gebhart/patrepeval huggingface dataset:
[Synthesis of N alpha-(4-methylbenzoyl)-4-amidinophenyl-alaninamides and -esters]. (1983)

To test their inhibitory activity against serine proteinases, especially thrombin, in comparison to the very potent N alpha-tosyl-4-amidinophenylalaninamides, the authors synthetized the compounds named in the title, which contain the p-toluoyl residue in place of the tosyl residue. These compounds were prepared from 4-cyanophenyl-alanine (1) by N-acylation to 2 and formation of the active ester 3 which was aminolyzed. The amides thus obtained were converted, via the thioamides and the thioimidic acid ester salts, to the amidine hydroiodides 16-19. The methyl ester 21 was afforded from 2 by means of the Pinner reaction.
Mass Spectrometric Approaches Using Electrospray Ionization Charge States and Hydrogen-Deuterium Exchange for Determining Protein Structures and Their Conformational Changes (2003)

Electrospray ionization (ESI) mass spectrometry (MS) is a powerful analytical tool for elucidating structural details of proteins in solution especially when coupled with amide hydrogen/deuterium (H/D) exchange analysis. ESI charge-state distributions and the envelopes of charges they form from proteins can provide an abundance of information on solution conformations that is not readily available through other biophysical techniques such as near ultraviolet circular dichroism (CD) and tryptophan fluorescence. The most compelling reason for the use of ESI-MS over nuclear magnetic resonance (NMR) for measuring H/D after exchange is that larger proteins and lesser amounts of samples can be studied. In addition, MS can provide structural details on transient or folding intermediates that may not be accessible by CD, fluorescence, and NMR because these techniques measure the average properties of large populations of proteins in solution. Correlations between measured H/D and calculated parameters that are often available from crystallographic data can be used to extend the range of structural details obtained on proteins. Molecular dynamics and energy minimization by simulation techniques such as assisted model building with energy refinement (AMBER) force field can be very useful in providing structural models of proteins that rationalize the experimental H/D exchange results. Charge-state envelopes and H/D exchange information from ESI-MS data used complementarily with NMR and CD data provides the most powerful approach available to understanding the structures and dynamics of proteins in solution.
Simulating cyber-attacks for fun and profit (2009)

We introduce a new simulation platform called Insight, created to design and simulate cyber-attacks against large arbitrary target scenarios. Insight has surprisingly low hardware and configuration requirements, while making the simulation a realistic experience from the attacker's standpoint. The s
Three-Dimensional Ovarian Organ Culture as a Tool to Study Normal Ovarian Surface Epithelial Wound Repair (2009)

Ovarian cancers are primarily derived from a single layer of epithelial cells surrounding the ovary, the ovarian surface epithelium (OSE). Ovarian surface proliferation is associated with ovulation and has been suggested to play a role in ovarian surface transformation and cancer progression. Aspects of ovarian surface repair after ovulation include proliferation, migration, and surface regeneration. To study ovarian surface repair, an organ culture system was developed that supports the proliferation, encapsulation, and repair of an artificially wounded surface. Wounded mouse ovaries embedded into an alginate hydrogel matrix have normal OSE cells as demonstrated by expression of cytokeratin 8, vimentin, N-cadherin, and a lack of E-cadherin. Normal OSE cells began proliferating and migrating around wounded surfaces after 1 d of culture. Organ cultures were propagated in medium supplemented with BSA and fetal bovine serum to determine optimal growth conditions. BSA cultured organs had OSE that proliferated significantly more than controls until d 4, whereas fetal bovine serum cultured organs had significantly more surface area encapsulated by OSE. Overall, a three-dimensional ovarian organ culture supports the growth of normal OSE in response to artificial wounding and provides a novel system for investigating wound repair as it relates to the possible role of ovulation and ovarian cancer.
Monocarboxylate Transporter 4 Is a Therapeutic Target in Non-small Cell Lung Cancer with Aerobic Glycolysis Preference (2020)

Targeting metabolic reprogramming is an emerging strategy in cancer therapy. However, clinical attempts to target metabolic reprogramming have been proved to be challenging, with metabolic heterogeneity of cancer being one of many reasons that causes treatment failure. Here, we stratified non-small cell lung cancer (NSCLC) cells, mainly lung adenocarcinoma, based on their metabolic phenotypes and demonstrated that the aerobic glycolysis-preference NSCLC cell subtype was resistant to the OXPHOS-targeting inhibitors. We identified that monocarboxylate transporter 4 (MCT4), a lactate transporter, was highly expressed in the aerobic glycolysis-preference subtype with function supporting the proliferation of these cells. Glucose could induce the expression of MCT4 in these cells through a ΔNp63α and Sp1-dependent pathway. Next, we showed that knockdown of MCT4 increased intracellular lactate concentration and induced a reactive oxygen species (ROS)-dependent cellular apoptosis in the aerobic glycolysis-preference NSCLC cell subtype. By scanning a panel of monoclonal antibodies with MCT4 neutralizing activity, we further identified a MCT4 immunoglobulin M (IgM) monoclonal antibody showing capable anti-proliferation efficacy on the aerobic glycolysis-preference NSCLC cell subtype. Our findings indicate that the metabolic heterogeneity is a critical factor for NSCLC therapy and manipulating the expression or function of MCT4 can be an effective strategy in targeting the aerobic glycolysis-preference NSCLC cell subtype.
Classification of the state-of-the-art dynamic web services composition techniques (2006)

Dynamic web service composition can serve applications or users on an on-demand basis. With dynamic composition, the application's capabilities can be extended at runtime so that theoretically an unlimited number of new services can be created from a limited set of service components, thus making applications no longer restricted to the original set of operations specified and envisioned at design and/or compile time. Moreover, dynamic composition is the only means to adapt the behaviour of running components in highly available applications such as, banking and telecommunication systems where services cannot be brought offline to upgrade or remove obsolete services. In this paper, we present a novel classification of the current state-of-the-art dynamic web services composition techniques with attention to the capabilities and limitations of the underlying approaches. The proposed taxonomy of these techniques is derived based on a comprehensive survey of what has been done so far in dynamic web service composition. Finally, we summarise our findings and present a vision for future research work in this area.
Stress‐induced borehole elongation: A comparison between the four‐arm dipmeter and the borehole televiewer in the Auburn Geothermal Well (1985)

The nature and origin of borehole elongation recorded by the four‐arm dipmeter calipers is studied utilizing information obtained from hydraulic fracturing stress measurements and borehole televiewer data taken in a well located in Auburn, New York. A preferred orientation N10°W‐S10°E, ±10° and a less prominant E‐W orientation of borehole elongation, was observed on two runs of the dipmeter. Comparisons of borehole geometry determined using the televiewer and the dipmeter show that both tools give the same orientation of borehole elongtion provided that the zone of elongation is longer than 30 cm. Comparisons of dipmeter caliper data with orientation of in situ stress and natural fractures, obtained from hydrofracturing tests and televiewer data show that the N10°W‐S10°E borehole elongations (1) are axisymmetric, (2) are aligned with the minimum horizontal stress S h , and (3) are not associated with natural fractures intersecting the well. These elongations are interpreted as stress‐induced well bore breakouts. The E‐W elongation direction is characterized by an asymmetric borehole cross section in thinly bedded rocks and is not caused by breakouts. This asymmetric geometry can be discriminated from breakouts using the oriented electric measurements provided by the dipmeter. This study demonstrates that the dipmeter can be used to determine the orientation of S h (by mapping breakouts), confirming the results of earlier less detailed studies, and provides a firm basis for mapping regional stress patterns using existing dipmeter data.
Analysis and evolution of journaling file systems (2005)

We develop and apply two new methods for analyzing file system behavior and evaluating file system changes. First, semantic block-level analysis (SBA) combines knowledge of on-disk data structures with a trace of disk traffic to infer file system behavior; in contrast to standard benchmarking approaches, SBA enables users to understand why the file system behaves as it does. Second, semantic trace playback (STP) enables traces of disk traffic to be easily modified to represent changes in the file system implementation; in contrast to directly modifying the file system, STP enables users to rapidly gauge the benefits of new policies. We use SBA to analyze Linux ext3, ReiserFS, JFS, and Windows NTFS; in the process, we uncover many strengths and weaknesses of these journaling file systems. We also apply STP to evaluate several modifications to ext3, demonstrating the benefits of various optimizations without incurring the costs of a real implementation.
Polymer-Initiated Photogeneration of Silver Nanoparticles in SPEEK/PVA Films:  Direct Metal Photopatterning (2003)

Cross-linking of sulfonated poly(ether-ether)ketone-poly(vinyl alcohol) (SPEEK-PVA) materials yields flexible polymer films, possessing high light-sensitivity and ion-exchange capabilities. Adsorbed Ag+ ions are photoreduced in the film under illumination (lambda = 350 nm), leading to metal nanoparticle formation in places where the film has been exposed to the light. Nanoparticles form via reduction of Ag+ by the polymeric alcohol radicals, generated in the system as a result of photochemical H-abstraction from PVA molecules by the excited carbonyl triplet state of SPEEK. Use of the films for direct metal photopatterning is demonstrated.
Band-Target Entropy Minimization. A Robust Algorithm for Pure Component Spectral Recovery. Application to Complex Randomized Mixtures of Six Components (2003)

A newly developed self-modeling curve resolution method, band-target entropy minimization (BTEM), is described. This method starts with the data decomposition of a set of spectroscopic mixture data using singular value decomposition. It is followed by the transformation of the orthonormal basis vectors/loading vectors into individual pure component spectra one at a time. The transformation is based in part on some seminal ideas borrowed from information entropy theory with the desire to maximize the simplicity of the recovered pure component spectrum. Thus, the proper estimate is obtained via minimization of the proposed information entropy function or via minimization of derivative and area of the spectral estimate. Nonnegativity constraints are also imposed on the recovered pure component spectral estimate and its corresponding concentrations. As its name suggests, in this method, one targets a spectral feature readily observed in loading vectors to retain, and then combinations of the loading vectors are searched to achieve the global minimum value of an appropriate objective function. The major advantage of this method is its one spectrum at a time approach and its capability of recovering minor components having low spectroscopic signals. To illustrate the application of BTEM, spectral resolution was performed on FT-IR measurements of very highly overlapping mixture spectra containing six organic species with a two-component background interference (air). BTEM estimates were also compared with the estimates obtained using other self-modeling curve resolution techniques, i.e., SIMPLISMA, IPCA, OPA-ALS, and SIMPLISMA-ALS.
Application of Fourier Transform Infrared Spectroscopy and Chemometrics for Differentiation of <i>Salmonella enterica</i> Serovar Enteritidis Phage Types (2010)

Fourier transform infrared (FT-IR) spectroscopy and chemometric techniques were used to discriminate five closely related Salmonella enterica serotype Enteritidis phage types, phage type 1 (PT1), PT1b, PT4b, PT6, and PT6a. Intact cells and outer membrane protein (OMP) extracts from bacterial cell membranes were subjected to FT-IR analysis in transmittance mode. Spectra were collected over a wavenumber range from 4,000 to 600 cm(-1). Partial least-squares discriminant analysis (PLS-DA) was used to develop calibration models based on preprocessed FT-IR spectra. The analysis based on OMP extracts provided greater separation between the Salmonella Enteritidis PT1-PT1b, PT4b, and PT6-PT6a groups than the intact cell analysis. When these three phage type groups were considered, the method based on OMP extract FT-IR spectra was 100% accurate. Moreover, complementary local models that considered only the PT1-PT1b and PT6-PT6a groups were developed, and the level of discrimination increased. PT1 and PT1b isolates were differentiated successfully with the local model using the entire OMP extract spectrum (98.3% correct predictions), whereas the accuracy of discrimination between PT6 and PT6a isolates was 86.0%. Isolates belonging to different phage types (PT19, PT20, and PT21) were used with the model to test its robustness. For the first time it was demonstrated that FT-IR analysis of OMP extracts can be used for construction of robust models that allow fast and accurate discrimination of different Salmonella Enteritidis phage types.
Percolation View of Novolak Dissolution. 5. The Dissolution of Exposed Resist Films (1996)

Dissolution inhibition produced by diazonaphthoquinones in novolak and in other phenolic resins is based on the formation of phenolic clusters. The principal result of the exposure of novolak−diazoquinone resist films to light is the dispersal of these clusters. It occurs through the thermal effect of the Wolff rearrangement that follows the photolysis of diazonaphthoquinone. Indenecarboxylic acid, which is the final product of irradiation, is converted to indenecarboxylate ion in the penetration zone of the dissolving films, where it adds to the concentration of hydrophilic percolation sites. This causes the dissolution rate of exposed resist films to be accelerated above that of pure novolak.
Two-Dimensional Nanoparticle Arrays Show the Organizational Power of Robust DNA Motifs (2006)

The bottom-up spatial organization of potential nanoelectronic components is a key intermediate step in the development of molecular electronics. We describe robust three-space-spanning DNA motifs that are used to organize nanoparticles in two dimensions. One strand of the motif ends in a gold nanoparticle; only one DNA strand is attached to the particle. By using two of the directions of the motif to produce a two-dimensional crystalline array, one direction is free to bind gold nanoparticles. Identical motifs, tailed in different sticky ends, enable the two-dimensional periodic ordering of 5 and 10 nm diameter gold nanoparticles.
Mathematical frontiers in optical solitons (2001)

Solitons are localized concentrations of field energy, resulting from a balance of dispersive and nonlinear effects. They are ubiquitous in the natural sciences. In recent years optical solitons have arisen in new and exciting contexts that differ in many ways from the original context of coherent propagation in a uniform medium. We review recent developments in incoherent spatial solitons and in gap solitons in periodic structures.
The generation of correlated Rayleigh random variates by inverse discrete Fourier transform (2000)

A number of different algorithms are used for the generation of correlated Rayleigh random variates. This paper presents an analysis of the statistical properties of methods based on the inverse discrete Fourier transform (IDFT). A modification of the algorithm of Smith (1975) is presented, the new method requiring exactly one-half the number of IDPT operations and roughly two-thirds the computer memory of the original method. Evaluations of and comparisons between various variate generation methods using meaningful quantitative measures are believed to be lacking. New quantitative quality measures for random variate generation have been proposed that are, in particular, meaningful and useful for digital communication system simulation. This paper presents the application of these measures to the IDFT method and three other methods of correlated variate generation, comparing the algorithms in terms of the quality of the generated samples and the required computational effort.
Prediction of Ballistic Missile Trajectories (1968)

Abstract : A critical problem in a missile defense system is that of predicting the trajectory and impact point for a ballistic reentry vehicle. This memorandum will describe methods of prediction as well as numerical results for several representative examples. There are several reports describing the estimation of the states of a ballistic missile; the ballistic trajectory and impact point will be predicted by using these estimated values.
Regulation of the Cerebral Circulation: Role of Endothelium and Potassium Channels (1998)

Several new concepts have emerged in relation to mechanisms that contribute to regulation of the cerebral circulation. This review focuses on some physiological mechanisms of cerebral vasodilatation and alteration of these mechanisms by disease states. One mechanism involves release of vasoactive factors by the endothelium that affect underlying vascular muscle. These factors include endothelium-derived relaxing factor (nitric oxide), prostacyclin, and endothelium-derived hyperpolarizing factor(s). The normal vasodilator influence of endothelium is impaired by some disease states. Under pathophysiological conditions, endothelium may produce potent contracting factors such as endothelin. Another major mechanism of regulation of cerebral vascular tone relates to potassium channels. Activation of potassium channels appears to mediate relaxation of cerebral vessels to diverse stimuli including receptor-mediated agonists, intracellular second messenger, and hypoxia. Endothelial- and potassium channel-based mechanisms are related because several endothelium-derived factors produce relaxation by activation of potassium channels. The influence of potassium channels may be altered by disease states including chronic hypertension, subarachnoid hemorrhage, and diabetes.
Space-Time Modelling of the Spread of Salmon Lice between and within Norwegian Marine Salmon Farms (2013)

Parasitic salmon lice are potentially harmful to salmonid hosts and farm produced lice pose a threat to wild salmonids. To control salmon lice infections in Norwegian salmonid farming, numbers of lice are regularly counted and lice abundance is reported from all salmonid farms every month. We have developed a stochastic space-time model where monthly lice abundance is modelled simultaneously for all farms. The set of farms is regarded as a network where the degree of contact between farms depends on their seaway distance. The expected lice abundance at each farm is modelled as a function of i) lice abundance in previous months at the same farm, ii) at neighbourhood farms, and iii) other, unspecified sources. In addition, the model includes explanatory variables such as seawater temperature and farm-numbers of fish. The model gives insight into factors that affect salmon lice abundance and contributing sources of infection. New findings in this study were that 66% of the expected salmon lice abundance was attributed to infection within farms, 28% was attributed to infection from neighbourhood farms and 6% to non-specified sources of infection. Furthermore, we present the relative risk of infection between neighbourhood farms as a function of seaway distance, which can be viewed as a between farm transmission kernel for salmon lice. The present modelling framework lays the foundation for development of future scenario simulation tools for examining the spread and abundance of salmon lice on farmed salmonids under different control regimes.
Effect of Trifunctional Monomers and Antioxidants on the Crosslinking Reaction of Polyethylene (1982)

The crosslinking reaction and oxidative stability of low-density polyethylene were studied in the presence of trifunctional monomers and antioxidants with electron beam. The trifunctional monomers used in this study are Trimethylolpropane triacrylate(TMPTA), Trimethylolpropane trimethacrylate(TMPTM) and Triallyl cyanurate(TAC). And the antioxidants are Irganox 1010 (Pentaerythritoltetrakis[3-(3,5-di-t-butyl-4-hydroxyphenyl)-propionatel]), Santo-nox R(4,4'-Thio-bis(3-methyl-6-t-butylphenol)), Nocrac D(N-phenyl--naphthylamine) and Bis-phenol A(4,4'-Isopropylidene bisphenol). Among the monomers, TMPTA is the best crosslinking agent and prvides polyethylene with oxidative stability. Among the antioxidants, Nocrac D is the best antioxidant for polyethylene.
α<sub>1</sub>‐Antitrypsin can increase insulin‐induced mitogenesis in various fibroblast and epithelial cell lines (2000)

alpha(1)-Antitrypsin (AT), the archetypal member of the superfamily of serine proteinase inhibitors, inhibits leukocyte elastase activity and thereby can prevent lung damage. Here we show that in fibroblasts from human fetal lung and mouse embryo as well as in certain epithelial cells AT can also enhance the stimulatory effects of insulin on DNA synthesis and cell proliferation. Warming of AT at a moderate (41 degrees C) temperature for a longer time (21 h) or at a higher (65 degrees C) temperature for 30 min before treatment increased its stimulatory effects on both DNA synthesis and activating phosphorylation of p42/p44 mitogen-activated protein kinases. The results suggest that AT may promote regeneration of damaged tissues under pathophysiological conditions which are associated with fever.
Ice Crystal Size Changes During Ripening in Freeze Concentration (1985)

Crystal sizes were measured photographically versus elapsed time for non-uniform ice crystal populations mixed at equilibrium temperatures with sugar solutions. The mass of ice did not change, but crystals smaller than a "neutral diameter," D(n), tended to melt because of their excess surface energy. This subcooled the solution with respect to larger crystals, which consequently grew. This process, "ripening," which slowly increases mean crystal sizes and D(n) is used to produce ice crystals large enough to be cleanly separated from freeze concentrated solutions. "Sequential analysis" was used to determine D(n) and follow changes in the diameters, D(i), of fractions of the ice crystal populations. Rates of change in D(i) for both growth and melting were roughly proportional to (I/D(n) - 1/D(i). Overall mass-transfer coefficients were not markedly different for growth and melting, and decreased from roughly 2 mm/s to roughly 0.5 mm/s as sugar concentration increased 10% to 42%. In 10% sucrose solutions, mass-transfer coefficients decreased from roughly 2 mm/s to roughly 1 mm/s when gelatin was added at levels which increased from 0% to 0.5%. Ripening in freeze concentrated liquid foods apparently can be accelerated by manipulating initial crystal size distributions and temporarily removing high molecular weight components.