gebhart/patrepeval huggingface dataset:
Securing systems against external programs (1998)

Internet users routinely and often unknowingly download and run programs, such as Java applets; and some Web servers let users upload external programs and run them on the server. Although the practice of executing these external programs has the sanction of widespread use, its security implications haven't yet been systematically addressed. In the brief, dynamic history of the Internet, such a situation is not unusual. New communication mechanisms and computing paradigms are often implemented before the security issues they engender have been rigorously analyzed. Our goal is to address this problem in the subdomain of external programs by systematically outlining security issues and classifying current solutions. Our focus is solely on protecting a host from external programs. We do not address the problem of protecting the communication medium or protecting an external program from runtime systems. Furthermore, we do not address the problem of correctly identifying the source of an external program (authentication). We start our inquiry by reviewing the relevant models of computation, followed by an overview of the security problems associated with them. We then classify both the problems and the existing solutions using a resource-centric model that distinguishes problems associated with resource access from those associated with resource consumption. Finally, we classify solutions to each problem according to how and when they are applied.
LQR-trees: Feedback motion planning on sparse randomized trees (2009)

Recent advances in the direct computation of Lyapunov functions using convex optimization make it possible to efficiently evaluate regions of stability for smooth nonlinear systems. Here we present a feedback motion planning algorithm which uses these results to efficiently combine locally-valid linear quadratic regulator (LQR) controllers into a nonlinear feedback policy which probabilistically covers the reachable area of a (bounded) state space with a region of stability, certifying that all initial conditions that are capable of reaching the goal will stabilize to the goal. We demonstrate the performance of this systematic nonlinear feedback control design algorithm on the model underactuated systems and discuss the potential for control of more complicated control problems like bipedal walking.
Targeting the Epidermal Growth Factor Receptor Can Counteract the Inhibition of Natural Killer Cell Function Exerted by Colorectal Tumor-Associated Fibroblasts (2018)

Mesenchymal stromal cells (MSC) present in the tumor microenvironment [usually named tumor-associated fibroblasts (TAF)] can exert immunosuppressive effects on T and natural killer (NK) lymphocytes, favoring tumor immune escape. We have analyzed this mechanism in colorectal carcinoma (CRC) and found that co-culture of NK cells with TAF can prevent the IL-2-mediated NKG2D upregulation. This leads to the impairment of NKG2D-mediated recognition of CRC cells, sparing the NK cell activation through DNAM1 or FcγRIIIA (CD16). <i>In situ</i>, TAF express detectable levels of epidermal growth factor receptor (EGFR); thus, the therapeutic anti-EGFR humanized antibody cetuximab can trigger the antibody-dependent cellular cytotoxicity of TAF, through the engagement of FcγRIIIA on NK cells. Importantly, in the tumor, we found a lymphoid infiltrate containing NKp46<sup>+</sup>CD3<sup>-</sup> NK cells, enriched in CD16<sup>+</sup> cells. This population, sorted and cultured with IL-2, could be triggered <i>via</i> CD16 and <i>via</i> NKG2D. Of note, <i>ex vivo</i> NKp46<sup>+</sup>CD3<sup>-</sup> cells were able to kill autologous TAF; <i>in vivo</i>, this might represent a control mechanism to reduce TAF-mediated regulatory effect on NK cell function. Altogether, these findings suggest that MSC from the neoplastic mucosa (TAF) of CRC patients can downregulate the immune cell recognition of CRC tumor cells. This immunosuppression can be relieved by the anti-EGFR antibody used in CRC immunotherapy.
A double Nyquist digital product detector for quadrature sampling (1992)

A technique for digitally obtaining the in-phase (I) and quadrature (Q) components of an IF signal is presented. Initially, the input bandpass signal is mixed to a carrier frequency that is one-fourth of the sampling rate of a single A/D converter. The digitized bandpass signal is converted into its I and Q components at one-half the A/D sample rate by a digital product detector (DPD) composed of a commutator, two sign alternators, and two FIR fractional-phase interpolator filters. This simple structure can yield image performance that is limited by A/D quantization using relatively low interpolator filter orders and IF bandwidths as large as one-half the sampling rate of the A/D converter. The DPD performs Nyquist limit demodulation of the sampled bandpass signal and, therefore, requires a minimal sampling rate. The theory of operation, an analytic proof, design methodology, and simulated performance results are presented. Simulated results show that -86 dB images can be obtained with 8-tap FIR interpolators and a 12 bit A/D converter. A VLSI implementation is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Applied Pyrolysis Handbook (2006)

Analytical pyrolysis allows scientists to use routine laboratory instrumentation for analyzing complex, opaque, or insoluble samples more effectively than other analytical techniques alone. Applied Pyrolysis Handbook, Second Edition is a practical guide to the application of pyrolysis techniques to various samples and sample types for a dive
Characterization of 4‐hydroxyphenylpyruvate dioxygenase (1992)

The primary structure of Pseudomonas 4-hydroxyphenylpyruvate dioxygenase was determined. Sequence degradation of the intact protein and of peptides from three different digests of the carboxymethylated protein established a 357-residue polypeptide chain with a free alpha-amino group. Hydroxylamine cleavage at a single Asn-Gly sequence was useful. Comparisons with known structures in data banks revealed no close relationship with other characterized proteins. The human enzyme has a related composition, suggesting that also the eukaryotic form belongs to this protein type, but with a blocked N-terminus like in many other eukaryotic intracellular proteins. Secondary structure predictions suggest an alpha/beta mixed structure, fairly typical of globular proteins, without long segments of hydrophobicity or charge, although a region in the middle of the C-terminal third of the subunit appears to have the most extreme properties. A ferric centre, correlating with enzyme activity and absorbance at 595 nm, has previously been assigned to tyrosinate coordination. The Tyr and His distributions, and the position of a single Cys residue, all suggest a few likely sites, outside the C-terminal segment, for this centre.
Natural guanidine derivatives (1999)

R. G. S. Berlinck, Nat. Prod. Rep., 1999, 16, 339 DOI: 10.1039/A900338J
Early events in hepatitis C virus infection of chimpanzees. (1990)

The cytoplasmic antigen and ultrastructural changes we described previously for chimpanzees (Pan troglodytes) infected with hepatitis C virus (HCV) or with hepatitis D virus have recently been shown to be indirect measures of viral replication and appear to represent a host response to the expression or action of interferon. The time of appearance of these changes in hepatocytes during HCV infection, when compared with similar changes in hepatitis D virus infection, suggests a very early replicative phase for HCV. To investigate the early events in HCV infection, we infected two chimpanzees with HCV and obtained blood and liver biopsy samples from them daily during the first 10 days of infection. The early stage of infection with regard to HCV replication, antigen expression, and ultrastructural changes was similar in both chimpanzees. When tested by cDNA/polymerase chain reaction, HCV sequences became detectable in the serum as early as 3 days after inoculation and remained positive through the peak of aminotransferase elevations. In one chimpanzee the peak of virus production appeared to be 7 weeks after inoculation, which was coincident with rising enzyme values. The cytoplasmic antigen, detected by immunofluorescence, and ultrastructural changes, detected by electron microscopy, became positive in hepatocytes 3 and 6 days, respectively, after HCV sequences were first detected in serum. Circulating anti-HCV appeared 13 weeks and 32 weeks after inoculation, respectively, in the chimpanzees. These data indicate a very early replicative phase for HCV and a potentially long period of infectivity before the appearance of anti-HCV.
Biochemical and genetic analysis of the yeast proteome with a movable ORF collection (2005)

Functional analysis of the proteome is an essential part of genomic research. To facilitate different proteomic approaches, a MORF (moveable ORF) library of 5854 yeast expression plasmids was constructed, each expressing a sequence-verified ORF as a C-terminal ORF fusion protein, under regulated control. Analysis of 5573 MORFs demonstrates that nearly all verified ORFs are expressed, suggests the authenticity of 48 ORFs characterized as dubious, and implicates specific processes including cytoskeletal organization and transcriptional control in growth inhibition caused by overexpression. Global analysis of glycosylated proteins identifies 109 new confirmed N-linked and 345 candidate glycoproteins, nearly doubling the known yeast glycome.
Interactions Between Human Mesenchymal Stem Cells and Natural Killer Cells (2005)

Mesenchymal stem cells (MSCs) are multipotent progenitor cells representing an attractive therapeutic tool for regenerative medicine. They possess unique immunomodulatory properties, being capable of suppressing T-cell responses and modifying dendritic cell differentiation, maturation, and function, whereas they are not inherently immunogenic, failing to induce alloreactivity to T cells and freshly isolated natural killer (NK) cells. To clarify the generation of host immune responses to implanted MSCs in tissue engineering and their potential use as immunosuppressive elements, the effect of MSCs on NK cells was investigated. We demonstrate that at low NK-to-MSC ratios, MSCs alter the phenotype of NK cells and suppress proliferation, cytokine secretion, and cyto-toxicity against HLA-class I- expressing targets. Some of these effects require cell-to-cell contact, whereas others are mediated by soluble factors, including transforming growth factor-beta1 and prostaglandin E2, suggesting the existence of diverse mechanisms for MSC-mediated NK-cell suppression. On the other hand, MSCs are susceptible to lysis by activated NK cells. Overall, these data improve our knowledge of interactions between MSCs and NK cells and consequently of their effect on innate immune responses and their contribution to the regulation of adaptive immunity, graft rejection, and cancer immunotherapy.
Atomic force microscopy and surface-enhanced Raman spectroscopy. I. Ag island films and Ag film over polymer nanosphere surfaces supported on glass (1993)

The surface roughness and nanometer scale structure of Ag films used for surface-enhanced Raman scattering (SERS) are characterized using atomic force microscopy (AFM). Two important types of thin film based SERS-active surface have been examined in this study: (1) Ag island films (AgIF’s) on smooth, insulating substrates and (2) thick Ag films evaporated over both preroughened and smooth substrates. AFM is demonstrated to be capable of quantitatively defining the three-dimensional (3D) structure of these roughened surfaces. The effects of mass thickness, dm, and thermal annealing on the nanostructure of AgIF’s are studied in detail. Particle size histograms are calculated from the AFM images for both ‘‘as-deposited’’ and annealed IF’s with dm=1.8 and 3.5 nm. Quantitative measurements of the SERS enhancement factor (EF) are coupled with the AFM data and interpreted within the framework of the electromagnetic theory of SERS. AFM images for thick evaporated Ag films over a monolayer of polymer nanospheres (AgFON) shows the clear presence of ‘‘random substructure roughness’’ reducing their utility as controlled roughness surfaces. Similar roughness structures are observed for thick evaporated Ag films on smooth, insulating substrates. Nevertheless, AgFON surfaces are demonstrated to be among the most strongly enhancing thin film based surfaces ever studied with EF’s comparable to those found for electrochemically roughened surfaces. Applications of FON surfaces to ultrahigh sensitivity SERS, anti-Stokes detected SERS, and surface-enhanced hyper-Raman spectroscopy (SEHRS) are reported.
Designing personal tele-embodiment (2002)

At the intersection of telerobotics, computer networking and human social interaction we have chosen to explore an area we identify as personal tele-embodiment. At the core of this research is an emphasis on the individual person rather than the intricate complexities of the machine. While the mechanical elements of our system are essential to its over-all functionality, our research is driven solely by the study and understanding of the social and psychological aspects of extended human-human interactions rather than the latest techno-gadgetry. In this paper we emphasize the importance of the human component and describe the development of one such simple, inexpensive, Internet-controlled, untethered telerobot or PRoP (personal roving presence) that provides several fundamental elements of personal tele-embodiment.
Discovery of a TNF-α Antagonist Using Chondroitin Sulfate Microarrays (2006)

We report the first example of synthetic chondroitin sulfate (CS) microarrays to rapidly identify glycosaminoglycan-protein interactions and probe the specificity of proteins for distinct sulfation sequences. Using the microarrays, we identify a novel interaction between CS and TNF-alpha, a proinflammatory cytokine involved in rheumatoid arthritis, Crohn's disease, and psoriasis. Moreover, we demonstrate that CS-E tetrasaccharides and polysaccharides enriched in the CS-E sulfation motif can inhibit the activity of this therapeutically important cytokine. We anticipate that carbohydrate microarrays will accelerate our understanding of glycosaminoglycan-protein interactions and the role of sulfation in modulating physiological and disease states.
ChemInform Abstract: Discovery of 4‐Amino‐5‐(3‐bromophenyl)‐7‐(6‐morpholino‐pyridin‐3‐yl)pyrido [2,3‐d]pyrimidine (VI), an Orally Active, Non‐Nucleoside Adenosine Kinase Inhibitor. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Some unexpected reactions involving diphenylketene (1992)

Diphenylketene reacted with the 2-azabicyclo[2.2.1]hept-5-enes 5, 6 and 10 by attack on nitrogen to give the piperidones 7, 8 and the cyclopentenols 11 respectively. The same ketene reacted with the cyclohexa-1,3-dienes 16 and 17 to give significant amounts of the [4 + 2] addition products 20 and 21 respectively. The initially formed product from the cycloaddition of the enol ether 23 and diphenylketene is unstable, rearranging to produce the unsaturated ester 24.
B lineage‐restricted rearrangement of a human Igx transgene (1997)

Recent drug-membrane interaction and quantitative structure-activity relationship studies of thioxanthenes and related compounds acting as multidrug resistance (MDR) modifiers pointed to the importance of the stereoisomery for their MDR reversing activity. Therefore a molecular modeling study of trans-(T) and cis-flupentixol (C) was performed in order to elucidate the observed discrepancy between equal binding potency to P-glycoprotein and different MDR reversing activity of the two stereoisomers. The results show that the 2 to 3-fold difference in MDR reversing activity of T compared to C might be related to a different orientation of the molecules in the membrane lipid environment. From the conformations generated by the SYBYL systematic search procedure those comprising local energy minima were selected and further optimized with semiempirical quantum chemistry methods. From the optimized conformations those that corresponded to 1H NMR results on drug conformations in lipid environment were selected for further molecular modeling studies. The electrostatic and lipophilic fields of T and C were compared in order to identify molecular properties related to the activity difference. The results show that the electrostatic fields of the drugs when similar in shape are dissimilar and that the lipophilic and hydrophilic regions are clearer separated in T in comparison with C. This imposes a better fitting of T compared to C to membrane lipid environment in accordance with the observed higher interaction strength of T with phospholipids.
Polymer-Polymer Phase Behavior (1991)

Different polymers can be combined into a single material in many ways, which can lead to a wide range of phase behaviors that directly influence the associated physical properties and ultimate applications. Four factors control polymer-polymer phase behavior: choice of monomers, molecular architecture, composition, and molecular size. Current theories and experiments that deal with the equilibrium thermodynamics and non-equilibrium dynamics of polymer mixtures are described in terms of these experimentally accessible parameters. Two representative molecular architectures, binary linear homopolymer mixtures and diblock copolymers, exhibiting macrophase separation and microphase segregation, respectively, are examined in some detail. Although these model systems are fairly well understood, a myriad of mixing scenarios, with both existing and unrealized materials applications, remain unexplored at a fundamental level.
PPARγ in adipocyte differentiation and metabolism – Novel insights from genome‐wide studies (2010)

Adipocyte differentiation is controlled by a tightly regulated transcriptional cascade in which PPARgamma and members of the C/EBP family are key players. Here we review the roles of PPARgamma and C/EBPs in adipocyte differentiation with emphasis on the recently published genome-wide binding profiles for PPARgamma and C/EBPalpha. Interestingly, these analyses show that PPARgamma and C/EBPalpha binding sites are associated with most genes that are induced during adipogenesis suggesting direct activation of many more adipocyte genes than previously anticipated. Furthermore, an extensive overlap between the C/EBPalpha and PPARgamma cistromes indicate a hitherto unrecognized direct crosstalk between these transcription factors. As more genome-wide data emerge in the future, this crosstalk will likely be found to include several other adipogenic transcription factors.
Sparse Dictionary Learning for Edit Propagation of High-Resolution Images (2014)

We introduce a method of sparse dictionary learning for edit propagation of high-resolution images or video. Previous approaches for edit propagation typically employ a global optimization over the whole set of image pixels, incurring a prohibitively high memory and time consumption for high-resolution images. Rather than propagating an edit pixel by pixel, we follow the principle of sparse representation to obtain a compact set of representative samples (or features) and perform edit propagation on the samples instead. The sparse set of samples provides an intrinsic basis for an input image, and the coding coefficients capture the linear relationship between all pixels and the samples. The representative set of samples is then optimized by a novel scheme which maximizes the KL-divergence between each sample pair to remove redundant samples. We show several applications of sparsity-based edit propagation including video recoloring, theme editing, and seamless cloning, operating on both color and texture features. We demonstrate that with a sample-to-pixel ratio in the order of 0.01%, signifying a significant reduction on memory consumption, our method still maintains a high-degree of visual fidelity.
Duncan Guthrie Institute of Medical Genetics, Glasgow, University of Glasgow, Scotland. (1982)

Unbalanced chromosome aberrations detected by routine chromosome diagnostic services can be used for gene mapping by gene dosage. This procedure, once discredited by early observations in Down's syndrome, has now provided some of the most precise intrachromosomal gene localizations known and these are reviewed. Cytogeneticists have an obligation to see that every opportunity is taken to obtain mapping information from suitable cases. Interpretation of cytogenetic findings may be improved by application of appropriate gene dosage studies, and examples are described in which a diagnosis was made possible by such studies. Cytogeneticists may also contribute to human gene mapping by application of the technique of in situ molecular hybridization. The localization of the immunoglobulin kappa light chain genes (IGKV) to the short arm of chromosome 2 reported at this workshop provides the first example of the localization of an unassigned, unique DNA gene sequence by this method. Combined with the use of chromosomal translocations, resolution of assignments to chromosomal sub-bands is possible, and, as suitable DNA clones become available, the technique should have wide applicability in human gene mapping.
Pixelwise Instance Segmentation with a Dynamically Instantiated Network (2017)

Semantic segmentation and object detection research have recently achieved rapid progress. However, the former task has no notion of different instances of the same object, and the latter operates at a coarse, bounding-box level. We propose an Instance Segmentation system that produces a segmentation map where each pixel is assigned an object class and instance identity label. Most approaches adapt object detectors to produce segments instead of boxes. In contrast, our method is based on an initial semantic segmentation module, which feeds into an instance subnetwork. This subnetwork uses the initial category-level segmentation, along with cues from the output of an object detector, within an end-to-end CRF to predict instances. This part of our model is dynamically instantiated to produce a variable number of instances per image. Our end-to-end approach requires no post-processing and considers the image holistically, instead of processing independent proposals. Therefore, unlike some related work, a pixel cannot belong to multiple instances. Furthermore, far more precise segmentations are achieved, as shown by our substantial improvements at high APr thresholds.