gebhart/patrepeval huggingface dataset:
Diacetyl reductase of <i>Lactobacillus casei</i> (1970)

Diacetyl reductase (diacetyl:reduced nicotinamide adenine dinucleotide (NADH) oxidoreductase, EC. 1.1.1.5) has been isolated from Lactobacillus casei. Cell sonication, ammonium sulfate fractionation, Sephadex gel filtration, DEAE-cellulose chromatography, and alumina gel adsorption were used to obtain the partially purified enzyme. Both NADH oxidase and diacetyl reductase activity were associated with the same fraction at all stages in purification. Growth in media containing added pyruvate resulted in a 10-fold increase in the NADH oxidase activity and a 3-fold increase in the diacetyl reductase activity of crude cell extracts on a protein basis. Purified preparations showed maximal reductase and oxidase activities at pH 4.5 and 5.0, respectively. Lineweaver–Burke plots yielded intersecting lines when NADH and diacetyl concentrations were varied, suggesting a flavin-linked reaction. The absorption spectrum of the purified preparation was characteristic of that of a flavoprotein. The product of the reduction of diacetyl was identified as acetoin. Acetoin and methylene blue were inactive as acceptors.
Abstraction-based misuse detection: high-level specifications and adaptable strategies (2002)

A typical misuse detection system contains: (1) a language for describing known techniques (called misuse signatures) used by attackers to penetrate the target system, and (2) monitoring programs for detecting the presence of an attack based on the given misuse signatures. In most of the systems appearing in the literature, however, the description of misuses is often in terms of a low level language (i.e. in terms of audit records of the target system), that either has limited expressiveness or is difficult to use. Moreover the monitoring algorithms are often fixed and do not adapt to a changing operating environment or to objectives of the site security officer. To overcome these limitations, the paper defines a high level language for abstract misuse signatures (MuSigs). Due to the use of high level concepts, a MuSig can represent misuses in a simple form and yet with high expressiveness. The paper also introduces a set of system directives provided by the system designer in support of high level concepts. The paper then discusses ways to translate MuSigs into monitoring program with the help of the system directives. The adaptability of the system is obtained by the ability for the site security officer to add or delete system directives to change the behavior of the monitoring program.
Electrically-Induced Memory Effect in Bacteriorhodopsin (1995)

Absorption spectrum of bacteriorhodopsin under an electric field was investigated. We found that the change driven by the field does not disappear even after removing the field at relative humidity below 5%. Furthermore, we found that the state induced by the electric field returns to the initial state with light illumination. We examined the effect of humidity on this phenomenon. As for a retinylidene chromophore, we suppose the following phenomenon may occur. The existence of water molecules promotes the hydration of the nitrogen atom in the retinylidene chromophore, and the pi-electrons in the chromophore are attracted to the nitrogen atom. Such a change is considered to be one cause that makes the electrically-induced state unstable at high relative humidity.
Detection by broad-range real-time PCR assay of Chlamydia species infecting human and animals (2006)

This new real-time PCR offers a sensitive, reproducible assay that produces results in <3 h. With panels of quantified Chlamydia species, this real-time PCR can be run with all real-time PCR equipment. Larger trials are needed to confirm the utility of this test in diagnosis and for therapeutic follow-up.
Antibiotics from Gliding Bacteria, LXXVIII. Ripostatin A, B, and C: Isolation and Structure and Structure Elucidation of Novel Metabolites from <i>Sorangium cellulosum</i> (1996)

Abstract Three closely related new metabolites named ripostatins were isolated from the myxobacterium Sorangium cellulosum and their structures elucidated by spectroscopic methods. Two of them, ripostatin A ( 1a, b ) and B ( 2a ), are 14‐membered macrolides with an acetic acid and a phenylalkyl side chain, whereas the third metabolite ripostatin C ( 3a ) is an acyclic derivative of ripostatin A. By application of the method of Helmchen the absolute stereochemistry could be determined as (11 R ,13 R ) for ripostatin A, 11 R ,13 S ,15 R for ripostatin B and 11 S for ripostatin C. The polyketide origin of A was revealed by feeding experiments with 13 C‐labeled precursors demonstrating the incorporation of one molecule of phenylacetic acid derived from phenylalanine, one propionate unit, and ten acetate units.
Bouquet formation in budding yeast: Initiation of recombination is not required for meiotic telomere clustering (1999)

Fluorescence in situ hybridization in combination with synaptonemal complex and spindle pole body immunostaining to both spread and structurally preserved nuclei from time course experiments disclosed prominent telomere clustering during meiotic prophase of the yeast Saccharomyces cerevisiae. It was found that centromere clustering, which dominates vegetative nuclear structure, is rapidly lost after induction of meiosis. Telomeres tightly clustered during leptotene/zygotene-equivalent stages in the vicinity of the spindle pole body, giving rise to a classical chromosomal bouquet arrangement. This arrangement dissolved later during prophase. Painting of chromosomes XI revealed that initially compacted chromosome territories adopt an outstretched morphology in bouquet nuclei. This conformational state was associated with alignment and pairing. Chromosome condensation during pachytene rendered condensed and compact bivalents, and dispersed telomeres. Both the spo11 and rad50S recombination mutants formed bouquets, demonstrating that bouquet formation is recombination and synapsis independent.
Physiological measures of vaginal vasocongestion. (1998)

This paper reviews reliability, specificity, and practical applicability of the two most promising and widely used methods for measuring blood flow within the vagina: the oxygenation-temperature method and vaginal photoplethysmography. It was concluded that the oxygenation-temperature method and vaginal pulse amplitude as measured by the photoplethysmograph are both specific indicators of physiological sexual arousal. Although vaginal pulse amplitude seems to be the method of choice for measuring vaginal vasocongestion up to orgasm, and the oxygenation-temperature method for measuring orgasm, these measures should not be used in isolation. It is argued that women's sexual function should be evaluated using vaginal vasocongestion measures in conjunction with subjective indices. Finally, the field is in need of studies comparing physiological and subjective sexual responses in clinical and non-clinical groups.
Investigation of the Mechanism of Colloidal Silicalite‐1 Crystallization by Using DLS, SAXS, and <sup>29</sup>Si NMR Spectroscopy (2010)

Colloidal silicalite-1 zeolite was crystallized from a concentrated clear sol prepared from tetraethylorthosilicate (TEOS) and aqueous tetrapropylammonium hydroxide (TPAOH) solution at 95 degrees C. The silicate speciation was monitored by using dynamic light scattering (DLS), synchrotron small-angle X-ray scattering (SAXS), and quantitative liquid-state (29)Si NMR spectroscopy. The silicon atoms were present in dissolved oligomers, two discrete nanoparticle populations approximately 2 and 6 nm in size, and crystals. On the basis of new insight into the evolution of the different nanoparticle populations and of the silicate connectivity in the nanoparticles, a refined crystallization mechanism was derived. Upon combining the reagents, different types of nanoparticles (ca. 2 nm) are formed. A fraction of these nanoparticles with the least condensed silicate structure does not participate in the crystallization process. After completion of the crystallization, they represent the residual silicon atoms. Nanoparticles with a more condensed silicate network grow until approximately 6 nm and evolve into building blocks for nucleation and growth of the silicalite-1 crystals. The silicate network connectivity of nanoparticles suitable for nucleation and growth increasingly resembles that of the final zeolite. This new insight into the two classes of nanoparticles will be useful to tune the syntheses of silicalite-1 for maximum yield.
Collection of cell-free DNA for genomic analysis of solid tumors in a clinical laboratory setting (2017)

The breadth of diagnostic procedures that utilize cell free DNA (cfDNA) from human plasma has increased dramatically in recent years. Here, we confirm that tumor-derived cfDNA fragments are similar in size distribution to cfDNA derived from normal tissues. Therefore, collection procedures optimized with healthy donor specimens are likely to be applicable to the diagnosis and monitoring of many different cancer types. We verify that the distribution and DNA sequences of fragmentation sites in cfDNA from both normal-germline and tumor-derived cfDNA are non-random. A broad survey of cfDNA from healthy donors suggests that average individuals possess ~6 ng of cfDNA per mL of plasma. Importantly, the cfDNA present in plasma samples that were initially collected as whole blood in K2-EDTA tubes and subsequently processed by centrifugation is stable for several days at ambient temperatures. This observation has the potential to significantly reduce the cost and logistical complexity of shipping clinical samples from the site of collection to centers proficient in diagnostic analysis. Finally, plasma samples collected with high-volume plasma collection devices possess abundant quantities of cfDNA. Since the quantity of analyzed cfDNA is directly proportional to sensitivity of diagnostic assays, this method of plasma collection, where available, could enable highly sensitive post-treatment disease monitoring and early detection of cancer in at-risk individuals.
Cardiac resynchronization therapy: evaluation of ventricular dysynchrony and patient selection. (2015)

Cardiac resynchronization therapy (CRT) is an established treatment modality for systolic heart failure. Aimed to produce simultaneous biventricular stimulation and correct the lack of ventricular synchrony in selected patients with congestive heart failure, CRT has shown to improve mortality and reduce hospital admissions when compared to medical treatment. At present, the indication criteria for the implantation of a CRT device include an ejection fraction of less than 35%, heart failure symptoms consistent with NYHA functional class III-IV and a QRS complex duration equal or longer than 120 milliseconds. It has been reported that 30% of patients who meet those criteria still may not derive clinical benefit from CRT. Due to the existing diversity of imagin modalities and resources for their process and analysis, a great expectation in terms of more accurate diagnosis of ventricular dyssynchrony has been raised. Reilable identification of dyssynchrony could allow us to better predict the favorable response of an individual patient to CRT and therefore offer this procedure to those individuals most likely to benefit. We review the available techniques for the study of ventricular dyssynchrony for CRT patient selection and the results of its application in clinical trials. Despite tremendous progress in the imaging technology available for the assessment and diagnosis of ventricular dyssynchrony, an ideal method has not been identified and the duration of QRS complex in the surface ECG remains the accepted criteria of dyssynchrony in the selection of patients for CRT.
Engineering PQQ-glucose dehydrogenase into an allosteric electrochemical Ca<sup>2+</sup> sensor (2015)

Electrochemical biosensors convert biological events to an electrical current. To date most electrochemical biosensors exploit activities of naturally occurring enzymes. Here we demonstrated that insertion of a calmodulin domain into the redox enzyme PQQ-glucose dehydrogenase resulted in a selective Ca(2+) biosensor that could be used to rapidly measure Ca(2+) concentrations in human biological fluids. We were able to convert a point-of-care glucometer into Ca(2+) monitor by refurbishing it with the developed biosensor. We propose that similar engineering strategies may be used to create highly specific electrochemical biosensors to other analytes. Compatibility with cheap and ubiquitous amperometric detectors is expected to accelerate progression of these biosensors into clinical applications.
Abstract 73: Aberrant Activation of γ2-AMPK Increases Cardiac Growth Through Cellular Hypertrophy and Hyperplasia (2012)

AMP-activated protein kinase (AMPK) is an energy sensor and a key regulator of cell metabolism, hence a promising drug target. Point mutations in the regulatory γ2-subunit (encoded by PRKAG2 gene) have been shown to cause a unique form of cardiomyopathy in humans characterized by cardiac growth, arrhythmias and glycogen storage. In previous studies, we demonstrated that the mutation of prkag2 (N488I) caused aberrant activation of AMPK leading to glycogen storage. However, elimination of glycogen storage by inhibiting glycogen synthase activity failed to normalize heart weight (HW) of the mutant mice. Here, we aimed to determine whether cardiac growth in PRKAG2 ardiomyopathy was dueto cellular hypertrophy or hyperplasia. We used transgenic mice expressing a mutant PRKAG2 (N488I) in the heart (TGγ2 N488I ) that faithfully recapitulated PRKAG2 cardiomyopathy. We determined HW and cardiac myocyte size in adult (2 months) and postnatal (2 weeks) hearts in WT and TGγ2 N488I . At 2 months, TGγ2 N488I hearts show a 2.4-fold increase in HW/BW (body weight) (10.3 ± 1.44 vs. 4.3± 0.17 mg/g) as well as cross-sectional cell surface area compared WT hearts (325 ± 13 vs. 155 ± 5.4 μm 2 ,p<0.01), suggesting cellular hypertrophy in adult TGγ2 N488I heart. Furthermore, we observed increased mTOR activity evidenced by enhanced phosphorylation of mTOR (Ser2448) as well as its downstream targets S6 and 4E-BP. The HW of TGγ2 N488I was partially inhibited by treatment with rapamycin, an inhibitor of mTOR. Interestingly, the length and width of isolated cardiomyocytes from 2 weeks old mice were not different between the WT and TGγ2 N488I heart in spite of a 50% increase of HW of TGγ2 N488I mice. We observed a 2- fold increase in the expression of a proliferation marker, proliferating cell nuclear antigen (PCNA) during postnatal cardiac growth. Expression of Cyclin genes including cyclin D1, D2 and E1 was greatly increased in TGγ2 N488I hearts (2.4 - 4 fold, p<0.01 vs. WT). Taken together, these data indicate that aberrant γ2-AMPK activation stimulates cardiac growth through increased cell number during postnatal growth period and increased cell size at adulthood. These results suggest a novel role of γ2-AMPK in the growth of cardiac myocytes.
A simple optical coherence tomography quantification method for choroidal neovascularization (2015)

Purpose: Therapeutic efficacy is routinely assessed by measurement of lesion size using flatmounted choroids and confocal microscopy in the laser-induced choroidal neovascularization (L-CNV) rodent model. We investigated whether optical coherence tomography (OCT) quantification, using an ellipsoid volume measurement, was comparable to standard ex vivo evaluation methods for this model and whether this approach could be used to monitor treatment-related lesion changes.\n\nMethods: Bruch's membrane was ruptured by argon laser in the dilated eyes of C57BL/6J mice, followed by intravitreal injections of anti-VEGF164 or vehicle, or no injection. In vivo OCT images were acquired using Micron III or InVivoVue systems at 7, 10, and/or 14 days post-laser and neovascular lesion volume was calculated as an ellipsoid. Subsequently, lesion volume was compared to that calculated from confocal Z-stack images of agglutinin-stained choroidal flatmounts.\n\nResults: Ellipsoid volume measurement of orthogonal 2-dimensional OCT images obtained from different imaging systems correlated with ex vivo lesion volumes for L-CNV (Spearman's ρ=0.82, 0.75, and 0.82 at days 7, 10, and 14, respectively). Ellipsoid volume calculation allowed temporal monitoring and evaluation of CNV lesions in response to antivascular endothelial growth factor treatment.\n\nConclusions: Ellipsoid volume measurements allow rapid, quantitative use of OCT for the assessment of CNV lesions in vivo. This novel method can be used with different OCT imaging systems with sensitivity to distinguish between treatment conditions. It may serve as a useful adjunct to the standard ex vivo confocal quantification, to assess therapeutic efficacy in preclinical models of CNV, and in models of other ocular diseases.
Recognizing design patterns in C++ programs with integration of Columbus and Maisa (2002)

. A method for recognizing design patterns from C++ programs is presented. The method consists of two separate phases, analysis and reverse engineering of the C++ code, and architectural pattern matching over the reverse-engineered intermediate code representation. It is shown how the pattern recognition eect can be realized by integrating two specialized software tools, the reverse engineering framework Columbus and the architectural metrics analyzer Maisa. The method and the integrated power of the tool set are illustrated with small experiments. Key Words design patterns, reverse engineering, source code parsing, C++, object-oriented design 1
Towards freely and correctly adjusted Dijkstra's algorithm with semantic decision tables for ontology based data matching (2010)

Researches on ontology based data matching have been recently explored. In this paper, we will focus on how to adapt Dijkstra's algorithm for matching two data sets and how to freely adjust the parameters of Dijkstra's algorithm by the end users. A novel approach of using semantic decision tables for the adjustment will be presented and discussed. This particular approach provides a generic, user friendly, simple yet powerful solution to control an algorithm in an elegant way. In order to present the matching result, we propose a formula called GRASIM, which uses the travel cost of the shortest path, to calculate the similarities between two data sets.
Structural and dynamical features of inteins and implications on protein splicing. (2014)

VOLUME 289 (2014) PAGES 14506–14511 PAGE 14507: The panel showing the capture and collapse folding mechanism of the Npu DnaE intein in Fig. 1C was incomplete. The complete panel is provided.
The high-current-density phase of the discharge in low-pressure high-power switches as a mode of the vacuum discharge (1992)

Concepts of the theory of near-cathode layers of vacuum arcs are extended to the range of lower values of the current density and of the temperature of the cathode surface. It is shown that these concepts describe the mode of the vacuum discharge with the near-cathode voltage drop on the level of several hundred volts. The main features of this mode correspond qualitatively to those of the high-current-density phase of the discharge in low-pressure high-power switches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Removal of lead and cadmium from aqueous waste streams using granular activated carbon (GAC) columns (1994)

The use of granular activated carbon (GAC) columns to treat metal-bearing wastewaters was investigated. Synthetic wastewaters containing Pb and Cd (10 or 50 mg/L), acetic acid (0.001 N) or EDTA (1:0.1 or 1:1 Me:EDTA molar ratios) were studied. For metal-only and metal-acetic acid experiments, significant quantities (as high as 325 bed volumes (BV)) of wastewater were treated prior to breakthrough (Ce = 0.03 Co). X/M values were as high as about 30 mg Pb/g carbon. For EDTA experiments, Ce was always >0.03 Co. The amount of metal not removed corresponded to the amount that was complexed by EDTA. Column pH is the critical parameter influencing column performance. The increase in effluent metal concentration corresponded with the decrease in column pH. GAC columns were successfully regenerated using a 1 L (≈ 8 BV) 0.1 N HNO3 rinse followed by a 1 L 0.1 N NaOH rinse. Column performance was not adversely affected by regeneration. When the regeneration step was used on virgin carbon, a dramatic improvement in column performance was observed and was attributed to the increase in carbon surface pH (pH≈11) and the deposition of OH− in the pore liquid. Possible removal mechanism are precipitation on the carbon surface and in the pore liquid, and adsorption.
Flying Small Target Detection for Anti-UAV Based on a Gaussian Mixture Model in a Compressive Sensing Domain (2019)

Addressing the problems of visual surveillance for anti-UAV, a new flying small target detection method is proposed based on Gaussian mixture background modeling in a compressive sensing domain and low-rank and sparse matrix decomposition of local image. First of all, images captured by stationary visual sensors are broken into patches and the candidate patches which perhaps contain targets are identified by using a Gaussian mixture background model in a compressive sensing domain. Subsequently, the candidate patches within a finite time period are separated into background images and target images by low-rank and sparse matrix decomposition. Finally, flying small target detection is achieved over separated target images by threshold segmentation. The experiment results using visible and infrared image sequences of flying UAV demonstrate that the proposed methods have effective detection performance and outperform the baseline methods in precision and recall evaluation.
Microphone array signal processing with application in three-dimensional spatial hearing (2005)

Microphone arrays are known to enhance the directionality and signal-to-noise ratio (SNR) over single-channel sensors. This is considered beneficial in many applications such as video-conferencing systems and hearing aids. However, this advantage comes at the price of the sensation of spatial hearing. The spatial cues due to diffractions of the head and torso are lost if the array is not fitted in the ears. In this paper we present a system that incorporates binaural hearing synthesis into array signal processing, in an attempt to recover the three-dimensional sound image that a human listener would naturally perceive. In the system, the superdirective beamformer is exploited to estimate the direction of arrival (DOA) of the incoming sound. The spatial sound image is restored by steering the beam to the direction found in the DOA session and filtering the array output with the corresponding Head Related Transfer Functions (HRTF). The algorithms have been implemented in real-time fashion using a digital signal processor. Objective and subjective experiments were performed to validate the proposed system. The experimental results showed that the accurate localization of the sound source is achievable using the array system.
Comparison of mobile phone user interface design preferences (2007)

This research study explores cross-cultural differences and similarities of user preferences of mobile phone features. Product interactive focus groups were conducted in India and in the United States; groups included users without any apparent disabilities and users with a visual disability of legal blindness. The analysis of the focus group sessions and post-task usability questionnaires provided an insight to the preferences of mobile phone interface components and gave a deeper understanding of the mobile culture in the two countries. These results are summarized to provide guidelines for designing cross-cultural user interfaces which are nationality specific and disability specific. A pyramid model for a holistic process of designing cell phones for users with disabilities is proposed which integrated the findings of this study and Jordan's [1] pleasurability framework