gebhart/patrepeval huggingface dataset:
A Declarative and Expressive Approach to Control Forwarding Paths in Carrier-Grade Networks (2015)

SDN simplifies network management by relying on declarativity (high-level interface) and expressiveness (network flexibility). We propose a solution to support those features while preserving high robustness and scalability as needed in carrier-grade networks. Our solution is based on (i) a two-layer architecture separating connectivity and optimization tasks; and (ii) a centralized optimizer called framework, which translates high-level goals expressed almost in natural language into compliant network configurations. Our evaluation on real and synthetic topologies shows that framework improves the state of the art by (i) achieving better trade-offs for classic goals covered by previous works, (ii) supporting a larger set of goals (refined traffic engineering and service chaining), and (iii) optimizing large ISP networks in few seconds. We also quantify the gains of our implementation, running Segment Routing on top of IS-IS, over possible alternatives (RSVP-TE and OpenFlow).
Texture Generation with Neural Cellular Automata (2021)

Neural Cellular Automata (NCA) have shown a remarkable ability to learn the required rules to "grow" images, classify morphologies, segment images, as well as to do general computation such as path-finding. We believe the inductive prior they introduce lends itself to the generation of textures. Textures in the natural world are often generated by variants of locally interacting reaction-diffusion systems. Human-made textures are likewise often generated in a local manner (textile weaving, for instance) or using rules with local dependencies (regular grids or geometric patterns). We demonstrate learning a texture generator from a single template image, with the generation method being embarrassingly parallel, exhibiting quick convergence and high fidelity of output, and requiring only some minimal assumptions around the underlying state manifold. Furthermore, we investigate properties of the learned models that are both useful and interesting, such as non-stationary dynamics and an inherent robustness to damage. Finally, we make qualitative claims that the behaviour exhibited by the NCA model is a learned, distributed, local algorithm to generate a texture, setting our method apart from existing work on texture generation. We discuss the advantages of such a paradigm.
v-src Inhibits Differentiation via an Extracellular Intermediate(s) (1985)

Murine 3T3L1 preadipocytes transformed by avian sarcoma virus were unable to differentiate in response to insulin or dexamethasone plus 1-methyl-3-isobutylxanthine, both potent inducers of differentiation of the nontransformed 3T3L1 parental line. Conditioned medium from transformed cells contained a relatively heat-stable factor(s) which inhibited the differentiation of untransformed parental 3T3L1 cells but did not induce any changes in their morphology. A protease-sensitive mitogen was also detected in the medium. The relationship between the two activities remains to be elucidated.
Structure-Based Design of Hepatitis CVirus Vaccines That Elicit NeutralizingAntibody Responses to a ConservedEpitope (2017)

Despite recent advances in therapeutic options, hepatitis C virus (HCV) remains a severe global disease burden, and a vaccine can substantially reduce its incidence. Due to its extremely high sequence variability, HCV can readily escape the immune response; thus, an effective vaccine must target conserved, functionally important epitopes. Using the structure of a broadly neutralizing antibody in complex with a conserved linear epitope from the HCV E2 envelope glycoprotein (residues 412 to 423; epitope I), we performed structure-based design of immunogens to induce antibody responses to this epitope. This resulted in epitope-based immunogens based on a cyclic defensin protein, as well as a bivalent immunogen with two copies of the epitope on the E2 surface. We solved the X-ray structure of a cyclic immunogen in complex with the HCV1 antibody and confirmed preservation of the epitope conformation and the HCV1 interface. Mice vaccinated with our designed immunogens produced robust antibody responses to epitope I, and their serum could neutralize HCV. Notably, the cyclic designs induced greater epitope-specific responses and neutralization than the native peptide epitope. Beyond successfully designing several novel HCV immunogens, this study demonstrates the principle that neutralizing anti-HCV antibodies can be induced by epitope-based, engineered vaccines and provides the basis for further efforts in structure-based design of HCV vaccines.\nIMPORTANCE: Hepatitis C virus is a leading cause of liver disease and liver cancer, with approximately 3% of the world's population infected. To combat this virus, an effective vaccine would have distinct advantages over current therapeutic options, yet experimental vaccines have not been successful to date, due in part to the virus's high sequence variability leading to immune escape. In this study, we rationally designed several vaccine immunogens based on the structure of a conserved epitope that is the target of broadly neutralizing antibodies. In vivo results in mice indicated that these antigens elicited epitope-specific neutralizing antibodies, with various degrees of potency and breadth. These promising results suggest that a rational design approach can be used to generate an effective vaccine for this virus.
B-DNA structure is intrinsically polymorphic: even at the level of base pair positions (2011)

Increasingly exact measurement of single crystal X-ray diffraction data offers detailed characterization of DNA conformation, hydration and electrostatics. However, instead of providing a more clear and unambiguous image of DNA, highly accurate diffraction data reveal polymorphism of the DNA atomic positions and conformation and hydration. Here we describe an accurate X-ray structure of B-DNA, painstakingly fit to a multistate model that contains multiple competing positions of most of the backbone and of entire base pairs. Two of ten base-pairs of CCAGGCCTGG are in multiple states distinguished primarily by differences in slide. Similarly, all the surrounding ions are seen to fractionally occupy discrete competing and overlapping sites. And finally, the vast majority of water molecules show strong evidence of multiple competing sites. Conventional resolution appears to give a false sense of homogeneity in conformation and interactions of DNA. In addition, conventional resolution yields an average structure that is not accurate, in that it is different from any of the multiple discrete structures observed at high resolution. Because base pair positional heterogeneity has not always been incorporated into model-building, even some high and ultrahigh-resolution structures of DNA do not indicate the full extent of conformational polymorphism.
P2Y1Purinoceptor-Mediated Ca2+Signaling and Ca2+Wave Propagation in Dorsal Spinal Cord Astrocytes (2000)

ATP is known to act as an extracellular messenger mediating the propagation of Ca(2+) waves in astrocyte networks. ATP mediates Ca(2+) waves by activating P2Y purinoceptors, which mobilize intracellular Ca(2+) in astrocytes. A number of P2Y purinoceptor subtypes have been discovered, but it is not known which P2Y subtypes participate in transmitting astrocyte Ca(2+) waves. Here, we show that ATP analogs that are selective agonists for the P2Y(1) subtype of purinoceptor caused release of intracellular Ca(2+) in astrocytes from the dorsal spinal cord. The Ca(2+) responses were blocked by adenosine-3'-phospho-5'-phosphosulfate, an antagonist known to selectively inhibit P2Y(1) but not other P2Y purinoceptor subtypes. Also, we show that P2Y(1) mRNA is expressed in dorsal spinal cord astrocytes. Furthermore, expression of P2Y(1) in an astrocytoma cell line lacking endogenous purinoceptors was sufficient to permit propagation of intercellular Ca(2+) waves. Finally, Ca(2+) wave propagation in dorsal spinal cord astrocytes was suppressed by pharmacologically blocking P2Y(1) purinoceptors. Together, these results indicate that dorsal spinal astrocytes express functional P2Y(1) purinoceptors, which participate in the transmission of Ca(2+) waves. Ca(2+) waves in astrocytes have been implicated as a major signaling pathway coordinating glial and neuronal activity; therefore, P2Y(1) purinoceptors may represent an important link in cell-cell signaling in the CNS.
Temperature-Dependent Hall and Field-Effect Mobility in Strongly Coupled All-Inorganic Nanocrystal Arrays (2014)

We report on the temperature-dependent Hall effect characteristics of nanocrystal (NC) arrays prepared from colloidal InAs NCs capped with metal chalcogenide complex (MCC) ligands (In2Se4(2-) and Cu7S4(-)). Our study demonstrates that Hall effect measurements are a powerful way of exploring the fundamental properties of NC solids. We found that solution-cast 5.3 nm InAs NC films capped with copper sulfide MCC ligands exhibited high Hall mobility values over 16 cm(2)/(V s). We also showed that the nature of MCC ligands can control doping in NC solids. The comparative study of the temperature-dependent Hall and field-effect mobility values provides valuable insights concerning the charge transport mechanism and points to the transition from a weak to a strong coupling regime in all-inorganic InAs NC solids.
Energy-efficient localization with OFDM transmission in multipath channels (2017)

In this paper, we investigate the green characteristic of orthogonal frequency-division multiplexing (OFDM) transmissions in terms of range estimation and localization in multipath channels, relative to the pseudo-random noise (PN) transmissions. Based on the analysis of the fundamental bounds in gentle multipath channels, we observe that the required transmit energy for OFDM is proved to be much more efficient than that of PN to acquire a fixed ranging and positioning accuracy. Furthermore, the localization performance and the optimal network topology for attaining the best accuracy are presented. Numerical results, for both gentle multipath channels and nonseparable multipath channels, show a consistency with the proposed theory.
Researchenhancement of HIV infection is donor-dependent and correlates with the levels of SEVI (2010)

Background: HIV-1 is usually transmitted in the presence of semen. We have shown that semen boosts HIV-1 infection and contains fragments of prostatic acid phosphatase (PAP) forming amyloid aggregates termed SEVI (semen-derived enhancer of viral infection) that promote virion attachment to target cells. Despite its importance for the global spread of HIV-1, however, the effect of semen on virus infection is controversial. Results: Here, we established methods allowing the meaningful analysis of semen by minimizing its cytotoxic effects and partly recapitulating the conditions encountered during sexual HIV-1 transmission. We show that semen rapidly and effectively enhances the infectivity of HIV-1, HIV-2, and SIV. This enhancement occurs independently of the viral genotype and coreceptor tropism as well as the virus producer and target cell type. Semen-mediated enhancement of HIV-1 infection was also observed under acidic pH conditions and in the presence of vaginal fluid. We further show that the potency of semen in boosting HIV-1 infection is donor dependent and correlates with the levels of SEVI. Conclusions: Our results show that semen strongly enhances the infectivity of HIV-1 and other primate lentiviruses and that SEVI contributes to this effect. Thus, SEVI may play an important role in the sexual transmission of HIV-1 and addition of SEVI inhibitors to microbicides may improve their efficacy.
Short Frame Length Approximation for IRSA (2020)

In this letter, we propose a short-frame (SF) approximation for the packet loss rate of Irregular Repetition Slotted ALOHA (IRSA) particularly suitable for very short frames, up to 50 slots. The reason for limiting the frame size is to allow low-latency communications, a typical requirement in Industrial Internet of Things (IIoT) applications. We extend the Error Floor approximation (EF) through a recursive evaluation of inter-related stopping sets (STs). The tighter approximation yields the user degree distribution that minimizes the packet loss rate (PLR). For a scenario with 10 slots and 5 users, the degree distribution optimized adopting the SF approximation results in a 20% lower PLR compared to the one optimized with the EF approximation.
Advanced Development of Space Photovoltaic Concentrators Using Robust Lenses, Multi-Junction Cells, & Graphene Radiators (2018)

At the past three PVSCs [1]–[3], our team has presented recent advances in our space photovoltaic concentrator technology. In the past year, under multiple NASA-funded research and technology development programs, our team has made much additional progress in the advanced development of space photovoltaic concentrators. New robust Fresnel lenses, new high-efficiency multi-junction cells, and new graphene radiators have been developed. The paper will present the latest advances in this technology.
Three distinct classes of regulatory cytokines control endothelial cell MHC antigen expression. Interactions with immune gamma interferon differentiate the effects of tumor necrosis factor and lymphotoxin from those of leukocyte alpha and fibroblast beta interferons. (1988)

Recombinant preparations of TNF and lymphotoxin (LT) increase the expression of class I MHC antigens on cultured human endothelial cells (EC) without inducing expression of class II antigens. These actions are similar to those of rIFN-alpha or rIFN-beta. However, TNF and LT differ from IFN-alpha/beta in that the former synergize with IFN-gamma for class I regulation whereas the latter do not. Furthermore, LT or TNF do not affect IFN-gamma-mediated class II induction at optimal class I inducing concentrations (100 U/ml), whereas IFN-alpha and IFN-beta (at their optimal concentrations of 1,000 U/ml) are strikingly inhibitory. LT and TNF also can further increase expression of class I antigens on cells already maximally stimulated by IFN-alpha or IFN-beta. A recombinant preparation of IL-6 (formerly called 26-kD protein, IFN-beta 2, or B cell stimulating factor 2) was without effect on class I expression in EC. These data make it seem unlikely that the actions of LT or TNF on EC expression of MHC antigens are mediated through autocrine or paracrine production of IFN-alpha, IFN-beta or IL-6. More importantly, they suggest that LT or TNF are more likely to be immunostimulatory, whereas IFN-alpha or IFN-beta are more likely to be immunoinhibitory in vivo, a consideration of potential relevance for cytokine administration to various patient populations.
Promoting Sustainable Print Behaviour (2012)

We have designed and developed the Personal Assessment Tool (PAT) to make users aware of the impact of their behavior on the environment and helping them to reduce it. PAT aims at promoting more sustainable print behavior in a corporate work environment. We have deployed and experimented PAT in our research center and describe this experiment along with preliminary findings and observations. From these findings we conclude that PAT definitely motivated the participating users to improve their print behavior. Nevertheless it also highlighted the constrained aspects of printing in a work environment calling for organizational changes of established work processes.
Effects of Boundary Layer Ingesting (BLI) Propulsion Systems on Engine Cycle Selection and HWB Vehicle Sizing (2012)

A methodology for analyzing the boundary layer ingestion technology on a hybrid wing body aircraft has been developed using a simplified boundary layer analysis based on computation fluid dynamic results. With certain assumptions, a method for calculating the boundary layer velocity profiles across the flight envelope was shown using a log-wake velocity profile. This boundary layer profile was integrated over the surface of an assumed “D-shape” inlet to produce the inlet total pressure, temperature, and the ratio of the area averaged Mach number to the free-stream Mach number. The resulting curves were used within the EDS multi-disciplinary environment to analyze an HWB aircraft with BLI and other N+2 technologies over a range of cycle design parameters and for varying inlet aspect ratios. Aerothermodynamic engine cycle design explorations are performed that show that the candidate engine cycle selection that minimizes design mission fuel burn depends greatly on the assumed negative impacts BLI has on the engine performance.
Correlation between the Charge of Proteins in Solution and in the Gas Phase Investigated by Protein Charge Ladders, Capillary Electrophoresis, and Electrospray Ionization Mass Spectrometry (1998)

Charge ladders of bovine carbonic anhydrase II, hen egg-white lysozyme, and bovine pancreatic trypsin inhibitor, prepared by partial acetylation of primary amino groups on the surface of the protein, have been analyzed by capillary electrophoresis (CE) and on-line electrospray ionization mass spectrometry (ESIMS) using solution conditions that maintain the native structure of the protein. CE was used to separate the proteins that constitute the charge ladder into individual “rungs”protein derivatives that have the same number of acetylated amino groups and approximately the same net charge in solution. ESI was used to produce ions in the gas phase of the proteins that constitute each rung of the charge ladder; the mass spectra of these ions were obtained and analyzed. The distributions in charge states observed in the gas phase for the groups of proteins comprising each rung of the charge ladders were narrow, consistent with the retention of a compact structure of the proteins in the gas phase, and substantially independent of the number of acetylated amino groups. The ions observed in the gas phase had surface charge densities in a relatively narrow range of ∼0.9−1.5 units of charge per 103 Å2 of surface area (as estimated from crystallographic structures). These results demonstrate that the distribution of charge states for proteins produced in the gas phase by ESI do not necessarily reflect the net charge of the protein in solution or the number of amino groups on the protein.
The p38 and NFκB signaling protein activation involved in glycitein protective effects on isoproterenol-treated H9c2 cardiomyoblast cells (2012)

Heart disease (HD) is greatly associated with gender and clinical evidence shows that increased serum norepinephrine levels are found in patients with HD. This study investigates the cardio-protective effect of glycitein, a selective estrogen receptor modulator (SERM) from soy bean extract, on H9c2 cardiomyoblast cells treated with isoproterenol (ISO, a norepinephrine analog). The image data and results from western blotting showed that ISO treatment was capable of inducing cellular apoptosis, especially the mitochondrial dependent pathway. Glycitein treatment could suppress mitochondrial pro-apoptotic proteins expression including caspase-9 and caspase-3 in H9c2 treated with ISO. In contrast, several survival proteins were expressed in H9c2 cells treated with glycitein, such as phosphor (p)-Akt, p-Bad and Akt. We confirmed that the protective role of glycitein was partially mediated through the expression of p-38 and NFκB proteins by adding several pathway inhibitors.
Kinetics of isocyanate amine reactions (1987)

Development of polyurea-urethane and polyurea reaction injection molding (RIM) systems has created a need for kinetics of polyurea formation. Adiabatic batch reactions in solution were used to determine heats of reaction and relative reactivity of several aromatic amines and n-butanol with phenyl isocyanate (PI). In addition to comparing times required to reach 25, 50 and 75% conversion for both catalyzed and uncatalyzed reactions, n-th order models with Arrhenius rate constants were used to fit some of the exotherms. The reaction of 3,5-diethyl toluene (2,4 and 2,6)-diamine and PI could not be modeled due to unequal reactivity of the two amine groups. This unequal reactivity was studied using high performance liquid chromatography (HPLC) separation of the reaction products. The reactions of primary aliphatic amines and aromatic isocyanates were too rapid to be monitored in the batch apparatus. With a flow apparatus the reaction half time was estimated to be ∼ 0.002 s.
The Protein Kinase KIS Impacts Gene Expression during Development and Fear Conditioning in Adult Mice (2012)

The brain-enriched protein kinase KIS (product of the gene UHMK1) has been shown to phosphorylate the human splicing factor SF1 in vitro. This phosphorylation in turn favors the formation of a U2AF(65)-SF1-RNA complex which occurs at the 3' end of introns at an early stage of spliceosome assembly. Here, we analyzed the effects of KIS knockout on mouse SF1 phosphorylation, physiology, adult behavior, and gene expression in the neonate brain. We found SF1 isoforms are differently expressed in KIS-ko mouse brains and fibroblasts. Re-expression of KIS in fibroblasts restores a wild type distribution of SF1 isoforms, confirming the link between KIS and SF1. Microarray analysis of transcripts in the neonate brain revealed a subtle down-regulation of brain specific genes including cys-loop ligand-gated ion channels and metabolic enzymes. Q-PCR analyses confirmed these defects and point to an increase of pre-mRNA over mRNA ratios, likely due to changes in splicing efficiency. While performing similarly in prepulse inhibition and most other behavioral tests, KIS-ko mice differ in spontaneous activity and contextual fear conditioning. This difference suggests that disregulation of gene expression due to KIS inactivation affects specific brain functions.
Cardiomyocyte Regeneration: A Consensus Statement. (2017)

Cell therapy is an exciting option for repairing the injured heart, one that has attracted considerable interest over the past 15 years. Consensus exists that the injection/infusion or tissue-based implantation of various cell types may exert therapeutic effects,1–3 and there is general agreement that additional molecular, translational, and clinical studies are required to define the optimal cell source, method of delivery, and underlying mechanism(s) of action.

One of the remaining questions in this field pertains to cardiomyocyte turnover under normal and diseased conditions and its contribution to the beneficial effects of cell therapy. Although results published in the literature have not been consistent, we believe that the time is ripe to formulate a consensus for many of the pertinent questions.

It is important to emphasize that the focus of this consensus statement is on cardiomyocyte renewal; it is not on cell therapy in general. Although we touch on some aspects of therapeutic strategies based on delivery of exogenous cells, our intent here is to define areas of agreement and areas requiring further elucidation related to the regenerative potential of the myocardium itself.

We have included references to the scientific literature throughout the document. Although it is impossible for us to include all publications in this expansive field, representative studies that corroborate statements herein have been cited.

1. Definition of cardiomyocyte renewal.
 In this consensus statement, the term cardiomyocyte renewal is defined as the ability to replace lost cardiomyocytes by new ones. It is distinct from the turnover of cardiac proteins or the generation of polyploid cardiomyocytes (ie, those harboring >2 sets of chromosomes), either by nuclear division giving rise to multinucleation or by duplication of DNA without nuclear division resulting in polyploid nuclei.

2. Naturally occurring cardiomyocyte renewal and proliferation.
 1. During normal mammalian development
 1. Growth of the heart during …