gebhart/patrepeval huggingface dataset:
Fluoride Inhibition of Enolase:  Crystal Structure and Thermodynamics<sup>,</sup> (2005)

Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2P(i) complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 A resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2P(i) complex (enolase phosphate inhibitory complex, EPIC) at 1.92 A resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 x 10(5) +/- 1.3 x 10(5), 1.2 x 10(5) +/- 0.2 x 10(5), 8.6 x 10(4) +/- 1.6 x 10(4), and 1.6 x 10(4) +/- 0.7 x 10(4) M(-1). The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.
Cell-cycle-dependent Regulation of Human aurora A Transcription Is Mediated by Periodic Repression of E4TF1 (2002)

Human aurora A is a serine-threonine kinase that controls various mitotic events. The transcription of aurora A mRNA varies throughout the cell cycle and peaks during G(2)/M. To clarify the transcriptional mechanism, we first cloned the 1.8-kb 5'-flanking region of aurora A including the first exon. Transient expression of aurora A promoter-luciferase constructs containing a series of 5'-truncated sequences or site-directed mutations identified a 7-bp sequence (CTTCCGG) from -85 to -79 as a positive regulatory element. Electromobility shift assays identified the binding of positive regulatory proteins to the CTTCCGG element. Anti-E4TF1-60 antibody generated a supershifted complex. Furthermore, coexpression of E4TF1-60 and E4TF1-53 markedly increased aurora A promoter activity. Synchronized cells transfected with the aurora A promoter-luciferase constructs revealed that the promoter activity of aurora A increased in the S phase and peaked at G(2)/M. In addition, we identified a tandem repressor element, CDE/CHR, just downstream of the CTTCCGG element, and mutation within this element led to a loss of cell cycle regulation. We conclude that the transcription of aurora A is positively regulated by E4TF1, a ubiquitously expressed ETS family protein, and that the CDE/CHR element was essential for the G(2)/M-specific transcription of aurora A.
Breath Ketone Testing: A New Biomarker for Diagnosis and Therapeutic Monitoring of Diabetic Ketosis (2014)

Breath testing for ketones has a high sensitivity and specificity and appears to be a noninvasive, convenient, and repeatable method for the diagnosis and therapeutic monitoring of diabetic ketosis.
Biotinylated DNA probes for exotoxin A and pilin genes in the differentiation of Pseudomonas aeruginosa strains (1988)

Biotin-labeled DNA probes derived from Pseudomonas aeruginosa exotoxin A and pilin genes were tested for their ability to distinguish strains among a selected group of P. aeruginosa isolates. Probing of Southern blots of restriction digests of DNA from test strains with the exotoxin A probe demonstrated a unique hybridization pattern for each independently isolated strain containing the exotoxin A gene. Two phenotypically distinct strains isolated from the same patient were found to be identical in their DNA hybridization patterns. By using a pilin gene probe, similar distinction was made between independent strains, while strains from the same source were confirmed to be identical. Furthermore, DNA from a strain of P. aeruginosa lacking the exotoxin A gene yielded a unique pattern of restriction fragments which hybridized to the pilin gene probe. The exotoxin A and the pilin probes may together prove to be useful tools in epidemiological surveys during outbreaks of P. aeruginosa infection.
Why Model-Based Test Automation is Different and What You Should Know to Get Started (2004)

Test engineers, their managers, as well as the project developers often have many different views and misconceptions about tools and methods that provide test automation support. This paper compares model-based testing with three other generations of test automation. Model-based test automation can be considered a fourth generation test automation. It supports defect prevention, early requirement defect identification, and automatic generation of tests from models, which eliminates manual test design and reduces cost. However, to be effective at adopting model-based test automation, there are specific skills that will be required to incorporate this type of test automation into an organization. The paper discusses the organizational, personnel, and development lessons learned from working with numerous companies and projects over the past several years. It recommends how to get started, how to select a project, and how to organize a project. Finally, the paper describes how to measure, track and estimate the project completion date during the first non-pilot project.
Detection of camera artifacts from camera images (2014)

Cameras are frequently used in state-of-the-art systems in order to get detailed information of the environment. However, when cameras are used outdoors they easily get dirty or scratches on the lens which leads to image artifacts that can deteriorate a system's performance. Little work has yet been done on how to detect and cope with such artifacts. Most of the previous work has concentrated on detecting a specific artifact like rain drops on the windshield of a car. In this paper, we show that on moving systems most artifacts can be detected by analyzing the frames in a stream of images from a camera for static image parts. Based on the observation that most artifacts are temporally stable in their position in the image we compute pixel-wise correlations between images. Since the system is moving the static artifacts will lead to a high correlation value while the pixels showing only scene elements will have a low correlation value. For testing this novel algorithm, we recorded some outdoor data with the three different artifacts: raindrops, dirt and scratches. The results of our new algorithm on this data show, that it reliably detects all three artifacts. Moreover, we show that our algorithm can be implemented efficiently by means of box-filters which allows it to be used as a self-checking routine running in background on low-power systems such as autonomous field robots or advanced driver assistant systems on a vehicle.
Compact lumped element model for TSV in 3D-ICs (2011)

A wide-band lumped element model for a through silicon via (TSV) is proposed based on electromagnetic simulations. Closed form expressions for the TSV parasitics based on the dimensional analysis method are introduced. The proposed model enables direct extraction of the TSV resistance, self-inductance, oxide capacitance, and parasitic elements due to the finite substrate resistivity. The model's compactness and compatibility with SPICE simulations allows the fast investigation of a TSV impact on a 3-D circuit performance. The parameters' values of the proposed TSV model are fitted to the simulated S-parameters up to 10 GHz with an error less than 5%. It is shown that a TSV capacitance is highly dependent on the positions of ground contacts and has a value of tens of femto farads in a typical current technology. This value is much higher than a minimum device capacitance and requires special design methodologies such as cascaded buffers. Coupling between TSVs will be handled in another paper.
Elongational flow and melt-spinning instability of concentrated suspensions of small particles in polymer melts (1981)

It is suggested that the existence of yield values in the elongational viscosity of concentrated suspensions of small particles in polymer melts leads to enhanced instability of uniaxial stretching and melt-spinning behavior. This is supported by analyses of filament stability. Severe instabilities are found in experiments on both simple stretching and melt spinning of filaments of suspensions of carbon black, titanium dioxide, and calcium carbonate in polystyrene. Necking and low elongations to break are observed in the former case. The melt-spinning results show “draw resonance” occurring at low drawdown ratios and high amplitudes of disturbances in the unstable region.
Evidence for Specific Antibodies and Antibody-independent Inhibitors in Milk which Inhibit the Virus-induced Hemagglutination (1972)

Evidence for Specific Antibodies and Antibody-independent Inhibitors in Milk which Inhibit the Virus-induced Hemagglutination Get access Minoru Saito, Minoru Saito Central Research Laboratory, Morinaga Milk Industry Co., Ltd., Meguro, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Yoshitsugu Harada, Yoshitsugu Harada Central Research Laboratory, Morinaga Milk Industry Co., Ltd., Meguro, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Kazunori Mizoguchi, Kazunori Mizoguchi Central Research Laboratory, Morinaga Milk Industry Co., Ltd., Meguro, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Munehiro Hirayama Munehiro Hirayama Central Research Laboratory, Morinaga Milk Industry Co., Ltd., Meguro, Tokyo, JapanSchool of Health Sciences, University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 36, Issue 8, 1 August 1972, Pages 1437–1439, https://doi.org/10.1080/00021369.1972.10860425 Published: 01 August 1972 Article history Received: 13 October 1971 Published: 01 August 1972
Dramatic Effects of Gallium Promotion on Methanol Steam Reforming Cu–ZnO Catalyst for Hydrogen Production: Formation of 5 Å Copper Clusters from Cu–ZnGaO<sub><i>x</i></sub> (2013)

A new class of copper, zinc, and gallium mixed oxides (CuZnGaOx) with different chemical compositions obtained by a coprecipitation technique is identified as a highly active catalyst for the low-temperature, direct steam reforming of methanol to supply hydrogen gas to portable fuel cell devices. Their catalytic activity and selectivity are found to be critically dependent on the copper surface area, catalyst structure, and metal–support interaction, etc. As a result, temperature-programmed reduction has been used to investigate the copper ion reducibility and resulting copper speciation; N2O chemisorption and advanced microscopies to determine specific copper surface area, dispersion, and particle size; XRD to investigate the catalyst structure; EPR spectroscopy to probe the environment of Cu2+ species; and AC impedance spectroscopy to probe the mobility of trapped ions in solids. It is proposed that Ga incorporation into Cu–Zn oxide leads to the formation of a nonstoichiometric cubic spinel phase containing interstitial Cu+ ions, which can produce in situ a high population of extremely small 5 Å copper clusters at high dispersion on a defective ZnGa2O4 surface for effective catalysis.
Expanding the Usability Toolkit: Using PowerPoint™ to Perform Website Analysis and Testing (2012)

Many usability software packages exist to serve the needs of user experience practitioners. However, these options are often expensive and possess steep learning curves. The purpose of this paper is to provide novice practitioners a usability toolkit that is easy to use, versatile, and affordable. Using basic presentation software, PowerPoint™, graduate students in a usability and redesign course performed card sorting tasks with several users and used the results to create website prototypes for usability testing. The detailed methods for deploying these usability techniques via PowerPoint™, as well as the benefits of these methods, will be explored.
Molecular Cloning and Characterization of Porcine Na+/K+-ATPase Isoforms α1, α2, α3 and the ATP1A3 Promoter (2013)

Na⁺/K⁺-ATPase maintains electrochemical gradients of Na⁺ and K⁺ essential for a variety of cellular functions including neuronal activity. The α-subunit of the Na⁺/K⁺-ATPase exists in four different isoforms (α1-α4) encoded by different genes. With a view to future use of pig as an animal model in studies of human diseases caused by Na⁺/K⁺-ATPase mutations, we have determined the porcine coding sequences of the α1-α3 genes, ATP1A1, ATP1A2, and ATP1A3, their chromosomal localization, and expression patterns. Our ATP1A1 sequence accords with the sequences from several species at five positions where the amino acid residue of the previously published porcine ATP1A1 sequence differs. These corrections include replacement of glutamine 841 with arginine. Analysis of the functional consequences of substitution of the arginine revealed its importance for Na⁺ binding, which can be explained by interaction of the arginine with the C-terminus, stabilizing one of the Na⁺ sites. Quantitative real-time PCR expression analyses of porcine ATP1A1, ATP1A2, and ATP1A3 mRNA showed that all three transcripts are expressed in the embryonic brain as early as 60 days of gestation. Expression of α3 is confined to neuronal tissue. Generally, the expression patterns of ATP1A1, ATP1A2, and ATP1A3 transcripts were found similar to their human counterparts, except for lack of α3 expression in porcine heart. These expression patterns were confirmed at the protein level. We also report the sequence of the porcine ATP1A3 promoter, which was found to be closely homologous to its human counterpart. The function and specificity of the porcine ATP1A3 promoter was analyzed in transgenic zebrafish, demonstrating that it is active and drives expression in embryonic brain and spinal cord. The results of the present study provide a sound basis for employing the ATP1A3 promoter in attempts to generate transgenic porcine models of neurological diseases caused by ATP1A3 mutations.
Pathogenesis of osteoarthritis‐like changes in the joints of mice deficient in type IX collagen (2006)

Lack of type IX collagen in Col9a1-/- mice results in age-dependent OA-like changes in the knee joints and TMJs.
Use of Fluid Attenuated Inversion Recovery (FLAIR) Pulse Sequences in MRI of the Brain (1992)

Fluid attenuated inversion recovery pulse sequences with a long echo time (TE) have been used to image the brain in one volunteer and four patients. The long inversion time used with this sequence suppresses the signal from CSF and the long TE produces very heavy T2 weighting. The marked reduction in flow artefact from CSF and the high T2 weighting enabled anatomical detail to be seen within the brain stem and produced high lesion contrast in areas close to CSF. Lesions were demonstrated with greater conspicuity than with conventional T2-weighted sequences in patients with cerebral infarction, low grade astrocytoma, and diplegia.
A Social Cognitive Framework for Career Choice Counseling (1996)

This article extends social cognitive career theory by suggesting how several of its major hypotheses can be applied to counseling persons with career choice difficulties. Several theory‐derived counseling strategies are described that can be used to assist clients in developing a broad array of career options, analyzing and overcoming barriers to career choice, and counteracting choice‐limiting self‐efficacy beliefs. Each strategy is illustrated with a case example. Future research needs related to the counseling model are discussed.
Overview of known non-human primate pathogens with potential to affect colonies used for toxicity testing (2009)

The increased demand for non-human primates (NHPs) in biomedical research has resulted in alternative sources of animals being used, which has allowed for importation of animals with varying background incidences of bacterial, viral, parasitic, and fungal pathogens. This can be of minimal consequence when animals from different sources are kept isolated. However, when NHPs from different sources with varying incidences of primary and opportunistic pathogens are mixed, there can be a rapid spread of these pathogens and an increase in the seroconversion of susceptible animals. If this process occurs during the conduct of a study, interpretation of that study can be confounded. Furthermore, NHPs imported from areas enzootic for pathogens such as Plasmodium or with high incidences of human diseases such as measles and tuberculosis can introduce diseases that can be a threat to colony health, have zoonotic risk, and can severely impact study outcome. Thus, knowledge of the common primary and opportunistic NHP infections, as well as reemerging pathogens, enables the toxicologist to use information on disease status for pre-study animal selection and intelligent study design. This is particularly important when immunomodulatory compounds are being investigated. Moreover, the toxicologic pathologist well versed in the common spontaneous infections, opportunistic pathogens, and background lesions in NHPs is able to assess possible drug-related effects in drug safety studies. This review identifies the common primary and opportunistic pathogens, as well as newly emerging infections of NHPs, that can directly or indirectly affect colony health and the interpretation of drug safety studies.
Interferon-γ Induction of the Human Leukocyte Antigen-E Gene Is Mediated through Binding of a Complex Containing STAT1α to a Distinct Interferon-γ-responsive Element (1996)

Expression of the human major histocompatibility complex (MHC) class I genes has been shown previously to increase at the transcriptional level following exposure to interferon-gamma (IFN-gamma). In this report we have examined the molecular mechanisms involved in the IFN-gamma-induced transcription of the human MHC class I gene, HLA-E. Functional analysis of CAT reporter gene constructs under the control of the HLA-E promoter transfected into U937 cells revealed the presence of a distinct IFN-gamma-responsive element, termed the interferon response region (IRR), that was necessary and sufficient to mediate the response to IFN-gamma. This cis-acting regulatory sequence contains an imperfect inverted repeat; the 5'-half of the IRR resembles the IFN-gamma activation site (GAS), and the 3'-half of the IRR resembles the interferon-stimulated response element (ISRE). Gel mobility shift assays demonstrated that the IRR bound a single, specific, IFN-gamma-induced complex (IRR-AC), which was formed rapidly following treatment with IFN-gamma and was independent of protein synthesis. Competition experiments with GAS and ISRE sequences from other IFN-inducible genes showed that GAS sequences competed for the IRR-AC, whereas ISRE sequences did not compete. Mutational analysis demonstrated that point mutations in either the 5'-half or 3'-half of the IRR prevented binding of the complex and abrogated or markedly reduced the IFN-gamma responsiveness of reporter gene constructs. Supershift analysis revealed that the IRR-AC contains a factor that was recognized by antibodies specific for the protein STAT1alpha (signal transducer and activator of transcription). Taken together, these findings suggest that the mechanism of IFN-gamma-induced transcription of the HLA-E gene is distinct from that of other MHC class I genes.
Observations on the systemic effect of topical clobetasol propionate (Dermovate). (1975)

Topical application of clobetasol propionate in a strength of 0-05% in cream or ointment (Dermovate) suppressed the hypothalamic-pituitary-adrenal axis in both normal people and patients with diseased skin. In normal people the 9 am serum cortisol level was suppressed when between 45 and 90 g was applied weekly. Insulin stress test results in patients with diseased skin showed an abnormally small response after long-term application of similar amounts. We conclude that long-term administration should be restricted to less than 50 g a week.
Design for Variation (2012)

ABSTRACT Statistical engineering is the study of how to best utilize and integrate statistical methods with other engineering disciplines and information technology to solve high-level, complex, multidisciplinary problems. Engineering disciplines apply the principles or “building blocks” of the sciences to design something new or to improve something already in existence, frequently a machine, tool, or structure (Hoerl and Snee 2010b Hoerl , R. W. , Snee , R. D. ( 2010b ). Statistics roundtable: Closing the gap . Quality Progress , 43 ( 5 ): 52 – 53 . [Google Scholar]). Statistical engineering involves the application of the principles of probability and statistics, in conjunction with the work of other engineers and scientists, to quantify and control variability, uncertainty, and risk in order to improve a process, product, or service. The design for variation (DFV) process developed at Pratt & Whitney and described in this article is shown to possess all attributes of a statistical engineering application. Design for variation, a strategic initiative at Pratt & Whitney, represents a large-scale improvement of engineering design and analysis processes in order to quantify and reduce variability, uncertainty, and risk, requiring the efforts of engineers, statisticians, and information technology specialists. This article also presents examples of the DFV process as applied to turbine airfoil cooling, high cycle fatigue, hollow fan blade producibility, and optimization of thermal management systems and overall system performance. The new ‘DFV-enabled’ processes help engineers to actively manage variability, uncertainty, and risk directly via design, materials, and process changes.
Human lysosomal alpha-glucosidase. Characterization of the catalytic site (1991)

The substrate analogue conduritol B epoxide (CBE) is demonstrated to be an active site-directed inhibitor of human lysosomal alpha-glucosidase. A competitive mode of inhibition is obtained with glycogen as natural and 4-methylumbelliferyl-alpha-D-glucopyranoside as artificial substrate. The inactivation of the enzyme is time and concentration dependent and results in the covalent binding of CBE. Catalytic activity is required for binding to occur. CBE-labeled peptides containing the catalytic residue of lysosomal alpha-glucosidase were isolated and identified by microsequencing and amino acid analysis. The peptides appeared to originate from a protein domain which is highly conserved among alpha-amylases, maltase, glucoamylases, and transglucanosylases. Based on the sequence similarity and the mechanism of CBE binding, Asp-518 is predicted to be the essential carboxylate in the active site of lysosomal alpha-glucosidase. The functional importance of Asp-518 and other residues around the catalytic site was studied by expression of in vitro mutagenized alpha-glucosidase cDNA in transiently transfected COS cells. Substitution of Asp-513 by Glu-513 is shown to interfere with the posttranslational modification and the intracellular transport of the alpha-glucosidase precursor. The residues Trp-516 and Asp-518 are demonstrated to be critical for catalytic function.