gebhart/patrepeval huggingface dataset:
Quantitative software security risk assessment model (2007)

Risk analysis is a process for considering possible risks and determining which are the most significant for any particular effort. Determining which risks to address and the optimum strategy for mitigating said risks is often an intuitive and qualitative process. An objective view of the risks inherent in a development effort requires a quantitative risk model. Quantitative risk models used in determining which risk factors to focus on, tend to use a traditional approach of annualized loss expectancy (ALE). This research uses empirical data that reflects the security posture of each vulnerability to calculate Loss Expectancy; a risk impact estimator. Data from open source vulnerability databases and results of predicted threat models are used as input to the risk model. Security factors that take into account the innate characteristics of each vulnerability are incorporated into the calculation of the risk model; resulting in an empirical assessment of the potential threats to a development effort based on the risk metric calculation.
Projecting human pharmacokinetics of monoclonal antibodies from nonclinical data: comparative evaluation of prediction approaches in early drug development (2015)

Currently, more than 350 monoclonal antibodies (mAbs) and mAb derivatives are under development as therapeutics. The prediction of mAb pharmacokinetics (PK)/pharmacodynamics (PD) plays a key role in starting dose selection for first-in-human (FIH) studies. This article presents a brief overview of the biology and mechanisms of absorption, distribution, metabolism and excretion (ADME) for mAbs. In addition, a detailed review of mAb human PK/PD prediction from nonclinical data is provided, including allometry for mAbs with linear or nonlinear PK, species-invariant time method, physiologically based PK (PBPK) modeling and target-mediated drug disposition (TMDD) model, bioavailability projection and immunogenicity impact on PK prediction. Finally, from an industry perspective a decision tree of mAb human PK projection is proposed to facilitate drug development.
Differential Reactivity of [beta]-Carotene Isomers from Dunaliella bardawil Toward Oxygen Radicals (1993)

Dunaliella bardawil accumulates massive amounts of [beta]-carotene in two isoforms, a 9-cis and an all-trans stereoisomer, when grown under high irradiance, as a means to protect the cells against photoinhibition (A. Ben-Amotz, A. Shaish, M. Avron [1989] Plant Physiol 91: 1040-1043). The purpose of this work has been to find out if the mechanism of protection involves scavenging of reactive oxygen species. For this purpose high- and low-[beta]-carotene-containing cells were compared with respect to their sensitivity to several external oxidants [H2O2, methyl viologen, rose bengal, and 2,2[prime]-azobis(2-amidinopropane)HCl]. All oxidants induce a light-stimulated degradation of [beta]-carotene and of chlorophyll. The degradation of [beta]-carotene precedes that of chlorophyll, indicating that it is more reactive toward oxidants. The 9-cis [beta]-carotene is degraded faster than the all-trans stereoisomer when exposed to oxidants, both in intact cells and in isolated [beta]-carotene globules, indicating that it is a more effective scavenger of reactive oxygen species. Comparison of the sensitivity to different oxidants, between high- and low-[beta]-carotene-containing cells, reveals similar rates of chlorophyll and [beta]-carotene degradation in the two populations. Survival tests toward H2O2 and rose bengal show that high-[beta]-carotene cells have a similar sensitivity toward H2O2 but are more resistant toward rose bengal, a photoactivated generator of singlet oxygen, possibly due to masking of the latter by [beta]-carotene. These results suggest that the protection mechanism of massively accumulated [beta]-carotene in Dunaliella against photoinhibition is not due to scavenging of reactive oxygen species.
Use of biological response modifiers in the treatment of cutaneous T-cell lymphoma (1998)

Cutaneous T-cell lymphoma (CTCL) is typically a skin-infiltrating, clonal proliferative disorder of CD4+ T cells that exhibit a T-helper type 2 cytokine phenotype. Therapeutic decisions are based on the extent of disease and the observations that host-antitumor responses occur and that these responses may be blunted by the immunosuppressive cytokines produced by the malignant T cells. Biologic response modifiers, which may enhance cell-mediated immunity and antitumor responses, are active agents in the treatment of CTCL. The rationale and use of biologic response modifiers to treat CTCL are reviewed in this article.
Acute Hyperglycemia Attenuates Endothelium-Dependent Vasodilation in Humans In Vivo (1998)

Acute hyperglycemia impairs endothelium-dependent vasodilation in healthy humans in vivo. This finding suggests that elevated glucose may contribute to the endothelial dysfunction observed in patients with diabetes mellitus.
RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta (2002)

We report the identification and characterization of the gene encoding the eighth and final human ribonuclease (RNase) of the highly diversified RNase A superfamily. The RNase 8 gene is linked to seven other RNase A superfamily genes on chromosome 14. It is expressed prominently in the placenta, but is not detected in any other tissues examined. Phylogenetic analysis suggests that RNase 7 is the closest relative of RNase 8 and that the pair likely resulted from a recent gene duplication event in primates. Further analysis reveals that the RNase 8 gene has incorporated non-silent mutations at an elevated rate (1.3 x 10(-9) substitutions/site/year) and that orthologous RNase 8 genes from 6 of 10 primate species examined have been deactivated by frameshifting deletions or point mutations at crucial structural or catalytic residues. The ribonucleolytic activity of recombinant human RNase 8 is among the lowest of members of this superfamily and it exhibits neither antiviral nor antibacterial activities characteristic of some other RNase A ribonucleases. The rapid evolution, species-limited deactivation and tissue-specific expression of RNase 8 suggest a unique physiological function and reiterates the evolutionary plasticity of the RNase A superfamily.
Agent-based traffic simulation and traffic signal timing optimization with GPU (2011)

With the advantage of simulating the details of a transportation system, the “microsimulation” of a traffic system has long been a hot topic in the Intelligent Transportation Systems (ITS) research. The Cellular Automata (CA) and the Multi-Agent System (MAS) modeling are two typical methods for the traffic microsimulation. However, the computing burden for the microsimulation and the optimization based on it is usually very heavy. In recent years the Graphics Processing Units (GPUs) have been applied successfully in many areas for parallel computing. Compared with the traditional CPU cluster, GPU has an obvious advantage of low cost of hardware and electricity consumption. In this paper we build an MAS model for a road network of four signalized intersections and we use a Genetic Algorithm (GA) to optimize the traffic signal timing with the objective of maximizing the number of the vehicles leaving the network in a given period of time. Both the simulation and the optimization are accelerated by GPU and a speedup by a factor of 195 is obtained. In the future we will extend the work to large scale road networks.
Relationship of Serum HER-2/neu and Serum CA 15-3 in Patients with Metastatic Breast Cancer (2002)

Serum HER-2/neu is a significant independent predictive and prognostic factor in hormone receptor-positive metastatic breast cancer, even when adjusted for tumor burden as measured by CA 15-3. The combination of increased serum HER-2/neu and increased serum CA 15-3 predicts a worse prognosis than does increased CA 15-3 alone.
Rh−DuPHOS-Catalyzed Enantioselective Hydrogenation of Enol Esters. Application to the Synthesis of Highly Enantioenriched α-Hydroxy Esters and 1,2-Diols (1998)

The asymmetric hydrogenation of α-(acetyloxy)- and α-(benzoyloxy)acrylates 4 catalyzed by cationic rhodium−DuPHOS complexes has been examined. A wide range of substrates (4) were prepared via a convenient Horner−Emmons condensation protocol, and subsequently hydrogenated under mild conditions (60 psi of H2) at substrate-to-catalyst ratios (S/C) of 500. Overall, enol ester substrates 4 were reduced by the cationic Et−DuPHOS−Rh catalysts with very high levels of enantioselectivity (93−99% ee). Importantly, substrates 4 bearing β-substituents could be employed as E/Z isomeric mixtures with no detrimental effect on the selectivity. Labeling studies indicated that no significant E/Z isomerization of the substrates occurs during the course of these reactions. Details concerning optimization of the reaction, interesting solvent effects, and deprotection procedures for the synthesis of highly enantioenriched α-hydroxy esters and 1,2-diols also are provided.
Selective inactivation of the Arg-Gly-Asp-Ser (RGDS) binding site in von Willebrand factor by site-directed mutagenesis. (1992)

In order to assess the requirement for the Arg-Gly-Asp-Ser (RGDS) consensus adhesion sequence in von Willebrand factor (vWF) for vWF binding to platelets and endothelial cells, point mutations were introduced into this sequence by site-directed mutagenesis. A glycine to alanine substitution yielded RADS-vWF, while an aspartate to glutamate substitution resulted in RGES-vWF. Recombinant RADS-vWF and RGES-vWF, purified from transformed Chinese hamster ovary cells, were compared with recombinant wild type vWF (WT-vWF) in functional assays with platelets and human umbilical vein endothelial cells (HU-VECs). High molecular weight RADS-vWF and RGES-vWF multimers inhibited binding of 125I-vWF to a mixture of insolubilized native type I and III collagen and competed effectively with 125I-vWF for binding to formalin-fixed platelets in the presence of ristocetin, indicating functional collagen and platelet glycoprotein Ib binding. However, RADS-vWF and RGES-vWF were unable to displace the binding of 125I-vWF to thrombin or ADP-activated platelets. The attachment of HUVECs to either RADS-vWF or RGES-vWF coated surfaces was reduced and spreading was almost completely inhibited, compared with WT-vWF. We conclude that point mutations of the RGDS sequence in vWF selectively impair binding to platelet glycoprotein IIb/IIIa and the HUVEC vitronectin receptor.
Reduced-Complexity Receiver Structures for Space–Time Bit-Interleaved Coded Modulation Systems (2007)

Transmission efficiency in radio channels can be considerably improved by using multiple transmit and receive antennas and employing a family of schemes called space-time (ST) coding. Both extended range and/or improved bandwidth efficiency can be achieved, compared with a radio link with a single transmit and receive antenna. Bit-interleaved coded modulation schemes give diversity gains on fading channels with higher order modulation constellations combined with conventional binary convolutional codes also for the case of a single transmit and receive antenna radio link. In this paper, we study a family of flexible bandwidth-efficient ST coding schemes which combine these two ideas in a narrowband flat-fading channel and single-carrier modems. We address receiver complexity for the case of a large number of transmit antennas and higher order modulation constellations. Especially, we focus on practical configurations, where the number of transmit antennas is greater than that of receive antennas. Simplified receivers using tentative decisions are proposed and evaluated by means of simulations. Tradeoffs between complexity reduction and performance loss are presented. We emphasize systems that are of particular interest in applications where the number of transmit antennas exceeds the number of receive antennas. A system with four transmit antennas with an eight-fold complexity reduction and a performance loss of about 1 dB is demonstrated
Promising role of curcumin against viral diseases emphasizing COVID-19 management: A review on the mechanistic insights with reference to host-pathogen interaction and immunomodulation (2021)

Curcumin has already acknowledged immense interest from both medical and scientific research because of its multifaceted activity. To date, the promising effects of curcumin were perceived against numerous inflammatory diseases. Besides, curcumin's role as a medicine has been studied in many virus infections like influenza, HIV, etc. There is a need to analyze the cellular mechanisms of curcumin including host-pathogen interaction and immunomodulatory effects, to explore the role of curcumin against COVID-19. With this background, our study suggests that curcumin can prevent COVID-19 infections by inhibiting the pathogen entry, viral genome replication and steps in the endosomal pathway along with inhibition of T-cell signalling by impairing the autophagy-mediated antigen-presenting pathway. This review explicit the possible mechanisms behind curcumin-induced cellular immunity and a therapeutive dosage of curcumin suggesting a preventive strategy against COVID-19.
Allergens from Brazil nut: immunochemical characterization. (1997)

The increase in the consumption of tropical nuts in the Northern Hemisphere during the last years, has evolved in a simultaneous enhancement of allergic IgE mediated (Hypersensitivity type 1) reported cases produced by this kind of food. The Brazil nut is the seed of the Bertholletia excelsa tree (Family Lecythidaceae) and, as in other seeds, proteins represent one of its major components making up 15-17% of its fresh weight and 50% of defatted flour. Of these, storage proteins are the most important ones, and the 12 S globulin legumin-like protein and the 2 S albumin have been described as the most representative. The 2 S protein, due to its high sulfur-rich amino acid content (3% cysteine and 18% methionine), is being studied, cloned and expressed in some important agronomic seeds (soybean, bean, oilseed rape) in order to enrich the nutritional quality of them. The case of a patient with serious clinical allergic symptoms (vomiting, diarrhoea and loss of consciousness) caused by oral contact with the Brazil nut, is presented. The patient gave a positive Skin Prick Test response to Brazil nut, kiwi and hazelnut extracts, and negative to regionally specific aeroallergens and other food extracts. The patient serum showed a high level of specific IgE by RAST to Brazil nut (> 17.5 PRU/ml, Class 4), and significative levels to hazelnut, and mustard. In vitro immunological studies (SDS-Immunoblotting and IEF-Immunoblotting) revealed IgE-binding proteins present in the extract. It was shown that not only the heavy (Mr 9) and light (Mr 4) subunits of the known allergenic 2 S albumin but also the alpha-subunits (Mr approximately 33.5 and 32) and at least one of the beta-subunits (Mr approximately 21) of the 12 S Brazil nut globulin, hitherto never involved in allergic problems, showed a strong IgE-binding capacity.
SnO2-Based Dye-Sensitized Hybrid Solar Cells Exhibiting Near Unity Absorbed Photon-to-Electron Conversion Efficiency (2010)

Improving the solar light harvesting and photon-to-electron conversion efficiency for hybrid, organic-inorganic photovoltaics are critical challenges. Titania based solid-state hybrid solar cells are moderately efficient at converting visible photons to electrons, but major electrical losses still remain. A material based paradigm shift is required to dramatically enhance the performance of these devices. Here, we present an investigation into solid-state dye-sensitized solar cells (SDSCs) incorporating a molecular hole-transporter and mesoporous tin oxide electrodes, in place of titania usually employed. We investigate the influence of treating the surface of the SnO(2) with different oxides and find that MgO "passivated" SnO(2) electrodes demonstrate an unprecedented absorbed photon-to-electron conversion efficiency of near unity across a broad spectral range. A dual surface treatment of TiO(2) followed by MgO enables tuning of the solar cell photovoltage, fill factor, and efficiency with visible light absorbing cells delivering 3% solar-to-electrical full sun power conversion efficiency.
Multifunctional polymeric micelles for delivery of drugs and siRNA (2014)

Polymeric micelles, self-assembling nano-constructs of amphiphilic copolymers with a core-shell structure have been used as versatile carriers for delivery of drugs as well as nucleic acids. They have gained immense popularity owing to a host of favorable properties including their capacity to effectively solubilize a variety of poorly soluble pharmaceutical agents, biocompatibility, longevity, high stability in vitro and in vivo and the ability to accumulate in pathological areas with compromised vasculature. Moreover, additional functions can be imparted to these micelles by engineering their surface with various ligands and cell-penetrating moieties to allow for specific targeting and intracellular accumulation, respectively, to load them with contrast agents to confer imaging capabilities, and incorporating stimuli-sensitive groups that allow drug release in response to small changes in the environment. Recently, there has been an increasing trend toward designing polymeric micelles which integrate a number of the above functions into a single carrier to give rise to "smart," multifunctional polymeric micelles. Such multifunctional micelles can be envisaged as key to improving the efficacy of current treatments which have seen a steady increase not only in hydrophobic small molecules, but also in biologics including therapeutic genes, antibodies and small interfering RNA (siRNA). The purpose of this review is to highlight recent advances in the development of multifunctional polymeric micelles specifically for delivery of drugs and siRNA. In spite of the tremendous potential of siRNA, its translation into clinics has been a significant challenge because of physiological barriers to its effective delivery and the lack of safe, effective and clinically suitable vehicles. To that end, we also discuss the potential and suitability of multifunctional polymeric micelles, including lipid-based micelles, as promising vehicles for both siRNA and drugs.
Yeast artificial chromosomes employed for random assembly of biosynthetic pathways and production of diverse compounds in Saccharomyces cerevisiae (2009)

The technology has many potential uses but is particularly suited for generating high numbers of structurally diverse compounds, some of which may not be amenable to chemical synthesis, thus greatly facilitating access to a huge chemical space in the search for new commercially interesting compounds.
Phototherapy of tumors (1983)

Abstract Lasers provide a means of delivering high intensity light to small well‐defined areas under precise control. The biological response depends on the light wavelength and intensity and the absorption characteristics of the target organ. The most important effects are thermal and include tissue vaporization, necrosis with later sloughing, and necrosis stimulating an inflammatory response which may lead to local fibrosis. The Carbon Dioxide Laser can cut or vaporize neoplastic tissue in areas accessible to rigid endoscopy, but the more penetrating Nd YAG and Argon laser beams can be transmitted via flexible fibers and have greater potential for destroying larger tumors without unacceptable damage to surrounding areas. More selective tumor phototherapy is possible in some organs by sensitization with HpD (hematoporphyrin derivative) and subsequent treatment with a dye laser. This effect is non‐thermal and depends on the production of singlet oxygen by activated HpD. The precision possible for local treatment of solid tumors with lasers is greater than for almost any other techniques, but careful quantitative studies are needed to establish the appropriate treatment parameters in any particular situation.
Cobalt‐Based Complexes for the Copolymerization of Propylene Oxide and CO2: Active and Selective Catalysts for Polycarbonate Synthesis (2003)

CO2 is an ideal feedstock for chemical synthesis; unfortunately its thermodynamic stability is a barrier to widespread use. Active cobalt catalysts for the copolymerization of propylene oxide and CO2 are reported (see scheme; L=N,N′-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexanediamine), which have excellent regioselectivity for polycarbonate synthesis without concomitant production of cyclic carbonate by-products. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2003/z52605_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Thrombosis and Haemostasis (2017)

Background The presence of dextran sulfate (DS) in reagents and the type of blood collection tube (citrate/citrated-theophylline-adenosine-dipyridamole [CTAD]) can lead to discrepancies between unfractionated heparin (UFH) anti-Xa levels.Objectives To evaluate the extent of the effect (1) of different reagents containing or not containing DS and (2) of the blood collection tubes, on UFH anti-Xa levels, in various clinical situations (NCT04700670).Methods We prospectively included patients from eight centers: group (G)1, cardiopulmonary bypass (CPB) after heparin neutralization (n ¼ 39); G2, cardiothoracic intensive
γ‐Substituted Peptide Nucleic Acids Constructed from L‐Lysine are a Versatile Scaffold for Multifunctional Display (2006)

On display: This model shows DNA (pink) annealed to a peptide nucleic acid (PNA; orange) containing several L-lysine γ side chains (LKγ-PNA) in the middle of the PNA oligomer. The LKγ-PNA side chains project away from the nucleobase pairs (purple) and line the periphery of the duplex. This strategy can be used for the multifunctional display of various functional groups from the PNA residues without diminishing the binding affinity or selectivity to DNA. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z603483_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Isolation and Characterization of Lipopolysaccharides (2008)

Lipopolysaccharide (LPS) is the signature glycolipid isolated from almost all Gram-negative bacteria. LPSs are well known for their ability to elicit the release of cytokines from eukaryotic cells including macrophages, neutrophils, and epithelial cells. LPS can be isolated free of contaminating nucleic acids and proteins by various techniques. In this review, we outline approaches for the isolation and preparation of LPSs for structural studies as well as preparation of very highly purified material for biological studies. Methods are also provided for the analysis of the purity and the structural composition of the LPSs. Finally, three methods for the isolation of lipid A are described.