gebhart/patrepeval huggingface dataset:
Human aldehyde dehydrogenase (1989)

An enzyme which catalyzes dehydrogenation of gamma-aminobutyraldehyde has been purified to homogeneity from human liver and identified as an isozyme of aldehyde dehydrogenase (EC 1.2.1.3); two other isozymes, previously obtained in a homogeneous form, are known as E1 and E2. Affinity chromatography on NAD-agarose (N6 with 8 carbon spacer) yields homogeneous enzyme which migrates as two components on isoelectric focusing with pI = 5.3 and 5.45. These two components, separated by fast protein liquid chromatography on a Mono-P HR 5/20 column, have similar Km values for gamma-aminobutyraldehyde, acetaldehyde, propionaldehyde, and NAD. The Km value for gamma-aminobutyraldehyde is 8.0-14.0 microM versus 760 microM for E1 and 512 microM for E2. The enzyme's molecular weight, subunit molecular weight, and amino acid composition are similar to those of the E1 and E2 isozymes. The enzyme also interacts with anti-E1 and anti-E2 antibodies; it is relatively insensitive to disulfiram inhibition and is neither activated nor inhibited by magnesium. Its absorption spectrum, where the ratio of 280/260 nm is 1.1 and a weak absorption is seen in the 340 nm range (Racker band), suggests the presence of bound coenzyme. gamma-Aminobutyraldehyde dehydrogenase (with Km value of 15 microM for gamma-aminobutyraldehyde) was previously partially purified from Pseudomonas fluorescens (Jakoby, W.B., and Fredericks, J. (1959) J. Biol. Chem. 234, 2145-2150) but never from a mammalian organism.
Efficient parallel solution of linear systems (1985)

The most efficient known parallel algorithms for inversion of a nonsingular n × n matrix A or solving a linear system Ax = b over the rationals require O(log n)2 time and M(n)n0.5 processors (where M(n) is the number of processors required in order to multiply two n × n rational matrices in time O(log n).) Furthermore, all known polylog time algorithms for those problems are unstable: they require the calculation to be done with perfect precision; otherwise they give no results at all.This paper describes parallel algorithms that have good numerical stability and remain efficient as n grows large. In particular, we describe a quadratically convergent iterative method that gives the inverse (within the relative precision 2-nO(1)) of an n × n rational matrix A with condition ≤ n0(1) in O(log n)2 time using M(n) processors. This is the optimum processor bound and the factor n0.5 improvement of known processor bounds for polylog time matrix inversion. It is the first known polylog time algorithm that is numerically stable. The algorithm relies on our method of computing an approximate inverse of A that involves O(log n) parallel steps and n2 processors.Also, we give a parallel algorithm for solution of a linear system Ax = b with a sparse n × n symmetric positive definite matrix A. If the graph G(A) (which has n vertices and has an edge for each nonzero entry of A) is s(n)-separable, then our algorithm requires only O((log n)(log s(n))2) time and |E| + M(s(n)) processors. The algorithm computes a recursive factorization of A so that the solution of any other linear system Ax = b′ with the same matrix A requires only O(log n log s(n)) time and |E| + s(n)2 processors.
Rear-end collision warning system on account of a rear-end monitoring camera (2009)

The objective of this study is to establish a rear-end collision warning system for an advance safety vehicle (ASV) by using a mounted rear-end monitoring camera. The paper attempted to analyze the driving environmental data and built up the rear-end collision warning logic on account of image processing. The main idea of the warning system is to prevent accidents caused by inattentive drivers. In recent years, the parking assistance system with ultrasonic sensors and rear-end camera, has almost become the basic equipment in vehicles. However, the parking assistance system is only activated when the equipped vehicle is reversing. This study tries to apply the rear-end monitoring camera's images as the rear-end collision surveillance for approaching driving. This improves the camera's utility when the parking assistance system in idleness. In this study, the practical system is mainly equipped to a testing car with an industry personal computer, an on-board LCD and a CCD camera. By image processing, the relative distance, velocity, and acceleration to the follower vehicle are measured. This paper developed the dynamic threshold from the relative data and the drivers' perceptive reaction time to issue the warning for the drivers. The α-β-γ filter was applied to process the relative data smoothly. The experiment result was successful on the off-line video tests. This study convinces that the developed rear-end warning system could appropriately warn the equipped driver when its following car does not keep in a safe distance.
Targeted cytosine methylation for <i>in vivo</i> detection of protein–DNA interactions (2003)

We report a technique, named targeted gene methylation (TAGM), for identifying in vivo protein-binding sites in chromatin. M.CviPI, a cytosine-5 DNA methyltransferase recognizing GC sites, is fused to a DNA-binding factor enabling simultaneous detection of targeted methylation, factor footprints, and chromatin structural changes by bisulfite genomic sequencing. Using TAGM with the yeast transactivator Pho4, methylation enrichments of up to 34- fold occur proximal to native Pho4-binding sites. Additionally, significant selective targeting of methylation is observed several hundred nucleotides away, suggesting the detection of long-range interactions due to higher-order chromatin structure. In contrast, at an extragenic locus lacking Pho4-binding sites, methylation levels are at the detection limit at early times after Pho4 transactivation. Notably, substantial amounts of methylation are targeted by Pho4-M.CviPI under repressive conditions when most of the transactivator is excluded from the nucleus. Thus, TAGM enables rapid detection of DNA-protein interactions even at low occupancies and has potential for identifying factor targets at the genome-wide level. Extension of TAGM from yeast to vertebrates, which use methylation to initiate and propagate repressed chromatin, could also provide a valuable strategy for heritable inactivation of gene expression.
Concurrent Naive and Memory CD8+ T Cell Responses to an Influenza A Virus (2001)

Memory Thy-1(+)CD8(+) T cells specific for the influenza A virus nucleoprotein (NP(366-374)) peptide were sorted after staining with the D(b)NP(366) tetramer, labeled with CFSE, and transferred into normal Thy-1.2(+) recipients. The donor D(b)NP(366)(+) T cells recovered 2 days later from the spleens of the Thy-1.2(+) hosts showed the CD62L(low)CD44(high)CD69(low) phenotype, characteristic of the population analyzed before transfer, and were present at frequencies equivalent to those detected previously in mice primed once by a single exposure to an influenza A virus. Analysis of CFSE-staining profiles established that resting tetramer(+) T cells divided slowly over the next 30 days, while the numbers in the spleen decreased about 3-fold. Intranasal infection shortly after cell transfer with a noncross-reactive influenza B virus induced some of the donor D(b)NP(366)(+) T cells to cycle, but there was no increase in the total number of transferred cells. By contrast, comparable challenge with an influenza A virus caused substantial clonal expansion, and loss of the CFSE label. Unexpectedly, the recruitment of naive Thy-1.2(+)CD8(+)D(b)NP(366)(+) host D(b)NP(366)(+) T cells following influenza A challenge was not obviously diminished by the presence of the memory Thy-1.1(+)CD8(+)D(b)NP(366)(+) donor D(b)NP(366)(+) set. Furthermore, the splenic response to an epitope (D(b)PA(224)) derived from the influenza acid polymerase (PA(224-233)) was significantly enhanced in the mice given the donor D(b)NP(366)(+) memory population. These experiments indicate that an apparent recall response may be comprised of both naive and memory CD8(+) T cells.
Administrative Decision-making and the Duty to Give Reasons: Can and Must Dissenters Explain Themselves? (2006)

If the right of a judge to dissent is unclear, then the right of an administrative tribunal member to issue dissenting reasons amounts to un-clarity on stilts (with apologies to Jeremy Bentham). As will be noted in the course of this article, there has been a distinct judicial reluctance to require such decision-makers to give any sort of reasons, let alone dissenting ones from minority members. However, the traditional reluctance appears to be wavering, and recent decisions have suggested that administrative decision-makers may have a general duty to give reasons for their decisions. Whether or not this developing duty requires dissenters to explain their reasons, or at least enables them to do so, is a matter that has been given little thought and is the subject of no commentary. This article therefore proposes to consider these issues at some length. Before the topic of dissenting reasons can be considered, it is first necessary to examine the general requirements imposed on administrative decision-makers to give reasons for their decisions. This article will then discuss recent developments in administrative law that are relevant to the position of minority tribunal members, and in particular, will assess whether a party has the right to know of the existence of a dissent and the identity of the dissenting member(s). After doing so, it will then consider whether the duty to give reasons obliges minority tribunal members to give dissenting reasons, in light of both the basis for that duty and indications from the case law. Finally, the existence of a right to give dissenting reasons, as opposed to an obligation to do so, will then be considered.
Modulation of cortical oscillatory activity during transcranial magnetic stimulation (2007)

Transcranial magnetic stimulation (TMS) can transiently modulate cortical excitability, with a net effect depending on the stimulation frequency (< or =1 Hz inhibition vs. > or =5 Hz facilitation, at least for the motor cortex). This possibility has generated interest in experiments aiming to improve deficits in clinical settings, as well as deficits in the cognitive domain. The aim of the present study was to investigate the on-line effects of low frequency (1 Hz) TMS on the EEG oscillatory activity in the healthy human brain, focusing particularly on the outcome of these modulatory effects in relation to the duration of the TMS stimulation. To this end, we used the event-related desynchronization/synchronization (ERD/ERS) approach to determine the patterns of oscillatory activity during two consecutive trains of sham and real TMS. Each train of stimulation was delivered to the left primary motor cortex (MI) of healthy subjects over a period of 10 min, while EEG rhythms were simultaneously recorded. Results indicated that TMS induced an increase in the power of brain rhythms that was related to the period of the stimulation, i.e. the synchronization of the alpha band increased with the duration of the stimulation, and this increase was inversely correlated with motor-evoked potentials (MEPs) amplitude. In conclusion, low frequency TMS over primary motor cortex induces a synchronization of the background oscillatory activity on the stimulated region. This induced modulation in brain oscillations seems to increase coherently with the duration of stimulation, suggesting that TMS effects may involve short-term modification of the neural circuitry sustaining MEPs characteristics.
B-spline method for energy minimization in grid-based molecular mechanics calculations (1998)

A method is described for molecular mechanics calculations based on a cubic B-spline approximation of the potential energy. This method is useful when parts of the system are allowed to remain fixed in position so that a potential energy grid can be precalculated and used to approximate the interaction energy between parts of a molecule or between molecules. We adapted and modified the conventional B-spline method to provide an approximation of the Empirical Conformational Energy Program for Peptides (ECEPP) potential energy function. The advantage of the B-spline method over simpler approximations is that the resulting B-spline function is C2 continuous, which allows minimization of the potential energy by any local minimization algorithm. The standard B-spline method provides a good approximation of the electrostatic energy; but in order to reproduce the Lennard–Jones and hydrogen-bonding functional forms accurately, it was necessary to modify the standard B-spline method. This modification of the B-spline method can also be used to improve the accuracy of trilinear interpolation for simulations that do not require continuous derivatives. As an example, we apply the B-spline method to rigid-body docking energy calculations using the ECEPP potential energy function. Energies are calculated for the complex of Phe-Pro-Arg with thrombin. For this system, we compare the performance of the B-spline method to that of the standard pairwise summation in terms of speed, accuracy, and overhead costs for a variety of grid spacings. In our rigid-body docking calculations, the B-spline method provided an accurate approximation of the total energy of the system, and it resulted in an 180-fold reduction in the time required for a single energy and gradient calculation for this system. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 71–85, 1998
Cluster analysis of neuropsychological test results among patients with traumatic brain injury (TBI): Implications for a model of TBI-related disability (1993)

Abstract Neuropsychological test data and educational attainment for 47 patients with traumatic brain injury (TBI) were submitted to cluster analysis. Relationships of cluster membership to injury severity (coma days) and disabilities (Portland Adaptability Inventory; PAI) were examined. Cluster 1 was composed of highly educated individuals with relatively mild initial injuries, neuropsychological impairment, and disabilities. Impairments for Cluster 1 appeared more significant in contrast to probably high preinjury functioning. Cluster 2, whose members had lowest test performances on measures of remote memory and reading, may have been marginally functioning prior to injury. Those in Cluster 2 had only mild initial injuries, but showed moderately extensive disabilities on the PAI. Patients in Cluster 3 had mild initial injuries, very mild neuropsychological impairments, and mild disabilities, characterized by difficulties with planning and irritability. Individuals in Clusters 4 and 5 had more severe initial injuries, neuropsychological impairments, and disabilities. Patients in Cluster 5 showed greater perseverative tendencies and socially inappropriate behavior than those in the other clusters. Results of this cluster analysis suggest a model of TBI-related disability which predicts level of chronic disability from preinjury functioning, injury severity, and impairments in remote memory and adaptive abilities.
Innovative approach to the design of low-cost Zr-based BMG composites with good glass formation (2013)

The high manufacturing cost for metallic glasses hampers actual commercial applications of this class of fascinating materials. In this letter, the effect of oxygen impurity on the glass forming ability and tensile properties of Zr-BMG composites were studied. Our results have demonstrated that oxygen was absorbed and concentrated only in the precipitated β-Zr phase, leading that the remainder molten metal retains good glass forming ability. The high oxygen concentration in the β-Zr phase induces a significant solid-solution strengthening effect, this resulting in an enhanced strength of the BMG composites without sacrificing their overall ductility. Based on this alloying strategy, we have successfully developed the low-cost Zr-based BMG composites with excellent tensile properties and good glass forming ability, using the low grade industrial raw materials processed under industrial vacuum systems. This finding is expected to greatly cut down the manufacturing cost and greatly promote the commercial applications of the BMG composites.
Repetition and Associative Context Effects in Speech Production (1991)

An experiment is reported that addresses the impact of lexical constraint on the production characteristics (mean duration and peak amplitude) of a given target word within a sentence production task. Subjects produced aloud sentences from memory that contained a target word (e.g., cat) that was either a repetition of an earlier word in the sentence (e.g., cat), associatively related to an earlier word in the sentence (e.g., dog), or unrelated to an earlier word in the sentence (e.g., son). The position within the sentence and phonetic environment of the target were equated across conditions. The results indicated that the mean durations for the target word were shorter in the repetition condition, compared to the associatively related condition, which in turn produced shorter production durations compared to the unrelated condition. In addition, the peak amplitude measurements indicated that the repeated condition produced relatively lower peak amplitudes for the target word, compared to the remaining two conditions which did not differ.
API QuadFERM+ with rapid DNase for identification of Neisseria spp. and Branhamella catarrhalis (1987)

The QuadFERM+ system (Analytab Products, Plainview, N.Y.), a 2-h carbohydrate degradation method for the identification of Neisseria spp., was evaluated along with a rapid DNase test for confirmation of Branhamella catarrhalis. QuadFERM+ identified 100% of 82 N. gonorrhoeae and 96% of 54 N. meningitidis strains. The two misidentified meningococcal strains were biochemically atypical and were also misidentified by the conventional method. Of 26 N. lactamica strains, 25 (96%) were correctly identified. Of 21 Neisseria spp., 14 (67%) produced carbohydrate reactions in agreement with the conventional procedure, and 7 strains produced detectable acid in the QuadFERM+ from maltose and sucrose but not glucose. All 9 N. cinerea and 30 B. catarrhalis strains were asaccharolytic by QuadFERM+. The rapid DNase test was positive for all B. catarrhalis strains and negative for all other organisms. Two beta-lactamase-positive N. gonorrhoeae strains and 25 (93%) of 27 beta-lactamase-positive B. catarrhalis strains were detected by the 2-h acidometric beta-lactamase test on the strip. QuadFERM+ with rapid DNase is a simple and easily interpretable method for identification of these organisms in the clinical laboratory.
Iterative mining of resource-releasing specifications (2011)

Software systems commonly use resources such as network connections or external file handles. Once finish using the resources, the software systems must release these resources by explicitly calling specific resource-releasing API methods. Failing to release resources properly could result in resource leaks or even outright system failures. Existing verification techniques could analyze software systems to detect defects related to failing to release resources. However, these techniques require resource-releasing specifications for specifying which API method acquires/releases certain resources, and such specifications are not well documented in practice, due to the large amount of manual effort required to document them. To address this issue, we propose an iterative mining approach, called RRFinder, to automatically mining resource-releasing specifications for API libraries in the form of (resource-acquiring, resource-releasing) API method pairs. RRFinder first identifies resource-releasing API methods, for which RRFinder then identifies the corresponding resource-acquiring API methods. To identify resource-releasing API methods, RRFinder performs an iterative process including three steps: model-based prediction, call-graph-based propagation, and class-hierarchy-based propagation. From heterogeneous information (e.g., source code, natural language), the model-based prediction employs a classification model to predict the likelihood that an API method is a resource-releasing method. The call-graph-based and class-hierarchy-based propagation propagates the likelihood information across methods. We evaluated RRFinder on eight open source libraries, and the results show that RRFinder achieved an average recall of 94.0% with precision of 86.6% in mining resource-releasing specifications, and the mined specifications are useful in detecting resource leak defects.
Controlling latent TB tuberculosis infection in high-burden countries: A neglected strategy to end TB (2019)

In a Perspective, Gavin Churchyard and Sue Swindells discuss the importance of strategies to target latent tuberculosis infection in high risk populations and thus disrupt a reservoir for new infections in high burden countries.
Efficient Total Syntheses of (−)‐Colombiasin A and (−)‐Elisapterosin B: Application of the Cr‐Catalyzed Asymmetric Quinone Diels–Alder Reaction (2005)

A made-to-order asymmetric catalytic reaction was applied in the key quinone Diels–Alder step of the total syntheses of the title compounds (see scheme for the synthesis of colombiasin A). The reaction was highly regio- and diastereoselective.
Emerging Technologies in Ethanol Production (1993)

The fuel ethanol industry is poised to adopt a wide range of technologies that would reduce costs at every stage of the production process. Improved enzymes and fermenter designs can reduce the time needed to convert corn to ethanol and lower capital costs. Membrane filtration can allow the recovery of high-value coproducts such as lactic acid. Adoption of these and other innovations in the next 5 years is expected in new ethanol plants constructed to cope with new demand resulting from Clean Air Act stipulations for cleaner burning fuel. Biomass (agricultural residues, municipal and yard waste, energy crops like switchgrass) can also be converted to ethanol, although commercial-scale ventures are limited by current technology. While biomass requires more handling and sorting before conversion, those costs may be offset by the abundance of biomass relative to corn.
Integrating transparent conductive oxides to improve the infrared response of silicon solar cells with passivating rear contacts (2018)

This work addresses the development of a transparent conductive oxide (TCO)/metal stack for n-type Si solar cells featuring a tunnel oxide passivating rear contact (TOPCon). While poly-Si based passivating contacts contacted by local fire-through metallization currently show an increased recombination at the metal contacts and a poor infrared (IR) response, we aim to realize a full-area metallization which maintains the high level of surface passivation and avoids IR losses. Some research groups have reported that sputtering TCOs on poly-Si based passivating contacts degrades the surface passivation and unlike the SHJ cells this degradation cannot be cured completely at Tcure ∼ 200°C. However, the higher thermal stability of TOPCon allows for higher Tcure of up to 400°C, which can effectively restore the surface passivation. On the other hand, the contact resistivity (ρc) of the TOPCon/ITO/metal contact increased by several orders of magnitude in our test structures during annealing at such high temperatures. Possible reasons like the formation of an interfacial oxide are currently under investigation. Increasing the poly-Si thickness and/or doping mitigated the effect of sputter damage, but this will come at the cost of more parasitic absorption. However, by adapting the sputter and the subsequent annealing process, we were able to realize low damage deposition of ITO (loss in implied Voc ∼ 7 mV) on thin, lowly doped poly-Si layers on textured wafers, yielding reasonable contact properties (ρc ∼ 40 mΩcm2; of the whole rear contact stack).