poly(G)-poly(C) DNA which substantiate a recent report indicating bandlike conduction for this particular form of DNA. Our results show that both guanine and cytosine give rise to conducting channels along the DNA strands. The conductivity results from the overlap of the pi orbitals along the base stacks. We also demonstrate that the measured increase of the threshold voltage with temperature in poly(G)-poly(C) DNA is the result of electron localization due to the structural disorder following high temperature.
Abrasive Blasting with Post-Process and In-Situ Characterization (2014)

Abrasive blasting is a common process for cleaning or roughening the surface of a material prior to the application of a coating. Although the process has been in practice for over 100 years, the lack of a comprehensive understanding of the complex interactions that exist with the process can still yield an inferior surface quality. Subsequently, parts can be rejected at one of many stages of the manufacturing process and/or fail unexpectedly upon deployment. The objective of this work is to evaluate the effect of selected input parameters on the characteristics of the blasted surface characteristics so that a more useful control strategy can be implemented. To characterize surface roughness, mechanical profilometry was used to collect average roughness parameter, Ra. Decreasing blast distance from 6” to 4” gave ΔRa = +0.22 µm and from 8” to 6” gave ΔRa = +0.22 µm. Increasing blast pressure from 42 psi to 60 psi decreased the Ra by 0.33 µm. Media pulsation reduced Ra by 0.56 µm and the use of new media reduced Ra by 0.47 µm. Although blasting under the same conditions and operator on different days led to ΔRa due to shorter blast times, there was no statistically significant variance in Ra attributed to blasting on different days. Conversely, a ΔRa = +0.46 µm was observed upon blasting samples with different cabinets. No significant ΔRa was found when switching between straight and Venturi nozzles or when using different operators. Furthermore, the feasibility of fiber optic sensing technologies was investigated as potential tools to provide real time feedback to the blast machine operator in terms of substrate temperature. Decreasing the blast distance from 6” to 4” led to ΔT = +9.2 °C, while decreasing the blast angle to 45° gave ΔT= -11.6 °C for 304 stainless steel substrates. Furthermore, increasing the blast pressure from 40 psi to 50 psi gave ΔT= +15.3 °C and changing from 50 psi to 60 psi gave ΔT= +9.9 °C. The blast distance change from 8” to 6” resulted in ΔT = +9.8 °C in thin stainless steel substrate temperature. The effects of substrate thickness or shape were evaluated, giving ΔT= +7.4 °C at 8” distance, ΔT= +20.2 °C at 60 psi pressure, and ΔT= -15.2 °C at 45° blasting when comparing thin stainless steel against 304 stainless steel (thick) temperatures. No significant ΔT in means was found when going from 6” to 8” distance on 304 stainless steel, 40 psi and 60 psi blasting of thin SS, as well as angled and perpendicular blasting of thin SS. Comparing thick 304 and thin stainless steel substrates at a 6” blast distance gave no significant ΔT.
Synthesis of Pyrrole, Pyrrolo[3,4-b]pyridine and Pyrrplo[3,2-b]pyridine Derivatives (1987)

The reaction of ethyl benzylidenecyanoacetate (1) with hippuric acid (2) in acetic anhydride leads t o pyrrole derivative 5 together with the acetyl derivative 2. Treatment of 5 with ethyl acetoacetate, acetylacetone and malononitrile give the pyrrolo[3,4-blpyridines 2, 12 and 2; respectively.Coupling of 5 and I with benzenediazonium chloride yield the phenylaza derivatives 5 and 9 respectively.On the other hand, ethyl cyanoacetate reacts with !t o give the pyrrolo[3,2-blpyridine derivative J?.Activated nitriles have been extensively utilized for the synthesis of polyfunctionally substituted heterocycles1-3.This paper deals with the synthesis of the pyrrole derivative 2 which was subsequently utilized for the synthesis of pyrrolo[3,4-blpyridine and pyrrolo[3,2-blpyridine derivatives.Compound 5 was obtained in good yield on refluxing 0.01 mole of ethyl benzylidenecyanoacetate
Assessment of regional long-axis function during dobutamine echocardiography (2001)

Echocardiographic analysis of regional left ventricular function is based upon the assessment of radial motion. Long-axis motion is an important contributor to overall function, but has been difficult to evaluate clinically until the recent development of tissue Doppler techniques. We sought to compare the standard visual assessment of radial motion with quantitative tissue Doppler measurement of peak systolic velocity, timing and strain rate (SRI) in 104 patients with known or suspected coronary artery disease undergoing dobutamine stress echocardiography (DbE). A standard DbE protocol was used with colour tissue Doppler images acquired in digital ciné-loop format. Peak systolic velocity (PSV), time to peak velocity (TPV) and SRI were assessed off-line by an independent operator. Wall motion was assessed by an experienced reader. Mean PSV, TPV and SRI values were compared with wall motion and the presence of coronary artery disease by angiography. A further analysis included assessing the extent of jeopardized myocardium by comparing average values of PSV, TPV and SRI against the previously validated angiographic score. Segments identified as having normal and abnormal radial wall motion showed significant differences in mean PSV (7.9±3.8 and 5.9±3.3 cm/s respectively; P < 0.001), TPV (84±40 and 95±48 ms respectively; P = 0.005) and SRI (-1.45±0.5 and -1.1±0.9 s-1 respectively; P < 0.001). The presence of a stenosed subtending coronary artery was also associated with significant differences from normally perfused segments for mean PSV (8.1±3.4 compared with 5.7±3.7 cm/s; P < 0.001), TPV (78±50 compared with 92±45 ms; P < 0.001) and SRI (-1.35±0.5 compared with -1.20±0.4 s-1; P = 0.05). PSV, TPV and SRI also varied significantly according to the extent of jeopardized myocardium within a vascular territory. These results suggest that peak systolic velocity, timing of contraction and SRI reflect the underlying physiological characteristics of the regional myocardium during DbE, and may potentially allow objective analysis of wall motion.
Quantum dot origin of luminescence in InGaN-GaN structures (2002)

We report on resonant photoluminescence (PL) of InGaN inclusions in a GaN matrix. The structures were grown on sapphire substrates using metal-organic chemical vapor deposition. Nonresonant pulsed excitation results in a broad PL peak, while resonant excitation into the nonresonant PL intensity maximum results in an evolution of a sharp resonant PL peak, having a spectral shape defined by the excitation laser pulse and a radiative decay time close to that revealed for PL under nonresonant excitation. Observation of a resonantly excited narrow PL line gives clear proof of the quantum dot nature of luminescence in InGaN-GaN samples. PL decay demonstrates strongly nonexponential behavior evidencing coexistence of quantum dots having similar ground-state transition energy, but very different electron-hole wave-function overlap.
Critical Evaluation of Platelet Aggregation in Whole Human Blood (1986)

Platelet aggregation studies generally are performed in platelet-rich plasma (PRP) by the turbidometric method. The authors compared this technic with the recently introduced impedance aggregometry in PRP and whole blood (WB). In healthy controls there was a good correlation between the two technics when aggregation was induced by ADP or collagen. As compared with PRP, platelets in WB were more sensitive to the aggregating effect of thrombin, ristocetin, and arachidonic acid. Platelet sensitivity to prostacyclin was increased in WB. The anti-platelet effect of a single oral dose of aspirin could be detected for a longer period in WB than in PRP. Platelet aggregation tests in WB from patients with platelet dysfunctions showed the same response pattern to different aggregating agents as in PRP. In contrast to turbidometry, the impedance method in PRP and WB enabled registration of platelet aggregation in a dose-dependent fashion in a sample from a patient with severe hyperlipoproteinemia. It is concluded that platelet aggregation can be studied conveniently with the impedance method in the more physiologic medium of WB. Providing the same information as the well-established turbidometry, the time-sparing impedance method needs less citrated blood. Moreover, our results show an increased sensitivity of the WB system to some aggregating and anti-platelet agents.
Transgenic HFE‐dependent induction of hepcidin in mice does not require transferrin receptor‐2 (2012)

Hereditary hemochomatosis (HH) is caused by mutations in several genes, including HFE and transferrin receptor-2 (TFR2). Loss of either protein decreases expression of the iron regulatory hormone hepcidin by the liver, leading to inappropriately high iron uptake from the diet, and resulting in systemic iron overload. In tissue culture, overexpressed HFE and TFR2 physically interact. Hepatocellular overexpression of Hfe in vivo increases hepcidin expression, despite an associated decrease in Tfr2. On this basis, we hypothesized that Tfr2 would not be required for Hfe-dependent up-regulation of hepcidin. We show that hepatocellular overexpression of Hfe in Tfr2(Y245X/Y245X) mice leads to hepcidin induction eventuating in iron deficiency and a hypochromic, microcytic anemia. Furthermore, coimmunoprecipitation studies using liver lysates did not provide evidence for physical interaction between Hfe and Tfr2 in vivo. In conclusion, we demonstrate that Tfr2 is not essential for Hfe-mediated induction of hepcidin expression, supporting the possibility that TFR2 may regulate iron metabolism in an HFE-independent manner.
Redefinition of Write Margin for Next-Generation SRAM and Write-Margin Monitoring Circuit (2006)

We redefine write margin in order to be able to quantify the effect of both PVT variation and write-margin improvement. A write-margin monitoring circuit based on this definition is implemented in a 90nm CMOS process. This circuit can be applied to an SRAM power supply circuit to improve the write margin
<title>Improved field-sequential-color technique for LCDs</title> (1994)

Dimension Technologies Inc. has devised and experimentally validated a technique for producing field-sequential-color illumination for liquid crystal displays (LCDs) that does not exhibit image breakup and can provide flicker free images at slower refresh speeds than other field-sequential-color techniques. The technique involves a combination of colored illumination patterns that are sequentially imaged within the pixels of an LCD. An optical bench version of this type of illumination system was used to evaluate the ability to produce white light, evaluate flicker performance, evaluate image breakup visibility, and perform reading tests. This work can lead to a superior means of producing color displays using monochrome LCDs. Application of the research by LCD manufacturers may allow that industry to produce simplified, less costly LCDs for color displays.