gebhart/patrepeval huggingface dataset:
Polyethylenimine Is a Strong Inhibitor of Human Papillomavirus and Cytomegalovirus Infection (2011)

Polyethylenimines are cationic polymers with potential as delivery vectors in gene therapy and with proven antimicrobial activity. However, the antiviral activity of polyethylenimines has not been addressed in detail thus far. We have studied the inhibitory effects of a linear 25-kDa polyethylenimine on infections with human papillomaviruses and human cytomegaloviruses. Preincubation of cells with polyethylenimine blocked primary attachment of both viruses to cells, resulting in a significant reduction of infection. In addition, the dissemination of human cytomegalovirus in culture cells was efficiently reduced by recurrent administration of polyethylenimine. Polyethylenimine concentrations required for inhibition of human papillomavirus and cytomegalovirus did not cause any cytotoxic effects. Polyethylenimines and their derivatives may thus be attractive molecules for the development of antiviral microbicides.
The action of a water-soluble carbodiimide on adenosine-5'-polyphosphates (1987)

When aqueous solutions of adenosine-5'-mono-, di-, or triphosphates are treated with a water soluble carbodiimide the major product is the expected diadenosine-5'-5'-polyphosphate. The yields of these pyrophosphates are greatly increased in the presence of the Mg2+ ion. Adenosine-5'-tetraphosphate behaves differently. The major product is adenosine-5'-monophosphate. We believe that this hydrolysis occurs via a cyclic trimetaphosphate intermediate.
Effects of Backbone Contacts 3‘ to the Abasic Site on the Cleavage and the Product Binding by Human Apurinic/Apyrimidinic Endonuclease (APE1) (2003)

The mammalian apurinic/apyrimidinic (AP) endonuclease (APE1) is a multifunctional protein that plays essential roles in DNA repair and gene regulation. We decomposed the APEs into 12 blocks of highly conserved sequence and structure (molegos). This analysis suggested that residues in molegos common to all APEs, but not to the less specific nuclease, DNase I, would dictate enhanced binding to damaged DNA. To test this hypothesis, alanine was substituted for N226 and N229, which form hydrogen bonds to the DNA backbone 3' of the AP sites in crystal structures of the APE1/DNA complex. While the cleavage rate at AP sites of both N226A and N229A mutants increased, their ability to bind to damaged DNA decreased. The ability of a double mutant (N226A/N229A) to bind damaged DNA was further decreased, while the V(max) was almost identical to that of the wild-type APE1. A double mutant at N226 and R177, a residue that binds to the same phosphate as N229, had a significantly decreased activity and substrate binding. As the affinity for product DNA was decreased in all the mutants, the enhanced reaction rate of the single mutants could be due to alleviation of product inhibition of the enzyme. We conclude that hydrogen bonds to phosphate groups 3' to the cleavage site is essential for APE1's binding to the product DNA, which may be necessary for efficient functioning of the base excision repair pathway. The results indicate that the molego analysis can aid in the redesign of proteins with altered binding affinity and activity.
Apolipoprotein E allele-dependent pathogenesis: A model for age-related retinal degeneration (2005)

Age-related macular degeneration (AMD) is a late-onset, multifactorial, neurodegenerative disease of the retina and the leading cause of irreversible vision loss in the elderly in the Western world. We describe here a murine model that combines three known AMD risk factors: advanced age, high fat cholesterol-rich (HF-C) diet, and apolipoprotein E (apoE) genotype. Eyes of aged, targeted replacement mice expressing human apoE2, apoE3, or apoE4 and maintained on a HF-C diet show apoE isoform-dependent pathologies of differential severity. ApoE4 mice are the most severely affected. They develop a constellation of changes that mimic the pathology associated with human AMD. These alterations include diffuse sub-retinal pigment epithelial deposits, drusenoid deposits, thickened Bruch's membrane, and atrophy, hypopigmentation, and hyperpigmentation of the retinal pigment epithelium. In extreme cases, apoE4 mice also develop marked choroidal neovascularization, a hallmark of exudative AMD. Neither age nor HF-C diet alone is sufficient to elicit these changes. We document choroidal neovascularization and other AMD-like ocular pathologies in an animal model that exploits known AMD risk factors. The model is additionally attractive because it is not complicated by invasive experimental intervention. Our findings in this model implicate the human apoE E4 allele as a susceptibility gene for AMD and support the hypothesis that common pathogenic mechanisms may underlie AMD and Alzheimer's disease.
Introducing Attribute-Based Access Control to AUTOSAR (2016)

<div class="section abstract"><div class="htmlview paragraph">Cyber security concerns in the automotive industry have been constantly increasing as automobiles are more computerized and networked. AUTOSAR is the standard architecture for automotive software development, addressing various aspects including security. The current version of AUTOSAR is concerned with only cryptography-based security for secure authentication at the communication level. However, there has been an increasing need for authorization security to control access on software resources such as data and services in the automobile. In this paper, we introduce attribute-based access control (ABAC) to AUTOSAR to address authorization in automotive software.</div></div>
Nonlinear circuit-reduction of high-speed interconnect networks using congruent transformation techniques (2001)

A new algorithm based on Krylov subspace methods is proposed for efficient simulation of large interconnect networks with nonlinear terminations. Reduction is obtained by projecting the original system described by nonlinear differential equations into a subspace of a lower dimension. The reduced circuit can be simulated using conventional numerical integration techniques. Significant reduction in computational expense is achieved as the size of the reduced equations is much less than that of the original system. The new algorithm is potentially useful for analysis of lossy coupled transmission lines with nonlinear terminations.
Immunoregulatory Properties of Fractions from Human Pregnancy Urine: Evidence That Human Chorionic Gonadotropin is Not Responsible (1977)

The immunologically privileged position of the histoin-compatible fetus and placenta is a striking example of a physiologic immunoregulatory mechanism. This study was designed to examine the effects of human chorionic gonadotropin (HCG) on the recognitive proliferative phase and the cytotoxic effector phase of in vitro cell-mediated immune responsiveness, since HCG has previously been reported to be immunosuppressive in vitro and in vivo. Commercial preparations of HCG were found to be potent inhibitors of lymphocyte proliferative responses to nonspecific mitogens like phytohemagglutinin (PHA), specific antigens such as streptolysin-O (SLO), and allogeneic cells as measured in the one-way mixed leukocyte response. Cytotoxic effector function of lymphocytes as measured by antibody-dependent cellular cytotoxicity (ADCC) and mitogen-induced cellular cytotoxicity were also markedly inhibited by these preparations. However, the 50% inhibitory concentration varied widely from lot to lot of these commercial materials. After dialysis, a portion of the inhibitory activity was lost from some but not all HCG lots. The dialysate from those lots with diminished activity was found to be immunosuppressive in vitro but contained no HCG detectable by radioimmunoassay. Following dialysis, the immunosuppressive activity of the various HCG lots remained variable and correlated poorly with values for HCG obtained by a double antibody radioimmunoassay. HCG preparations purified to a homogeneity sufficient for amino acid sequence were found to be only minimally immunosuppressive to the in vitro PHA response and had almost no effect on proliferative responses to antigens and allogeneic cells. These data do not support the concept of a primary immunoregulatory role for HCG, but they suggest that other uncharacterized compounds partially co-purified from pregnant urine along with HCG may have such immunoregulatory activity. Further characterization and identification of this immunoregulatory material(s) is essential, since it appears to have many of the properties of an ideal immunosuppressive compound: a) nontoxicity, b) ready reversibility, c) activity at very low concentration, and d) activity on a broad range of cellular immune functions.
SIP application to multimedia telecontrol of power systems (2004)

At present, in our project we are researching about the viability of the enhancement of the basic telecontrol information supplied by SCADA systems by adding multimedia content. SIP is a simple and light protocol, with client-server architecture, which allows to achieve voice and video communications through a data IP network, in similar way as the well-known and widespread HTTP protocol works. So, we consider SIP it good choice to integrate multimedia in telecontrol operation.
Atroposelective Biaryl Coupling with Chiral Catalysts:  Total Synthesis of the Antileishmanial Naphthylisoquinoline Alkaloids Ancistrotanzanine B and Ancistroealaine A (2003)

[reaction: see text] The first total synthesis of the naphthylisoquinoline alkaloid ancistrotanzanine B and its atropo-diastereomer, ancistroealaine A, is described. The key step is the construction of the rotationally hindered and thus stereogenic biaryl axis by Suzuki coupling. While only weak internal asymmetric inductions by the stereogenic center in the dihydroisoquinoline part were observed, much better atropisomeric ratios in favor of ancistrotanzanine B were achieved by the use of chiral catalysts. Both alkaloids, in particular ancistrotanzanine B, show high antileishmanial activities.
The Effects of Voxel Localization and Time of Echo on the Diagnostic Accuracy of Cystic Brain Tumors in 3 Tesla Magnetic Resonance Spectroscopy (2012)

Selection of voxels with the guide of chemical shift imaging map yields to 100% diagnostic sensitivity. If not accessible, the use of the union of peripheral and central voxels enhances the sensitivity when compared to usage of peripheral or central voxels solely.
Recent Advances in Determining the Pathogenesis of Canine Monocytic Ehrlichiosis (1999)

Canine monocytic ehrlichiosis (CME) is a potentially fatal tick-borne disease caused by the rickettsia Ehrlichia canis ([16][1]). The etiologic agent was first recognized in Algeria in 1935 ([8][2]). Since then, it has been reported worldwide, causing extensive morbidity and mortality among domestic
Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds (2003)

The van der Waals volume is a widely used descriptor in modeling physicochemical properties. However, the calculation of the van der Waals volume (V(vdW)) is rather time-consuming, from Bondi group contributions, for a large data set. A new method for calculating van der Waals volume has been developed, based on Bondi radii. The method, termed Atomic and Bond Contributions of van der Waals volume (VABC), is very simple and fast. The only information needed for calculating VABC is atomic contributions and the number of atoms, bonds, and rings. Then, the van der Waals volume (A(3)/molecule) can be calculated from the following formula: V(vdW) = summation operator all atom contributions - 5.92N(B) - 14.7R(A) - 3.8R(NR) (N(B) is the number of bonds, R(A) is the number of aromatic rings, and R(NA) is the number of nonaromatic rings). The number of bonds present (N(B)) can be simply calculated by N(B) = N - 1 + R(A) + R(NA) (where N is the total number of atoms). A simple Excel spread sheet has been made to calculate van der Waals volumes for a wide range of 677 organic compounds, including 237 drug compounds. The results show that the van der Waals volumes calculated from VABC are equivalent to the computer-calculated van der Waals volumes for organic compounds.
Thyroid transcription factor (TTF) ‐1 regulates the expression of midkine (MK) during lung morphogenesis (2003)

Midkine (MK) is a 13-kDa heparin-binding growth factor that is thought to mediate developmental processes, including vasculogenesis, cell migration, and proliferation in various organs. To determine whether MK plays a role during lung morphogenesis, immunostaining for MK was assessed in mouse lung from embryonic day (E) 13 to postnatal day (PN) 24. MK was detected in mesenchymal and respiratory epithelial cells of the peripheral mouse lung from E13.0 to E15.5. From E18.5 to PN1, MK was observed primarily in epithelial cells lining conducting airways and peripheral lung saccules. By PN10, expression was no longer observed in respiratory epithelial cells but was readily detected in small blood vessels in the alveolar region of the lung. Although most respiratory epithelial cells uniformly expressed MK before E13.0, MK was restricted to subsets of cells by E18.5, colocalizing with the Clara cell secretory protein (CCSP) marker in conducting airways and with pro-SPC, a marker specific for alveolar type II pneumocytes. By PN10, MK was not detected in respiratory epithelial cells of the conducting airways and was closely associated with capillary networks. The sites of intense MK staining in the respiratory epithelial cells correlated with sites of expression of thyroid transcription factor (TTF) -1, a transcription factor regulating formation and gene expression in the lung parenchyma. TTF-1 enhanced transcription of the mouse MK gene promoter, acting on TTF-1 regulatory elements located in the 5'-region of the gene. Furthermore, MK expression was not detected in lungs of TTF-1 null mice. TTF-1 regulates expression of MK in the lung. The temporal/spatial distribution of midkine is consistent with a potential role in paracrine signaling during lung morphogenesis.
Clinical Course and Flow Cytometric Analysis of Paroxysmal Nocturnal Hemoglobinuria in the United States and Japan (2004)

: To determine and directly compare the clinical course of white and Asian patients with paroxysmal nocturnal hemoglobinuria (PNH), data were collected for epidemiologic analysis on 176 patients from Duke University and 209 patients from Japan. White patients were younger with significantly more classical symptoms of PNH including thrombosis, hemoglobinuria, and infection, while Asian patients were older with more marrow aplasia. The mean fraction of CD59-negative polymorphonuclear cells (PMN) at initial analysis was higher among Duke patients than Japanese patients. In both cohorts, however, a larger PNH clone was associated with classical PNH symptoms, while a smaller PNH clone was associated with marrow aplasia. Thrombosis was significantly more prevalent in white patients than Asian patients, and was associated with a significantly higher proportion of CD59-negative PMN. For individual patients, CD59-negative populations varied considerably over time, but a decreasing PNH clone portended hematopoietic failure. Survival analysis revealed a similar death rate in each group, although causes of death were different and significantly more Duke patients died from thrombosis. Japanese patients had a longer mean survival time (32.1 yr vs. 19.4 yr), although Kaplan-Meier survival curves were not significantly different. Poor survival in both groups was associated with age over 50 years, severe leukopenia/neutropenia at diagnosis, and severe infection as a complication; additionally, thrombosis at diagnosis or follow-up for Duke patients and renal failure for Japanese patients were poor prognostic factors. These data identify important differences between white and Asian patients with PNH. Identification of prognostic factors will help the design of prospective clinical trials for PNH.
Differential Expression of Proliferation-Associated Molecules in Individual Micrometastatic Carcinoma Cells (1993)

Although support from clinical follow-up is still needed, this study demonstrates that, beyond the mere presence of micrometastatic cells in bone marrow, useful prognostic information can be obtained by analysis of additional cell growth markers.
JUCS - Journal of Universal Computer Science (2020)

Since there have been a number of online social networking services (SNS), we have been experiencing new social phenomena around us.Traditional social network analysis methods [Gan and Zhu 2007, Jung 2010] might have difficulties efficiently understanding the large-scale social data from such SNS [Jung 2012].Moreover, as the area of social networks is a highly cross-disciplinary one, we aim to foster and develop sustainable collaborations between Computer Science and Informatics, Sociology, Cognitive Science and Psychology, Geographic and Environmental Science, Biology, and Health and Social Sciences [Jung 2009a].This will provide an opportunity to push further the discussion regarding the potential of social networks and their applications across these communities.Due to their scale, complexity and dynamics, these networks are extremely difficult to analyze in terms of traditional social network analysis methods .On the other hand, the data about human communication, common activities and collaboration simultaneously provide new opportunities for new applications [Jung 2008b, Jung 2008a].Thus, this special issue is focused on an analysis of these large-scale social structures and what is more important to identify the areas where social network analysis can be applied and provide the knowledge that is not accessible for other types of analysis.Additionally, applications of social networks analysis can be investigated either from a static or dynamic perspective.We seek for business and industrial applications of social network analysis that help to solve real-world problems.The area of social networks analysis and its applications bring together researchers and practitioners from different fields and the main goal of this special issue is to provide an opportunity to share visions, research achievements and solutions as well as to establish worldwide cooperative research and development.At the same time, we want to provide a platform
Thermal conductivity of GaN films: Effects of impurities and dislocations (2002)

We report details of the calculation of the lattice thermal conductivity κ in wurtzite GaN. Numerical simulations are performed for n-type wurtzite GaN with different density of silicon dopants, point defects and threading dislocations. Using the material specific model we verified the experimentally observed linear decrease of the room-temperature thermal conductivity with the logarithm of the carrier density n. The decrease was attributed mostly to the increased phonon relaxation on dopants. Our calculations show that the increase in the doping density from 1017 to 1018 cm−3 leads to about a factor of 2 decrease in thermal conductivity from 1.77 W/cm K to 0.86 W/cm K. We have also established that the room-temperature thermal conductivity in GaN can be limited by dislocations when their density is high, e.g., ND&gt;1010 cm−2. The obtained results are in good agreement with experimental data. The developed calculation procedure can be used for accurate simulation of self-heating effects in GaN-based devices.
Fuel Deoxygenation and Aircraft Thermal Management (2006)

Phyre Technologies, Inc., under Phase I and Phase II Small Business Innovative Research (SBIR) programs, has developed a proprietary and unique deoxygenation system which is capable of reducing the dissolved oxygen levels in aviation fuel to 1 ppm or below. This technological breakthrough is expected to allow the development of compact, lightweight and highly efficient fuel deoxygenation systems that can substantially increase the thermal stability of military and commercial aviation jet fuels including diesel and kerosenebased fuels that are used in ground-based turbine-powered generators. In addition to the deoxygenation of fuel, this system is also capable of deoxygenating fuel tank ullage space gas – thereby operating both as a fuel deoxygenator and a more environmentally friendly alternative to conventional OBIGGS. In this paper the overall design of the equipment, operating conditions and results of initial testing of jet and diesel fuels will be discussed.
Dynamic Impact Response of Human Cadaveric Forearms Using a Wrist Brace (1998)

The purpose of this study was to compare the dynamic impact response of braced and unbraced cadaveric wrists using a commercially available wrist guard. Twelve arms were harvested from six cadavers. Each pair of forearms, one with and one without a brace, were impacted using a modified guillotine-type drop fixture placed over a force platform. Using a piece-wise linear regression analysis, we identified four phases of dynamic loading in the vertical force profile before fracture. These phases included an initial linear loading phase starting at impact, followed by a nonlinear phase, a second rapid linear loading phase, and a final nonlinear loading phase to failure. Three transition points were identified that defined the boundaries of the linear loading phases. Vertical force and impulse were significantly higher (P < 0.01) at each transition point and at failure in all braced specimens compared with unbraced specimens. However, the most noticeable differences were found during the initial two loading phases. Time to each transition point and to failure was not significantly different (P > 0.27) between the braced and unbraced wrists. The results of this study differ from those obtained under more quasistatic loading conditions. Dynamic impact testing suggests that wrist guards may have a prophylactic effect during low-energy dynamic impact situations.
Palladium-Catalyzed Mono-<i>N</i>-allylation of Unprotected Anthranilic Acids with Allylic Alcohols in Aqueous Media (2011)

Palladium-catalyzed N-allylation of anthranilic acids 1a-j with allyl alcohol 2a in the presence of Pd(OAc)(2), sodium diphenylphosphinobenzene-3-sulfonate (TPPMS) in THF-H(2)O at room temperature gave only mono-N-allylated anthranilic acids 3a-j in good yields (70-98%). The reactions of 4-bromoanthranilic acid 1i with 2-methyl-3-buten-2-ol 2b showed complete chemoselectivity in N-allylation (neutral conditions) and C-vinylation (basic conditions). In our catalytic system, the keys to success are use of an unprotected anthranilic acid as a starting material and the presence of water in the reaction medium. The carboxyl group of anthranilic acid and water may play important roles for the smooth generation of the π-allyl palladium species by activation of the hydroxyl group of the allylic alcohol.
Inertial-Kinect Fusion for Outdoor 3D Navigation (2013)

The lightweight and low-cost 3D sensing device, such as Microsoft Kinect, has gained much attention in computer vision and robotics community.Although quite promising and successful for indoor applications, its outdoor usage has been significantly hampered by its short detection range (around 4 meters) coupled with ambient infrared interference.This paper addresses the theoretical and practical development of an Inertial-Kinect fused SLAM framework that can handle the 3D to 2D degeneration in Kinect sensing, called a depth dropout problem.The vision node is designed to provide either full 6DOF or partial 5DOF vehicle pose measurements depending on the depth availability, whilst the low-cost inertial system designed in house (less than $40AUD) enables continuous metric mapping and navigation.Indoor and outdoor experiment results are provided, demonstrating the robustness of the proposed approach in a challenging environmental conditions.