gebhart/patrepeval huggingface dataset:
Thienocinnolinone Alkanoic Acid Derivatives as Aldose Reductase Inhibitors (2005)

A new series of 8-halogen-4,4a,5,6-tetrahydrothieno[2,3-h]cinnolinone-N2-alkanoic acids was prepared and tested for aldose reductase (ALR2) inhibitory activities. These compounds showed significant inhibitory activity against bovine lens ALR2, with the best compound 2e showing an IC(50) value of 31.4 microM. The presence of the C8-substituents here studied (Cl, Br) on the thienocinnolinone scaffold caused a decrease of the inhibitory potency by a factor of about 4 with respect to the unsubstituted parent compound, while the presence of a C8-methyl group, considered in a previous paper decreased the activity by a factor of about 2. Moreover, the length of the N2 alkanoic chain influences strongly the enzyme inhibitory activity. While most of the carboxylic acids ALR2 inhibitors are acetic acid derivatives, in the case of thienocinnolinone compounds, homologues higher than acetic acids showed to be more active.
Problem Statement of Network Slicing in IP/MPLS Networks (2016)

The research and standardization of IMT-2020 (a.k.a. 5G) are in
progress in several industry communities and standard organizations.
The goal of 5G is to integrate various services, each of which has a
set of unique requirements, into a single network, such that each
service has a customized suited to its needs. The concept
Network Slicing is widely discussed and considered as the key
mechanism to meet the diverse service requirements concurrently with
the same physical infrastructure. This document provides an
overview of the concept network slicing in the current IMT-2020
(a.k.a. 5G) related works, and discusses the corresponding
requirements on IP/MPLS network, which will be used as the mobile
transport for 5G.
Retinoic Acid Receptor β,γ-Selective Ligands: Synthesis and Biological Activity of 6-Substituted 2-Naphthoic Acid Retinoids (1996)

In search for retinoic acid receptor (RAR) selective ligands, a series of 6-substituted 2-naphthoic acid retinoids were synthesized and evaluated in vitro in a transactivation assay and a competition binding assay for all RARs. These derivatives, in general, showed RAR beta,gamma selectivity. Among these naphthoic acids, oxime derivative 12 was identified as a potent RAR gamma-selective retinoid, while olefinic derivative 11 was found to be comparable to retinoic acid and slightly RAR beta,gamma selective. For the bioassays, a general correlation was observed between the binding affinity of the ligand to the receptors and the potency of the compounds in the transactivation assay. The structure-activity relationship of these naphthoic acids will be discussed.
Efficient and Color-Tunable Mn-Doped ZnSe Nanocrystal Emitters:  Control of Optical Performance via Greener Synthetic Chemistry (2007)

Formation of Mn-doped ZnSe quantum dots (Mn:ZnSe d-dots) using nucleation-doping strategy was studied systematically and optimized through greener approaches. The resulting d-dots were with high ( approximately 50%) photoluminescence (PL) quantum yield (QY), which was achieved by the controlled formation of small-sized MnSe nanoclusters as the core and a diffused interface between the nanocluster core and the ZnSe overcoating layers. Synthesis of the d-dots under high temperatures (240-300 degrees C) was achieved by varying the structure of the metal carboxylate precursors, concentration of the inhibitors, free fatty acid, and concentration of the activation reagents, fatty amines. Highly emissive d-dots synthesized under desired conditions were found to be extremely stable upon thermal treatment up to the boiling point of the solvent (about 300 degrees C), which was quantitatively studied using in situ measurements. The PL peak of the d-dots was controllably tuned in a surprisingly large optical window, from 565 to 610 nm. These highly emissive and stable d-dots possess characteristics of practical emissive materials, especially for applications requiring high power, high concentration of emitters, and under tough conditions.
Structure and conformation of saframycin R determined by high field 1H and 13C NMR and its interactions with DNA in solution. (1983)

The chemical structure and conformation of the new antitumor antibiotic saframycin R have been determined by high field 1H and 13C NMR as well as FAB mass spectrometry. Unlike other members of the saframycin family, saframycin R contains a reduced quinone ring bearing a glycolic ester moiety. Saframycin R exhibits acid promoted equilibrium and reversible covalent binding to DNA templates and, in the presence of a reducing agent, oxygen dependent single strand scission of supercoiled DNA. The extent of DNA scission is enhanced by in situ porcine carboxyl esterase or base catalyzed cleavage of the glycolic ester function plausibly by the release of the more reactive reduced saframycin A. This suggests that saframycin R may be regarded as a less toxic pro-drug for the active forms of saframycins A or S.
Posttranslational oligomerization and cooperative acid activation of mixed influenza hemagglutinin trimers. (1988)

The influenza virus hemagglutinin (HA) is a well-characterized integral membrane glycoprotein composed of three identical subunits. We have analyzed the formation of mixed trimers in cells expressing two different HA gene products. The results show efficient and essentially random assembly of functional hybrid trimers provided that the HAs are from the same HA subtype. Trimerization is thus a posttranslational event, and subunits are recruited randomly from a common pool of monomers in the endoplasmic reticulum. Mixed trimers were not observed between HAs derived from different subtypes, indicating that the trimerization event is sequence specific. Mixed trimers containing mutant subunits were, moreover, used to establish that the acid-induced conformational change involved in the membrane fusion activity of HA is a highly cooperative event.
Viscoacoustic waveform inversion of velocity structures in the time domain (2014)

ABSTRACT Because of the conversion of elastic energy into heat, seismic waves are attenuated and dispersed as they propagate. The attenuation effects can reduce the resolution of velocity models obtained from waveform inversion or even cause the inversion to produce incorrect results. Using a viscoacoustic model consisting of a single standard linear solid, we discovered a theoretical framework of viscoacoustic waveform inversion in the time domain for velocity estimation. We derived and found the viscoacoustic wave equations for forward modeling and their adjoint to compensate for the attenuation effects in viscoacoustic waveform inversion. The wave equations were numerically solved by high-order finite-difference methods on centered grids to extrapolate seismic wavefields. The finite-difference methods were implemented satisfying stability conditions, which are also presented. Numerical examples proved that the forward viscoacoustic wave equation can simulate attenuative behaviors very well in amplitude attenuation and phase dispersion. We tested acoustic and viscoacoustic waveform inversions with a modified Marmousi model and a 3D field data set from the deep-water Gulf of Mexico for comparison. The tests with the modified Marmousi model illustrated that the seismic attenuation can have large effects on waveform inversion and that choosing the most suitable inversion method was important to obtain the best inversion results for a specific seismic data volume. The tests with the field data set indicated that the inverted velocity models determined from the acoustic and viscoacoustic inversions were helpful to improve images and offset gathers obtained from migration. Compared to the acoustic inversion, viscoacoustic inversion is a realistic approach for real earth materials because the attenuation effects are compensated.
Pharmaceutical co-crystals - a review (2009)

Co-crystallization alters the molecular interactions and composition of pharmaceutical materials, and is considered better alternatives to optimize drug properties. Co-crystals consists of API and a stoichiometric amount of a pharmaceutically acceptable co-crystal former. Pharmaceutical co-crystals are nonionic supramolecular complexes and can be used to address physical property issues such as solubility, stability and bioavailability in pharmaceutical development without changing the chemical composition of the API. Co-crystals can be constructed through several types of interaction, including hydrogen bonding, pi-stacking, and van der Waals forces. Co-crystals High Throughput provides information on relationship between formation and chemical structure of the API and conformer. Factors affecting co-crystal stability are reported and a co-crystal is only expected to form if it is thermodynamically more stable than the crystals of its components. Phase transformations induced during processing/storage affects the mechanisms of conversion of crystalline drugs to co-crystals. Pharmaceutical co-crystals could play a major part in the future of API formulation and can be employed for chiral resolution.
Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. (1983)

Two 19-base-long oligonucleotides were synthesized, one complementary to the normal human beta-globin gene (beta A) and one complementary to the sickle cell beta-globin gene (beta S). The nonadecanucleotides were radioactively labeled and used as probes in DNA hybridization. Under appropriate hybridization conditions, these probes can be used to distinguish the beta A gene from the beta S allele. The DNA from individuals homozygous for the normal beta-globin gene (beta A beta A) only hybridized with the beta A specific probe; the DNA from those homozygous for the sickle cell beta-globin gene (beta S beta S) only hybridized with the beta S specific probe. The DNA from heterozygous individuals (beta A beta S) hybridized with both probes. This allele-specific hybridization behavior of oligonucleotides provides a general method for diagnosis of any genetic disease which involves a point mutation in the DNA sequence of a single-copy gene.
Fumarate reduction and product formation by the Reiter strain of Treponema phagedenis (1982)

The catabolic pathways for butyrate, acetate, succinate, and ethanol formation by the Reiter strain of Treponema phagedenis were investigated. Enzyme activities were demonstrated for glucose catabolism to pyruvate by the Embden-Meyerhof-Parnas pathway. Butyrate formation from acetyl-coenzyme A (acetyl-CoA) does not generate ATP by substrate level phosphorylation and involves NAD+-dependent 3-hydroxybutyryl-CoA dehydrogenase and NAD(P)+-independent butyryl-CoA dehydrogenase activities. Butyrate is formed from butyryl-CoA in a CoA transphorase reaction. Phosphate acetyltransferase and acetate kinase activities convert acetyl-CoA to acetate. An NADP+-dependent alcohol dehydrogenase participates in ethanol formation; however, the manner in which acetyl-CoA is reduced to acetaldehyde is unclear. A membrane-associated fumarate reductase was found which utilized reduced ferredoxin or flavin nucleotides as physiological electron donors. Additional electron carriers may also be involved in electron transfer for fumarate reduction. Strains of Treponema denticola, T. vincentii, and T. minutum utilized fumarate without succinate formation, whereas strains of T. phagedenis and T. refringens formed succinate from exogenously supplied fumarate.
Microgrids for Service Restoration to Critical Load in a Resilient Distribution System (2016)

Microgrids can act as emergency sources to serve critical loads when utility power is unavailable. This paper proposes a resiliency-based methodology that uses microgrids to restore critical loads on distribution feeders after a major disaster. Due to limited capacity of distributed generators (DGs) within microgrids, dynamic performance of the DGs during the restoration process becomes essential. In this paper, the stability of microgrids, limits on frequency deviation, and limits on transient voltage and current of DGs are incorporated as constraints of the critical load restoration problem. The limits on the amount of generation resources within microgrids are also considered. By introducing the concepts of restoration tree and load group, restoration of critical loads is transformed into a maximum coverage problem, which is a linear integer program (LIP). The restoration paths and actions are determined for critical loads by solving the LIP. A 4-feeder, 1069-bus unbalanced test system with four microgrids is utilized to demonstrate the effectiveness of the proposed method. The method is applied to the distribution system in Pullman, WA, resulting in a strategy that uses generators on the Washington State University campus to restore service to the Hospital and City Hall in Pullman.
Accessory cell function of human B cells. I. Production of both interleukin 1-like activity and an interleukin 1 inhibitory factor by an EBV-transformed human B cell line. (1984)

In the present paper we report that the ROHA -9 cell line, an Epstein-Barr virus (EBV)-transformed human B cell line with accessory cell capabilities, constitutively secretes a soluble factor with the biochemical and biological characteristics of human monocyte-derived IL-1. The IL-1 derived from ROHA -9 augmented murine thymocyte proliferation and enhanced the proliferative response of human T lymphocytes to concanavalin A (Con A). The ROHA -9-derived IL-1 activity eluted from Sephacryl S-200 in two peaks, at 15- 18K and 32- 35K mol wt, eluted from DEAE-Sephacel at 50-80 and 110-130 mM NaCl, and showed charge heterogeneity with peaks at pI 7.3, 6.1, and 4.1 on isoelectrofocusing (IEF). These findings suggest that B cells may elaborate an IL-1-like activity. During the logarithmic growth of ROHA -9 cells, a inhibitory factor that inhibited the response of mouse thymocytes to IL-1 was also produced. This factor had a mol wt of 95K on Sephacryl S-200, eluted at 150 mM NaCl on DEAE-Sephacel and showed a peak of pI 4.7 on preparative IEF. The inhibitory factor appeared to be selective in its effects on IL-1 responses, since it did not inhibit the activity of IL-2 on mouse thymocytes or on the growth of the IL-2-dependent CT6 cell line. This "contra-IL-1" inhibited the response of murine thymocytes to suboptimal (1 microgram/ml) but not optimal (10 micrograms/ml) doses of Con A and the response of human peripheral blood lymphocytes to streptolysin O ( SLO ) or to alloantigens. Moreover, the factor could be absorbed by mouse thymocytes but not by CT6 cells, and such thymocytes pretreated with contra-IL-1 failed to response to IL-1. Although this inhibitor is the product of a transformed B cell line, it may be representative of regulatory substances that normally control IL-1 activities either at the extracellular or intracellular level.
Matrix radiance transfer (2003)

Precomputed Radiance Transfer allows interactive rendering of objects illuminated by low-frequency environment maps, including self-shadowing and interreflections. The expensive integration of incident lighting is partially precomputed and stored as matrices.Incorporating anisotropic, glossy BRDFs into precomputed radiance transfer has been previously shown to be possible, but none of the previous methods offer real-time performance. We propose a new method, matrix radiance transfer, which significantly speeds up exit radiance computation and allows anisotropic BRDFs. We generalize the previous radiance transfer methods to work with a matrix representation of the BRDF and optimize exit radiance computation by expressing the exit radiance in a new, directionally locally supported basis set instead of the spherical harmonics. To determine exit radiance, our method performs four dot products per vertex in contrast to previous methods, where a full matrix-vector multiply is required. Image quality can be controlled by adapting the number of basis functions. We compress our radiance transfer matrices through principal component analysis (PCA). We show that it is possible to render directly from the PCA representation, which also enables the user to trade interactively between quality and speed.
Potentiation of cytochrome P450/cyclophosphamide-based cancer gene therapy by coexpression of the P450 reductase gene. (1997)

Intratumoral expression of cytochrome P450 2B1 sensitizes tumor cells to the cytotoxic action of the alkylating agent prodrug cyclophosphamide (CPA) and provides a novel strategy for cancer gene therapy that may enhance the selectivity and the effectiveness of this class of antitumor drugs [L. Chen and D. J. Waxman, Cancer Res., 55: 581-589, 1995]. P450-catalyzed drug metabolism is obligatorily dependent on electron input from the flavoenzyme NADPH-P450 reductase (RED), which is widely expressed in many cell types, including tumor cells. Here, we investigate the potential utility of combining RED gene transfer with CPA-based P450 gene therapy. Rat 9L gliosarcoma cells stably expressing either basal or elevated (up to 10-fold increase) levels of RED, in the presence or absence of P450 2B1, were selected and characterized. RED overexpression substantially increased the sensitivity of these cells to CPA, but only when combined with P450 2B1 expression. An enhanced cytotoxic response was also obtained when recombinant adenovirus encoding P450 2B1 was used to deliver the P450 gene to RED-overexpressing tumor cells. CPA cytotoxicity was substantially decreased by the RED inhibitor diphenyleneiodonium chloride or by the P450 inhibitor metyrapone, providing evidence of its dependence on the catalytic contributions of both protein components of the P450 metabolic pathway. Conditioned media from P450 2B1-expressing and RED-overexpressing tumor cells treated with CPA exhibited increased formation of the primary 4-hydroxy metabolite and greater cell contact-independent bystander cytotoxic potential compared to tumor cells containing P450 2B1 and basal levels of RED. Evaluation of the impact of P450/RED combination gene therapy using a s.c. solid tumor model/tumor excision assay revealed a dramatic 50-100-fold increase in tumor cell kill in vivo over that provided by liver drug activation alone. These findings establish the importance of endogenous RED levels as a determinant of the sensitivity of tumor cells to CPA/P450 gene therapy and demonstrate the striking therapeutic effectiveness of an anticancer prodrug activation strategy based on the combination of a cytochrome P450 gene with the gene encoding RED.
Investigation of the stereoregularity of poly(vinyl alcohol) (1964)

Abstract Studies of the steric structures of poly(vinyl alcohol), as deduced from studies of the structures of its esters, particularly poly(vinyl formate) are described. Two types of tactic poly(vinyl formate) crystallize with different structures, corresponding to their different molecular structures. Therefore, the type of molecular stereoregularity in poly(vinyl formate) samples can be deduced from an examination of the crystals produced by a given crystallization treatment. From the results of the study of the poly(vinyl formate) crystals, some conclusions can be drawn concerning the steric structure of poly(vinyl alcohol). Crystallizabilities of other tactic poly(vinyl esters) have also been investigated.
Static detection of security vulnerabilities in scripting languages (2006)

We present a static analysis algorithm for detecting security vulnerabilities in PHP, a popular server-side scripting language for building web applications. Our analysis employs a novel three-tier architecture to capture information at decreasing levels of granularity at the intrablock, intraprocedural, and interprocedural level. This architecture enables us to handle dynamic features of scripting languages that have not been adequately addressed by previous techniques. We demonstrate the effectiveness of our approach on six popular open source PHP code bases, finding 105 previously unknown security vulnerabilities, most of which we believe are remotely exploitable. 1
Mesodermal Control of Neural Cell Identity: Floor Plate Induction by the Notochord (1990)

The floor plate is a specialized group of midline neuroepithelial cells that appears to regulate cell differentiation and axonal growth in the developing vertebrate nervous system. A floor plate-specific chemoattractant was used as a marker to examine the role of the notochord in avian floor plate development. Expression of this chemoattractant in lateral cells of the neural plate and neural tube was induced by an ectopic notochord, and midline neural tube cells did not express the chemoattractant after removal of the notochord early in development. These results provide evidence that a local signal from the notochord induces the functional properties of the floor plate.
Combination of Decompressive Craniectomy and Mild Hypothermia Ameliorates Infarction Volume After Permanent Focal Ischemia in Rats (2001)

Early DC significantly reduces infarction size and improves neurological outcome in MCA infarction in rats. Temporary mild hypothermia delays infarct evolution but does not significantly reduce definite infarction size or improve neurological outcome. Combined hypothermia and DC yield significant additional benefit.
Ligand binding properties of the human erythropoietin receptor extracellular domain expressed in Escherichia coli. (1992)

We developed an assay to directly measure the ligand binding properties of the cloned human erythropoietin receptor (EpoR). The cDNA encoding the extracellular domain of the human EpoR was amplified by polymerase chain reaction and ligated into the prokaryotic expression vector pGEX3X. Synthesis in Escherichia coli was induced and a soluble glutathione S-transferase fusion protein, EREx, was purified by erythropoietin affinity chromatography. Purified EREx was bound to GSH agarose beads and used in a solid phase ligand binding assay. Specific binding of 125I-erythropoietin to EREx beads was demonstrated. A single affinity class (Kd = 1.5 nM) of the binding site was evident on Scatchard analysis. The Kd of this site is quantitatively equivalent to that of the "low" affinity cellular binding site. Kinetic analysis of ligand binding to EREx revealed both the on and off rates to be rapid, with t1/2 of 60 and 40 s, respectively. EREx ligand binding exhibits no obvious metal ion dependence or cross-competition by other hemopoietins. Antibodies to EREx block the binding of erythropoietin to the cellular EpoR. We conclude that the 66-kDa EpoR protein is capable of specific ligand binding and that no covalent modifications or associated molecules are required for this interaction. We speculate that the "high" affinity cellular binding site (Kd less than 0.2 nM) results from the interaction of the EpoR with another molecule, either additional EpoR or associated subunits, that decreases the ligand off rate.