gebhart/patrepeval huggingface dataset:
Hirudin: amino-terminal residues play a major role in the interaction with thrombin. (1991)

Amino acid substitutions within the amino-terminal 5 residues of the thrombin-specific inhibitor hirudin dramatically alter its ability to inhibit the thrombin-catalyzed hydrolysis of both a chromogenic substrate and fibrinogen. Replacing the highly conserved Tyr-3 residue with Trp or Phe increases hirudin's affinity for thrombin 3-6-fold (decreases the inhibition constant, Ki) whereas Thr results in a 450-fold increase in Ki. A more extensive modification involving deletion of the amino-terminal Val, and Tyr-3----Val, Thr-4----Gln, and Asp-5----Ile replacement, results in a large reduction in thrombin inhibitory activity corresponding to greater than a 10(7)-fold increase in Ki and a 10(3)-fold increase in IC50, using D-Phe-L-pipecolyl-Arg-p-nitroanilide (S-2238) and fibrinogen, respectively, as substrates. Kinetic analysis of these mutant proteins and synthetic peptide fragments and available structural information on thrombin and hirudin derived from protein crystallography and two-dimensional NMR studies indicate that the amino-terminal region of hirudin binds at the apolar binding/active site region of thrombin, with Tyr-3 occupying the S3 specificity site. The large effect of these modifications on hirudin activity suggests that alteration of the amino-terminal segment can destabilize the interaction of other regions of hirudin with thrombin.
Reductive Cleavage of Acetals/Ketals with ZrCl<sub>4</sub>/NaBH<sub>4</sub> (1999)

Abstract Reductive cleavage of acetals/ketals with zirconium tetrachloride-sodium borohydride leading to the formation of ether alcohols is described.
A Qualitative Review on 3D Coarse Registration Methods (2015)

3D registration or matching is a crucial step in 3D model reconstruction. Registration applications span along a variety of research fields, including computational geometry, computer vision, and geometric modeling. This variety of applications produces many diverse approaches to the problem but at the same time yields divergent notations and a lack of standardized algorithms and guidelines to classify existing methods. In this article, we review the state of the art of the 3D rigid registration topic (focused on Coarse Matching) and offer qualitative comparison between the most relevant approaches. Furthermore, we propose a pipeline to classify the existing methods and define a standard formal notation, offering a global point of view of the literature. Our discussion, based on the results presented in the analyzed papers, shows how, although certain aspects of the registration process still need to be tested further in real application situations, the registration pipeline as a whole has progressed steadily. As a result of this progress in all registration aspects, it is now possible to put together algorithms that are able to tackle new and challenging problems with unprecedented data sizes and meeting strict precision criteria.
Tricyclic trisaminomethanes (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTricyclic trisaminomethanesThomas J. AtkinsCite this: J. Am. Chem. Soc. 1980, 102, 20, 6364–6365Publication Date (Print):September 1, 1980Publication History Published online1 May 2002Published inissue 1 September 1980https://pubs.acs.org/doi/10.1021/ja00540a044https://doi.org/10.1021/ja00540a044research-articleACS PublicationsRequest reuse permissionsArticle Views1210Altmetric-Citations99LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A study of noise in charge-coupled devices (1975)

The report describes the results of a twelve-month program that was heavily weighted toward quantitative experimental characterization designed to establish the appropriate analytic models for the various spatial and temporal noise sources in CCDs that can be used to accurately predict the limiting performance of CCD functions. Low noise input and output techniques were refined to the point that bulk trapping was observed in a four-phase, 150-stage buried channel divice. Surface state trapping levels ranging from 800 to 2000 electrons were observed, in good agreement with the theoretical levels predicted using (N sub ss) values obtained for double-pulse experiments. Other noise sources treated included fixed-pattern or spatial noise, dark current, partition noise, and burst noise.
On the determination of functions from their integral values along certain manifolds (1986)

When one integrates a function of two variables x,y - a point function f(P) in the plane - subject to suitable regularity conditions along an arbitrary straight line g then one obtains in the integral values F(g), a line function. In Part A of the present paper the problem which is solved is the inversion of this linear functional transformation, that is the following questions are answered: can every line function satisfying suitable regularity conditions be regarded as constructed in this way? If so, is f uniquely known from F and how can f be calculated? In Part B a solution of the dual problem of calculating a line function F(g) from its point mean values f(P) is solved in a certain sense. Finally, in Part C certain generalizations are discussed, prompted by consideration of non-Euclidean manifolds as well as higher dimensional spaces. The treatment of these problems, themselves of interest, gains enhanced importance through the numerous relationships that exist between this topic and the theory of logarithmic and Newtonian potentials. These are mentioned at appropriate places in the text.
Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci (2018)

In C. elegans, efficient RNA silencing requires small RNA amplification mediated by RNA-dependent RNA polymerases (RdRPs). RRF-1, an RdRP, and other Mutator complex proteins localize to Mutator foci, which are perinuclear germline foci that associate with nuclear pores and P granules to facilitate small RNA amplification. The Mutator complex protein MUT-16 is critical for Mutator foci assembly. By analyzing small deletions of MUT-16, we identify specific regions of the protein that recruit other Mutator complex components and demonstrate that it acts as a scaffolding protein. We further determine that the C-terminal region of MUT-16, a portion of which contains predicted intrinsic disorder, is necessary and sufficient to promote Mutator foci formation. Finally, we establish that MUT-16 foci have many properties consistent with a phase-separated condensate and propose that Mutator foci form through liquid-liquid phase separation of MUT-16. P granules, which contain additional RNA silencing proteins, have previously been shown to have liquid-like properties. Thus, RNA silencing in C. elegans germ cells may rely on multiple phase-separated compartments through which sorting, processing, and silencing of mRNAs occurs.
Magnetorheological Fluid Based Torque Transmission Clutches (1999)

Applications of magnetorheological (MR) fluids in torque transmission clutches are investigated in this study. Quick time response and variable rheological properties of MR fluids in response to an applied magnetic field are utilized in generating the variable torque transmission. Magnitude of the transmitted torque is adjusted by the level of the magnetic field applied over the MR fluid in the clutch mechanism. In this experimental study, the MR torque transmission clutch configuration considered was based on a concentric cylinder geometry. The MR clutch was fabricated and tested during the study. An experimental set-up was prepared based on a power motor, magnetic field generation system, and the MR clutch mechanism. Coiled wires in a solenoid configuration were used to generate the magnetic field. The wires were coiled over the clutch housing and electric current was sent to the wires. The electric current level determined the magnitude of the applied magnetic field. The clutch cylinders were sealed and the space in between the cylinders was filled with the MR fluid. By driving the clutch with the power motor, and applying varying magnetic field levels, variations in the transmitted torque was obtained. Continuous measurements were made between the input and output power and the transmitted torque for different magnetic field levels and different motor speeds. The torque transmission capabilities of MR clutch configurations were evaluated from the study. MR clutch mechanisms can potentially be used in underwater robotic systems where controlled continuous torque transmission is desirable.
The Future of Work and Leisure. By Stanley Parker (1972)

(1972). The Future of Work and Leisure. By Stanley Parker. Journal of Leisure Research: Vol. 4, No. 3, pp. 222-223.
Laser Gas Nitriding of Ti-6AI-4V Alloy (1997)

Abstract Laser gas nitriding of Ti-6A1-4V has been investigated with both CO2 and Nd:YAG lasers. Results indicate that Nd:YAG laser in pulse mode provides a better surface finish and a lower cracking severity than CO2 laser. A crack-free nitrided layer has been obtained by optimizing the processing parameters. Titanium nitride (TiN) significantly increases the hardness of the nitrided surfaces. The amount of titanium nitride produced depends on the processing parameters, such as laser pulse energy and nitrogen concentration. With optimized parameters, the nitrided surface is somewhat rougher than the polished base metal but much smoother than the shot peened surface. The shrinkage effect in the laser melt zone produces surface residual tensile stresses regardless of the processing environment. Preheating or stress relieving after laser nitriding can significantly reduce the residual tensile stress level.
Electrocoagulation applications for industrial wastewaters: a critical review (2012)

Cost-effective methods are required to treat a wide range of wastewater pollutants in a diverse range of conditions. As compared with traditional treatment methods, electrocoagulation provides a relatively compact and robust treatment alternative in which sacrificial metal anodes initiate electrochemical reactions that provide active metal cations for coagulation and flocculation. The inherent advantage of electrocoagulation is that no coagulants have to be added to the wastewater and hence the salinity of the water does not increase after treatment. Electrocoagulation is a complex process involving a multitude of pollutant removal mechanisms operating synergistically. Although numerous publications have appeared in the recent past, the lack of a holistic and systematic approach has resulted in the design of several treatment units without considering the complexity of the system and process control mechanisms. Due to the fact that electrocoagulation is thought to be an enigmatic, promising treatment tech...
Boundless memory allocations for memory safety and high availability (2011)

Spatial memory errors (like buffer overflows) are still a major threat for applications written in C. Most recent work focuses on memory safety - when a memory error is detected at runtime, the application is aborted. Our goal is not only to increase the memory safety of applications but also to increase the application's availability. Therefore, we need to tolerate spatial memory errors at runtime. We have implemented a compiler extension, Boundless, that automatically adds the tolerance feature to C applications at compile time. We show that this can increase the availability of applications. Our measurements also indicate that Boundless has a lower performance overhead than SoftBound, a state-of-the-art approach to detect spatial memory errors. Our performance gains result from a novel way to represent pointers. Nevertheless, Boundless is compatible with existing C code. Additionally, Boundless provides a trade-off to reduce the runtime overhead even further: We introduce vulnerability specific patching for spatial memory errors to tolerate only known vulnerabilities. Vulnerability specific patching has an even lower runtime overhead than full tolerance.
Reduced Nitric Oxide Production and Altered Myocardial Metabolism During the Decompensation of Pacing-Induced Heart Failure in the Conscious Dog (1998)

Abstract —The aim of the present study was to determine whether cardiac nitric oxide (NO) production changes during the progression of pacing-induced heart failure and whether this occurs in association with alterations in myocardial metabolism. Dogs (n=8) were instrumented and the heart paced until left ventricular end-diastolic pressure reached 25 mm Hg and clinical signs of severe failure were evident. Every week, hemodynamic measurements were recorded and blood samples were withdrawn from the aorta and the coronary sinus for measurement of NO metabolites, O 2 content, free fatty acids (FFAs), and lactate and glucose concentrations. Cardiac production of NO metabolites or consumption of O 2 or utilization of substrates was calculated as coronary sinus-arterial difference times coronary flow. In end-stage failure, occurring at 29±1.6 days, left ventricular end-diastolic pressure was 25±1 mm Hg, left ventricular systolic pressure was 92±3 mm Hg, mean arterial pressure was 75±2.5 mm Hg, and dP/dt max was 1219±73 mm Hg/s (all P <0.05). These changes in hemodynamics were associated with a fall of cardiac NO metabolite production from 0.37±0.16 to −0.28±0.13 nmol/beat ( P <0.05). O 2 consumption and lactate uptake did not change significantly from control, while FFA uptake decreased from 0.16±0.03 to 0.05±0.01 μEq/beat and glucose uptake increased from −2.3±7.0 to 41±10 μg/beat ( P <0.05). The cardiac respiratory quotient also increased significantly by 28%. In 14 normal dogs the same measurements were performed at control and 1 hour after we injected 30 mg/kg of nitro- l -arginine, a competitive inhibitor of NO synthase. O 2 consumption increased from 0.05±0.002 mL/beat at control to 0.071±0.003 mL/beat after nitro- l -arginine, while FFA uptake decreased from 0.1±0.01 to 0.06±0.01 μEq/beat, lactate uptake increased from 0.15±0.04 to 0.31±0.03 μmol/beat, glucose uptake increased from 8.2±5.0 to 35.4±9.5 μg/beat, and RQ increased by 23% (all P <0.05). Our results indicate that basal cardiac production of NO falls below normal levels during cardiac decompensation and that there are shifts in substrate utilization. This switch in myocardial substrate utilization also occurs after acute pharmacological blockade of NO production in normal dogs.
Two Distinct Sets of NS2A Molecules Are Responsible for Dengue Virus RNA Synthesis and Virion Assembly (2014)

Dengue virus (DENV) represents the most prevalent mosquito-borne human pathogen. Understanding the replication of DENV is essential for development of vaccines and therapeutics. Here we characterized the function of DENV-2 NS2A using a systematic mutagenesis approach. The mutagenesis results revealed two distinct sets of NS2A mutations: one set of mutations that result in defects in viral RNA synthesis and another set of mutations that result in defects in virion assembly. trans-Complementation analysis showed that mutants defective in viral RNA synthesis could not be rescued by wild-type NS2A; in contrast, mutants defective in virion assembly could be successfully rescued by wild-type NS2A or even by a mutant NS2A that is incompetent to support viral RNA synthesis. These results support a model in which two distinct sets of NS2A molecules are responsible for DENV RNA synthesis (located in the viral replication complex) and virion assembly (located in the virion assembly/budding site). The study confirms and extends our understanding of the two critical roles of flavivirus NS2A in viral RNA synthesis and virion assembly.
Biofertilizing Efficiency of Brown and Green Algae on Growth, Biochemical and Yield Parameters of Cyamopsis tetragonolaba (L.) Taub. (2010)

The effect of liquid extracts of marine algae Sargassum wightii and Ulva lactuca when applied as soil drench to cluster bean plant increased the growth, biochemical and yield of the plant. Liquid extracts of Sargassum wightii (1.5%) and Ulva lactuca (1.0%) was found to have maximum influence on growth parameters viz., shoot length, root length, total fresh and dry weight, leaf area and moisture content. Further, there was a significant increase in biochemical parameters such as photosynthetic pigments, protein content, amino acids, reducing sugar, ascorbic acid, nitrate reductase activity. Similarly, enhancement in yield parameters such as number of pods per plant, pod weight, pod length and number of seeds per pod were also observed. Higher concentrations of both algal extracts were found to show inhibitive effect on all above parameters studied.
Stereoselective Total Synthesis of (±)-Peribysin E (2011)

Radical cyclization of iodoketone 3 afforded cis-hydrindanone 8. Compound 8 was converted into key intermediate 5 via conventional transformations. Annulation of a spiro-lactal unit to 5 was pursued with three different approaches. In the first approach, radical cyclization of propargyl ester 17 provided spiro-lactone 18 with an undesired stereochemistry. Attempts to invert the stereochemistry at the spiro-center via retro-aldol and aldol condensation of compound 20 failed. In the second approach, key intermediate 5 was transformed into 23. Acylation of compound 23 gave 24 as a single diastereomer with the desired stereochemistry but in low yield. NBS bromination of 24 followed by lactone formation gave 26 in low yield. Alternatively, allylic oxidation of 24 with SeO(2) followed by lactonization gave 26 also in low yield. Finally, a third approach employing a semipinacol-type rearrangement of epoxy-alcohol 33 gave aldehyde 34 with the desired stereochemistry. Treatment of compound 34 with HCl in MeOH effected spiro-lactal formation and provided (±)-peribysin E. The overall yield of our synthesis is 3.2% from 2-methylcyclohenen-1-one.
Segmentation of the body and lungs from Compton scatter and photopeak window data in SPECT: a Monte-Carlo investigation (1996)

In SPECT imaging of the chest, nonuniform attenuation correction requires use of a patient specific attenuation (mu) map. Such a map can be obtained by estimating the regions of (1) the lungs and (2) the soft tissues and bones, and then assigning an appropriate value of attenuation coefficient (mu) to each region. The authors proposed a method to segment such regions from the Compton scatter and photopeak window SPECT slices of Tc-99m Sestamibi studies. The Compton scatter slices are used to segment the body outline and to estimate the regions of the lungs. Locations of the back bone and sternum are estimated from the photopeak window slices to assist in the segmentation. To investigate the accuracy of using Compton scatter slices in estimating the regions of the body and the lungs, a Monte-Carlo SPECT simulation of an anthropomorphic phantom with an activity distribution and noise characteristics similar to patient data was conducted. Energy windows of various widths were simulated for use in locating a suitable Compton scatter window for imaging, The effects of attenuation correction using a mu map based on segmentation were also studied. The results demonstrated for the activity and mu maps studied herein that: (1) reasonable contrast could be obtained from Compton scatter data for the segmentation of the lung regions, (2) true positive rates of 99% and 89% for determining the body and lung regions, respectively, with total error rates of 4% and 29%, could be achieved, (3) usage of a mu map based on segmentation for attenuation correction improved relative quantification over filtered backprojection, (4) variations in the assigned mu value of 40% smaller or 40% larger in the lung regions had an insignificant impact on the results of relative quantification, (5) a wide energy window away from the photopeak window for recording scattered events could benefit both the segmentation of the lung regions and the attenuation correction of the activity in the myocardium region, and (6) usage of a smaller than true mu value in the lung regions of an assigned mu map might benefit attenuation correction for absolute quantification.
Pterostilbene-Isothiocyanate Conjugate Suppresses Growth of Prostate Cancer Cells Irrespective of Androgen Receptor Status (2014)

Chemotherapy and anti-hormonal therapies are the most common treatments for non-organ-confined prostate cancer (PCa). However, the effectiveness of these therapies is limited, thus necessitating the development of alternative approaches. The present study focused on analyzing the role of pterostilbene (PTER)-isothiocyanate (ITC) conjugate--a novel class of hybrid compound synthesized by appending an ITC moiety on PTER backbone--in regulating the functions of androgen receptor (AR), thereby causing apoptosis of PCa cells. The conjugate molecule caused 50% growth inhibition (IC50) at 40 ± 1.12 and 45 ± 1.50 μM in AR positive (LNCaP) and negative (PC-3) cells, respectively. The reduced proliferation of PC-3 as well as LNCaP cells by conjugate correlated with accumulation of cells in G2/M phase and induction of caspase dependent apoptosis. Both PI3K/Akt and MAPK/ERK pathways played an important and differential role in conjugate-induced apoptosis of these PCa cells. While the inhibitor of Akt (A6730) or Akt-specific small interference RNA (siRNA) greatly sensitized PC-3 cells to conjugate-induced apoptosis, on the contrary, apoptosis was accelerated by inhibition of ERK (by PD98059 or ERK siRNA) in case of LNCaP cells, both ultimately culminating in the expression of cleaved caspase-3 protein. Moreover, anti-androgenic activity of the conjugate was mediated by decreased expression of AR and its co-activators (SRC-1, GRIP-1), thus interfering in their interactions with AR. All these data suggests that conjugate-induced inhibition of cell proliferation and induction of apoptosis are partly mediated by the down regulation of AR, Akt, and ERK signaling. These observations provide a rationale for devising novel therapeutic approaches for treating PCa by using conjugate alone or in combination with other therapeutics.