gebhart/patrepeval huggingface dataset:
Use of Artificial Neural Networks in a QSAR Study of Anti-HIV Activity for a Large Group of HEPT Derivatives (1999)

Anti-HIV activity for a set of 107 inhibitors of the HIV-1 reverse transcriptase, derivatives of 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT), was modeled with the aid of chemometric techniques. The activity of these compounds was estimated by means of multiple linear regression (MLR) and artificial neural network (ANN) techniques and compared with the previous works. The results obtained using the MLR method indicate that the anti-HIV activity of the HEPT derivatives depends on the reverse of standard shadow area on the YZ plane and the ratio of the partial charges of the most positive atom to the most negative atom of the molecule. The best computational neural network model was a fully-connected, feed-forward method with a 6-6-1 architecture. The mean-square error for the prediction set using this network was 0.372 compared with 0.780 obtained using the MLR technique. Comparison of the quality of the ANN of this work with different MLR models shows that ANN has a better predictive power.
Life Prediction for Turbopropulsion Systems Under Dwell Fatigue Conditions (2012)

The objective of this investigation was to develop an innovative methodology for life and reliability prediction of hot-section components in advanced turbopropulsion systems. A set of three generic time-dependent crack growth models was implemented and integrated into the Darwin® probabilistic life-prediction code. Using the enhanced risk analysis tool and material constants calibrated to IN 718 data, the effect of time-dependent crack growth on the risk of fracture in a turboengine component was demonstrated for a generic rotor design and a realistic mission profile. The results of this investigation confirmed that time-dependent crack growth and cycle-dependent crack growth in IN 718 can be treated by a simple summation of the crack increments over a mission. For the temperatures considered, time-dependent crack growth in IN 718 can be considered as a K-controlled environmentally-induced degradation process. Software implementation of the generic time-dependent crack growth models in Darwin provides a pathway for potential evaluation of the effects of multiple damage modes on the risk of component fracture at high service temperatures.
Notch signaling in kidney development (2003)

Notch signaling is required for kidney development, and the expression of Notch genes is increased in response to kidney damage. Further studies of Notch signaling will be important in order to understand kidney development and tissue repair.
Critical Role for Casein Kinase 2 and Phosphoinositide-3-Kinase in the Interferon-γ–Induced Expression of Monocyte Chemoattractant Protein-1 and Other Key Genes Implicated in Atherosclerosis (2007)

These studies provide novel insights into the role of PI3K/AKT and CK2 in IFN-gamma signaling relevant to changes in macrophage gene expression during atherosclerosis.
GRIN: a graph based RDF index (2007)

RDF (“Resource Description Framework”) is now a widely used World Wide Web Consortium standard. However, methods to index large volumes of RDF data are still in their infancy. In this paper, we focus on providing a very lightweight indexing mechanism for certain kinds of RDF queries, namely graph-based queries where there is a need to traverse edges in the graph determined by an RDF database. Our approach uses the idea of drawing circles around selected “center” vertices in the graph where the circle would encompass those vertices in the graph that are within a given distance of the “center” vertex. We come up with methods of finding such “center” vertices and identifying the radius of the circles and then leverage this to build an index called GRIN. We compare GRIN with three existing RDF indexex: Jena, Sesame, and RDFBroker. We compared (i) the time to answer graph based queries, (ii) memory needed to store the index, and (iii) the time to build the index. GRIN outperforms Jena, Sesame and RDFBroker on all three measures for graph based queries (for other types of queries, it may be worth building one of these other indexes and using it), at the expense of using a larger amount of memory when answering queries.
Speech perception using combinations of auditory, visual, and tactile information. (1989)

Four normally-hearing subjects were trained and tested with all combinations of a highly-degraded auditory input, a visual input via lipreading, and a tactile input using a multichannel electrotactile speech processor. The speech perception of the subjects was assessed with closed sets of vowels, consonants, and multisyllabic words; with open sets of words and sentences, and with speech tracking. When the visual input was added to any combination of other inputs, a significant improvement occurred for every test. Similarly, the auditory input produced a significant improvement for all tests except closed-set vowel recognition. The tactile input produced scores that were significantly greater than chance in isolation, but combined less effectively with the other modalities. The addition of the tactile input did produce significant improvements for vowel recognition in the auditory-tactile condition, for consonant recognition in the auditory-tactile and visual-tactile conditions, and in open-set word recognition in the visual-tactile condition. Information transmission analysis of the features of vowels and consonants indicated that the information from auditory and visual inputs were integrated much more effectively than information from the tactile input. The less effective combination might be due to lack of training with the tactile input, or to more fundamental limitations in the processing of multimodal stimuli.
Eyelid Anatomy (1992)

Appropriate shape, contour, height and mobility of the lids are essential to adequate protection and function of the eyes as well as overall appearance. A thorough understanding of eyelid anatomy is therefore necessary to achieve optimal surgical results. For the purpose of this discussion the eyelids can be divided into the following structural planes: 1) skin and subcutaneous tissue; 2) orbicularis muscle and submuscular fibroadipose layer; 3) orbital septum; 4) preaponeurotic fat; 5) eyelid retractors; and 6) the tarsi and conjunctiva.
Transgenic Mice Expressing Lipoprotein Lipase in Adipose Tissue (2003)

Lipoprotein lipase (LPL) is a key enzyme in lipoprotein and adipocyte metabolism. Defects in LPL can lead to hypertriglyceridemia and the subsequent development of atherosclerosis. The mechanisms of regulation of this enzyme are complex and may occur at multiple levels of gene expression. Because the 3'-untranslated region (UTR) is involved in LPL translational regulation, transgenic mice were generated with adipose tissue expression of an LPL construct either with or without the proximal 3'-UTR and driven by the aP2 promoter. Both transgenic mouse colonies were viable and expressed the transgene, resulting in a 2-fold increase in LPL activity in white adipose tissue. Neither mouse colony exhibited any obvious phenotype in terms of body weight, plasma lipids, glucose, and non-esterified fatty acid levels. In the mice expressing hLPL with an intact 3'-UTR, hLPL mRNA expression approximately paralleled hLPL activity. However in the mice without the proximal 3'-UTR, hLPL mRNA was low in the setting of large amounts of hLPL protein and LPL activity. In previous studies, the 3'-UTR of LPL was critical for the inhibitory effects of constitutively expressed hormones, such as thyroid hormone and catecholamines. Therefore, these data suggest that the absence of the 3'-UTR results in a translationally unrepressed LPL, resulting in a moderate overexpression of adipose LPL activity.
Similarities and Differences in the Structure−Activity Relationships of Capsaicin and Resiniferatoxin Analogues (1996)

Structure-activity relationships in analogues of the irritant natural product capsaicin have previously been rationalized by subdivision of the molecule into three structural regions (A,B, and C). The hypothesis that resiniferatoxin (RTX), which is a high-potency ligand for the same receptor and which has superficial structural similarities with capsaicin, could be analogously subdivided has been investigated. The effects of making parallel changes in the two structural series have been studied in a cellular functional assay which is predictive of analgesic activity. Parallel structural changes in the two series lead to markedly different consequences on biological activity; the 3- and 4-position aryl substituents (corresponding to the capsaicin 'A-region') which are strictly required for activity in capsaicin analogues are not important in RTX analogues. The homovanillyl C-20 ester group in RTX (corresponding to the capsaicin 'B-region') is more potent than the corresponding amide, in contrast to the capsaicin analogues. Structural variations to the diterpene moiety suggest that the functionalized 5-membered diterpene ring of RTX is an important structural determinant for high potency. Modeling studies indicate that the 3D position of the alpha-hydroxy ketone moiety in the 5-membered ring is markedly different in the phorbol (inactive) analogues and RTX (active) series. This difference appears to be due to the influence of the strained ortho ester group in RTX, which acts as a local conformational constraint. The reduced activity of an analogue substituted in this region and the inactivity of a simplified analogue in which this unit is entirely removed support this conclusion.
Small-Molecule Theranostic Probes: A Promising Future in Neurodegenerative Diseases (2013)

Prion diseases are fatal neurodegenerative illnesses, which include Creutzfeldt-Jakob disease in humans and scrapie, chronic wasting disease, and bovine spongiform encephalopathy in animals. They are caused by unconventional infectious agents consisting primarily of misfolded, aggregated, β -sheet-rich isoforms, denoted prions, of the physiological cellular prion protein (PrP(C)). Many lines of evidence suggest that prions (PrP(Sc)) act both as a template for this conversion and as a neurotoxic agent causing neuronal dysfunction and cell death. As such, PrP(Sc) may be considered as both a neuropathological hallmark of the disease and a therapeutic target. Several diagnostic imaging probes have been developed to monitor cerebral amyloid lesions in patients with neurodegenerative disorders (such as Alzheimer's disease, Parkinson's disease, and prion disease). Examples of these probes are Congo red, thioflavin T, and their derivatives. We synthesized a series of styryl derivatives, denoted theranostics, and studied their therapeutic and/or diagnostic potentials. Here we review the salient traits of these small molecules that are able to detect and modulate aggregated forms of several proteins involved in protein misfolding diseases. We then highlight the importance of further studies for their practical implications in therapy and diagnostics.
Examination of shape complementarity in docking ofUnbound proteins (1999)

Here we carry out an examination of shape complementarity as a criterion in protein-protein docking and binding. Specifically, we examine the quality of shape complementarity as a critical determinant not only in the docking of 26 protein-protein "bound" complexed cases, but in particular, of 19 "unbound" protein-protein cases, where the structures have been determined separately. In all cases, entire molecular surfaces are utilized in the docking, with no consideration of the location of the active site, or of particular residues/atoms in either the receptor or the ligand that participate in the binding. To evaluate the goodness of the strictly geometry-based shape complementarity in the docking process as compared to the main favorable and unfavorable energy components, we study systematically a potential correlation between each of these components and the root mean square deviation (RMSD) of the "unbound" protein-protein cases. Specifically, we examine the non-polar buried surface area, polar buried surface area, buried surface area relating to groups bearing unsatisfied buried charges, and the number of hydrogen bonds in all docked protein-protein interfaces. For these cases, where the two proteins have been crystallized separately, and where entire molecular surfaces are considered without a predefinition of the binding site, no correlation is observed. None of these parameters appears to consistently improve on shape complementarity in the docking of unbound molecules. These findings argue that simplicity in the docking process, utilizing geometrical shape criteria may capture many of the essential features in protein-protein docking. In particular, they further reinforce the long held notion of the importance of molecular surface shape complementarity in the binding, and hence in docking. This is particularly interesting in light of the fact that the structures of the docked pairs have been determined separately, allowing side chains on the surface of the proteins to move relatively freely. This study has been enabled by our efficient, computer vision-based docking algorithms. The fast CPU matching times, on the order of minutes on a PC, allow such large-scale docking experiments of large molecules, which may not be feasible by other techniques. Proteins 1999;36:307-317.
All-trans- and 9-cis-retinoic acid inhibit growth of normal human and murine B cell precursors (1995)

In the present paper we demonstrate that physiologic levels (10 nM) of both all-trans- and 9-cis-retinoic acid (RA) are potent inhibitors of the growth of human as well as murine B cell precursors in vitro. Ten nanomolar concentrations of all-trans- and 9-cis-RA reduced the DNA synthesis ([3H]thymidine uptake) of human B cell precursors (CD19+ IgM-) stimulated with O-tetradecanoylphorbol-13-acetate and ionomycin by approximately 55% and 70%, respectively. Human B cell precursors stimulated with low m.w. B cell growth factor were also inhibited by RA. Ten nanomolar concentrations of either isoform of RA reduced DNA synthesis by approximately 50%. No effect of RA on differentiation to sIgM positive cells was noted. The potent growth-inhibiting effect of RA on human B cell precursors was confirmed in the murine cell system. B lymphopoiesis from murine hematopoietic precursors (Lin-B220(+)-containing cells) was induced by stimulation with IL-7. Concentrations of all-trans- and 9-cis-RA as low as 10 pM reduced the colony-forming ability of the IL-7-stimulated Lin-B220(+)-containing cells. Ten nanomolar concentrations of either isoform reduced colony formation by approximately 60%. RA was not toxic to the cells, as the inhibition of colony formation after 24 h was reversible at concentrations as high as 1 microM. The growth-inhibiting effect of RA was directly mediated, as revealed by single cell analysis of the Lin-B220(+)-containing cells. Thus, vitamin A appears to have an important role in regulation of B lymphopoiesis.
Blood Glucose Area Under the Curve: Methodological Aspects (1990)

To specify the influence of methods used in estimating area under the curve (AUC) and the meaning of total and incremental AUC, 75 glycemic responses to a mixed meal were studied in 75 diabetic patients, 39 with insulin-dependent diabetes mellitus and 36 with non-insulin-dependent diabetes mellitus. AUC was integrated with five computerized methods: polynomial interpolation of third and fourth degree, trapezoidal rule, Simpson's integration, and cubic interpolatory splines. Although these methods gave significantly different results (P less than 0.001), a strong correlation was found between estimations of AUC with different methods (r greater than 0.99, P less than 0.001). In addition, variation between methods was less than or equal to 2%, whereas the coefficient of variation between subjects was 38%. Total AUC was strongly correlated with basal blood glucose value (r = 0.90, P less than 0.001), whereas incremental and positive AUC were not (r = 0.12 and 0.07, respectively, NS). Incremental and positive AUC were strongly correlated with glycemic rise (r = 0.89 and 0.93, respectively, P less than 0.001), whereas total AUC was only slightly so (r = 0.31, P less than 0.01). Incremental and positive AUC gave slightly but significantly different information on glucose response. These results suggest that variations related to the method used in estimating AUC are not clinically relevant and that a simple method such as trapezoidal rule can be used. Total AUC is a descriptive factor related to basal blood glucose value, whereas incremental and positive AUC more accurately describe glycemic response to foods.
Lipase‐catalyzed methanolysis of triricinolein in organic solvent to produce 1,2(2,3)‐diricinolein (2003)

The objective of this study was to find the optimal parameters for lipase-catalyzed methanolysis of triricinolein to produce 1,2(2,3)-diricinolein. Four different immobilized lipases were tested, Candida antarctica type B (CALB), Rhizomucor miehei (RML), Pseudomonas cepacia (PCL), and Penicillium roquefortii (PRL). n-Hexane and diisopropyl ether (DIPE) were examined as reaction media at three different water activities (a(w)), 0.11, 0.53, and 0.97. The consumption of triricinolein and the formation of 1,2(2,3)-diricinolein, methyl ricinoleate, and ricinoleic acid were followed for up to 48 h. PRL gave the highest yield of 1,2(2,3)-diricinolein. Moreover, this lipase showed the highest specificity for the studied reaction, i.e., high selectivity for the reaction with triricinolein but low for 1,2(2,3)-diricinolein. Recoveries of 93 and 88% DAG were obtained using PRL in DIPE at a(w) of 0.11 and 0.53, respectively. Further, NMR studies showed that a higher purity of the 1,2(2,3)-isomer vs. the 1,3-isomer was achieved at higher a(w) (88% at a(w) = 0.53), compared to lower a(w) (71% at a(w) = 0.11). The DAG obtained was acylated by the DAG acyltransferase from Arabidopsis thaliana. Therefore, this enzymatic product is a useful enzyme substrate for lipid biosynthesis. Accordingly, the use of PRL in DIPE at a(w) 0.53 is considered optimal for the synthesis of 1,2(2,3)-diricinolein from triricinolein.
Total Synthesis of dl-Febrifugine and dl-Isofebrifugine. (1999)

Racemic compounds (1 and 2) of the antimalarial agents febrifugine (d-1) and isofebrilugine (d-2) were synthesized using an unusual Claisen rearrangement of allyl enol ether (7) and the stereoselective reduction of 2-allyl-3-piperidone (8). This method is widely applicable to the synthesis of derivatives needed to study the structure-activity relationship of febrifugine.
Transitional Platoon Maneuvers In An Automated Highway System (1992)

This report deals with an introduction to the control aspect of platoon maneuvers in Automated Highway Systems. The different platoon maneuvers include lane changes, merge procedures and split procedures. The first part of the report consists of a review of the existing literature in this area. The survey is split up into the quasi-synchronous and vehicle follower controller methods of approach to the problem. The subsequent sections deal with the mathematical description of the problem with two representations of the system under study, varying only in level of model complexity. The simplified model has been studied with a linear based control as well as the nonlinear sliding mode approach. The results only reinforce the need for nonlinear systems analysis and control. The sliding control technique has also been applied to study the detailed version of the plant.
Regulating the Deficit After Bowsher v. Synar (1987)

Although acknowledging that "Gramm-Rudman-Hollings " was enacted "to meet a national fiscal emergency . . . of unprecedented magnitude," in Bowsher v. Synar the Supreme Court nevertheless declared its key provision unconstitutional.\nSection 251 of Gramm-Rudman-Hollings directed the Comptroller General to prepare a report to the President and Congress specifying program-by-program budget reductions necessary to prevent the deficit for the coming fiscal year from exceeding the maximum permitted by the statute. Seven justices agreed that this provision violates the Constitution.
Diagnosing disconjugate eye movements (2008)

Along with conventional measures of saccades, such as peak velocity, phase planes provide a useful tool to determine the site, extent, and pathogenesis of disconjugacy. We hypothesize that the pale global extraocular muscle fibers, which drive the high-acceleration component of saccades, receive a neural command that ensures initial ocular conjugacy.
Strong and efficient cache side-channel protection using hardware transactional memory (2017)

Cache-based side-channel attacks are a serious problem in multi-tenant environments, for example, modern cloud data centers. We address this problem with Cloak, a new technique that uses hardware transactional memory to prevent adversarial observation of cache misses on sensitive code and data. We show that Cloak provides strong protection against all known cache-based side-channel attacks with low performance overhead. We demonstrate the efficacy of our approach by retrofitting vulnerable code with Cloak and experimentally confirming immunity against state-of-the-art attacks. We also show that by applying Cloak to code running inside Intel SGX enclaves we can effectively block information leakage through cache side channels from enclaves, thus addressing one of the main weaknesses of SGX.
Renal bioavailability of selenium after supplementation with different forms of selenium: Ion probe and mass spectrometry study (2000)

The bioavailability and safety of three different forms of selenium was evaluated in nephrocytes by secondary ion mass spectrometry. The distribution of the element in kidney cortex and the variations of selenium concentrations were established in mice supplemented with sodium selenite, selenomethionine, or Selenion®. Images of physiological selenium revealed the element in proximal tubules and found it to be particularly concentrated on the basal lamina of nephrocytes but undetectable in distal tubules. After treatments, the selenium images and the concentrations depended on the chemical form administered. The highest renal selenium concentrations were observed for selenomethionine and Selenion®. Early toxic effects of selenium supplementation were revealed only for high-dose sodium selenite as accumulations in some lysosomes. The widespread distribution of selenomethionine and Selenion® in proximal and distal tubular cells suggested that both were metabolized as methionine. Our results show the importance of physiological selenium in proximal tubule metabolism and bring to evidence that the bioavailability and safety of selenium depend on the chemical form administered. J. Trace Elem. Exp. Med. 13:367–380, 2000. © 2000 Wiley-Liss, Inc.
Single-Laser Multi-Terabit/s Systems (2013)

Optical communication systems carry the bulk of all data traffic worldwide. This book introduces multi-Terabit/s transmission systems and three key technologies for next generation networks. A software-defined multi-format transmitter, an optical comb source and an optical processing scheme for the fast Fourier transform for Tbit/s signals. Three world records demonstrate the potential: The first single laser 10 Tbit/s and 26 Tbit/s OFDM and the first 32.5 Tbit/s Nyquist WDM experiments.