gebhart/patrepeval huggingface dataset:
Information leakage from optical emanations (2002)

A previously unknown form of compromising emanations has been discovered. LED status indicators on data communication equipment, under certain conditions, are shown to carry a modulated optical signal that is significantly correlated with information being processed by the device. Physical access is not required; the attacker gains access to all data going through the device, including plaintext in the case of data encryption systems. Experiments show that it is possible to intercept data under realistic conditions at a considerable distance. Many different sorts of devices, including modems and Internet Protocol routers, were found to be vulnerable. A taxonomy of compromising optical emanations is developed, and design changes are described that will successfully block this kind of "Optical Tempest" attack.
Rating scales for analgesics in sore throat (1984)

Clinical Pharmacology and Therapeutics (1984) 36, 151–156; doi:10.1038/clpt.1984.154
Renin inhibitors containing conformationally restricted P1-P1' dipeptide mimetics (1991)

A series of renin inhibitors containing lactam-bridged P1-P1' dipeptide mimetics based on the ACHPA (4(S)-amino-5-cyclohexyl-3(S)-hydroxypentanoic acid) design was studied. The inhibitors were obtained by aldol addition of various lactams with N alpha-Boc-L-cyclohexylalaninal, followed by Boc group removal and acylation with Boc-Phe-His. The aldol diastereomer having the S configuration at the two newly generated stereogenic centers gave optimal enzyme inhibition. Potency was further enhanced in the gamma-lactam ring series by substitution with small hydrophobic groups to mimic the P1' side chain of the renin substrate. Thus, 2(S)-[(Boc-L-phenylalanyl-L-histidyl)amino]-3-cyclohexyl-1(S)-hydroxyl-1 - (1,5,5-trimethyl-2-oxopyrrolidin-3(S)-yl)propane (34) has an IC50 of 1.3 nM in the human plasma renin assay. A variety of substituents on the lactam nitrogen are tolerated and can be used to vary the physical properties of the inhibitor. By using a model of the human renin active site, the conformation of 34 in the enzyme-inhibitor complex is proposed. This modeled conformation is very similar to the solid-state conformation of 2(S)-[(Boc-L-phenylalanyl-L-histidyl)amino]-3-cyclohexyl-1(S)-hydroxyl- 1-(1-methyl-2-oxopyrrolidin-3(S)-yl)propane (36), the structure of which was determined by single-crystal X-ray diffraction analysis. The most potent ACH-PA-lactam renin inhibitors show good selectivity when assayed against other types of aspartic proteinases. By varying the lactam ring substituents, potent and selective inhibitors of cathepsin D and cathepsin E can be obtained.
Purification and properties of the cellular prion protein from Syrian hamster brain (1992)

The cellular prion protein (PrPC) is encoded by a chromosomal gene, and its scrapie isoform (PrPSc) features in all aspects of the prion diseases. Prior to the studies reported here, purification of PrPC has only been accomplished using immunoaffinity chromatography yielding small amounts of protein. Brain homogenates contain two PrPC forms designated PrPC-I and -II. These proteins were purified from a microsomal fraction by detergent extraction and separated by immobilized Cu2+ ion affinity chromatography. PrPC-II appears to be generated from PrPC-I by limited proteolysis of the N-terminus. Fractions enriched for PrPC-I were purified further by cation-exchange chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Greater than 90% of the final product migrated as a broad band of M(r) 33-35 kDa as judged by silver staining after SDS-PAGE. Digestion of PrPC-I with peptide-N-glycosidase (PNGase) compressed the band and shifted its mobility giving an M(r) of 27 kDa. The protocol described should be amenable to large-scale preparation of PrPC, enabling physical comparisons of PrPC and PrPSc.
Photoinitiated Growth of Sub-7 nm Silver Nanowires within a Chemically Active Organic Nanotubular Template (2010)

Self-assembled supramolecular nanotubes of J-aggregated amphiphilic cyanine dye in aqueous solution are employed as chemically active templates for the photoinitiated formation of silver nanowires with a very small and homogeneous diameter of (6.4 +/- 0.5) nm. Key features of the template are (1) its small and well-defined diameter; (2) its photochemical activity, which allows photoinitiation of the structure formation; and (3) the processability in aqueous solution. The latter includes the potential to remove the template after the reaction, or to functionalize it further, e.g. with optoelectronically active polycations, providing access to quasi one-dimensional hybrid structures with well-defined metallic nanowires as a core.
Arthritogenic Monoclonal Antibodies from K/BxN Mice (2002)

Arthritis in the K/BxN mouse model is provoked by pathogenic antibodies (Abs) directed against a ubiquitously expressed protein, glucose-6-phosphate isomerase (GPI). To begin dissecting the repertoire of arthritogenic immunoglobulins (Igs) in the K/BxN model, and to provide a basis for comparison with RA patients we have generated anti-GPI monoclonal Abs (mAbs) from spontaneously activated B cells in the lymphoid organs of arthritic mice. B cell clones with anti-GPI specificities were present at extraordinarily high frequencies in the spleen, and less frequently in other lymphoid organs and in the synovial fluid. None of the anti-GPI mAbs induced arthritis when injected individually into healthy recipients, but most were effective when combined in pairs or larger pools. Arthritogenic combinations depended on mAbs of the IgG1 isotype, which bound to GPI with Kd in the 10(-9) M range, with no indication of cooperative binding between complementing pairs. Pathogenicity was not associated with recognition of a particular epitope, but the ability to form mAb/GPI multimers by simultaneous recognition of different epitopes was clearly required, consistent with the known role of complement and FcRs in this model. Sequence analysis revealed structural similarities amongst the mAbs, indicating that a particular subset of B cells may evade tolerance in K/BxN mice, and that affinity maturation by somatic mutation likely takes place. These results confirm that GPI itself, rather than a cross-reactive molecule, is the target of pathogenic Igs.
Particle Size Distribution Measurement from Millimeters to Nanometers and from Rods to Platelets (2002)

LTP
Investigation of GaN crystal quality on silicon substrates using GaN/AlN superlattice structures (2007)

Abstract The crystal quality of GaN thin film on silicon using GaN/AlN superlattice structures was investigated. The growth was carried out on Si(111) for GaN(0001) in a metal‐organic vapor phase epitaxy system. Various GaN/AlN superlattice intermediate layers have been designed to decrease the dislocation density. The results showed that the etch pit density could be greatly reduced by one order of magnitude. Cross‐sectional transmission electron microscopy (XTEM) study confirmed the efficiency of GaN/AlN superlattice in blocking threading dislocation propagation in GaN crystal. The design of nine period GaN/AlN (20nm/2nm) superlattice has been evidenced to be effective in reducing the dislocation density and improving the crystal quality. In addition, the dislocation bending in GaN/AlN interface and dislocation merging is investigated. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
A facile, stereoselective [2 + 2] photoreaction mediated by cucurbit[8]uril (2001)

The [2 + 2] photoreaction of (E)-diaminostilbene dihydrochloride proceeds with large rate acceleration and high stereoselectivity via formation of a stable 1:2 host-guest complex with curcurbit[8]uril in solution.
Scene-context-dependent reference-frame placement for MPEG video coding (1999)

The MPEG video-compression standard effectively exploits spatial, temporal, and coding redundancies in the algorithm. In its generic form, however, only a minimal amount of scene adaptation is performed. Video can be further compressed by taking advantage of scenes where the temporal statistics allow larger interreference-frame distances. This paper proposes the use of motion analysis (MA) to adapt to scene content. The actual picture type [intracoded (I), predicted (P), or bidirectionally coded (B)] decision is made by examining the accumulation of motion measurements since the last reference frame (either I or P) was labeled. The proposed MA-based adaptive reference frame-placement scheme outperforms the standard fixed-reference frame-placement and adaptive schemes based on histogram of difference. When compared with the standard fixed scheme, depending on the video contents, this proposed algorithm can achieve from 2 to 13.9% savings in bits while maintaining similar quality.
An abuttable CCD imager for visible and X-ray focal plane arrays (1991)

A frame-transfer silicon charge-coupled-device (CCD) imager has been developed that can be closely abutted to other imagers on three sides of the imaging array. It is intended for use in multichip arrays. The device has 420*420 pixels in the imaging and frame-store regions and is constructed using a three-phase triple-polysilicon process. Particular emphasis has been placed on achieving low-noise charge detection for low-light-level imaging in the visible and maximum energy resolution for X-ray spectroscopic applications. Noise levels of 6 electrons at 1-MHz and less than 3 electrons at 100-kHz data rates have been achieved. Imagers have been fabricated on 1000- Omega cm material to maximize quantum efficiency and minimize split events in the soft X-ray regime.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Impacto de la selección de los mecanismos de pago en la producción de atención de salud: ¿están en línea con los objetivos sanitarios? (2008)

The current mechanisms of financial transfer in the Chilean Health Care System imply incentives that are not up to the challenges of the Health Reform initiated in 2002. According to the authors, important modifications are required. We present empirical evidence of the undesired effects of those mechanisms on the overall generation of health services in the last few years. Starting in 2005, the Health Reform introduced Explicit Guarantees (GES) for the provision of certain services, and these are linked to the mechanisms of payment to the providers. There has been a general decrease in the activities of the National Health Services System, an increase of emergency care and in the purchase of external services via the Explicit Guarantees and also via the Free Choice option included in the public system. The reduction of the general activity of the public system is not matched by a fall in productivity: what we observe is a change in the case mix, which is induced mainly by the Explicit Guarantees scheme and its associated commitments. A reduction of access to non GES care may be under way. We describe the general outline of a proposed change in the financial transfer mechanisms, which is being discussed in the health sector.
Heparin Blockade of Thrombin-Induced Smooth Muscle Cell Migration Involves Inhibition of Epidermal Growth Factor (EGF) Receptor Transactivation by Heparin-Binding EGF-Like Growth Factor (2000)

Agonists of G protein-coupled receptors, such as thrombin, act in part by transactivating the epidermal growth factor (EGF) receptor (EGFR). Although at first a ligand-independent mechanism for EGFR transactivation was postulated, it has recently been shown that this transactivation by various G protein-coupled receptor agonists can involve heparin-binding EGF-like growth factor (HB-EGF). Because thrombin stimulation of vascular smooth muscle cell migration is blocked by heparin and because heparin can displace HB-EGF, we investigated the possibility that thrombin stimulation of smooth muscle cells (SMCs) depends on EGFR activation by HB-EGF. In rat SMCs, EGFR phosphorylation and extracellular signal-regulated kinase (ERK) activation in response to thrombin are inhibited not only by the EGFR inhibitor AG1478 and by EGFR blocking antibody but also by heparin and by neutralizing HB-EGF antibody. HB-EGF-dependent signaling induced by thrombin is inhibited by batimastat, which suggests a requirement for pro-HB-EGF shedding by a metalloproteinase. We further demonstrate that this novel pathway is required for the migration of rat and baboon SMCs in response to thrombin. We conclude from these data that the inhibitory effect of heparin on SMC migration induced by thrombin relies, at least in part, on a blockade of HB-EGF-mediated EGFR transactivation.
Fundamental limits of reconstruction-based superresolution algorithms under local translation (2004)

Superresolution is a technique that can produce images of a higher resolution than that of the originally captured ones. Nevertheless, improvement in resolution using such a technique is very limited in practice. This makes it significant to study the problem: "Do fundamental limits exist for superresolution?" In this paper, we focus on a major class of superresolution algorithms, called the reconstruction-based algorithms, which compute high-resolution images by simulating the image formation process. Assuming local translation among low-resolution images, this paper is the first attempt to determine the explicit limits of reconstruction-based algorithms, under both real and synthetic conditions. Based on the perturbation theory of linear systems, we obtain the superresolution limits from the conditioning analysis of the coefficient matrix. Moreover, we determine the number of low-resolution images that are sufficient to achieve the limit. Both real and synthetic experiments are carried out to verify our analysis.
A causal role for ERG in neoplastic transformation of prostate epithelium (2008)

A significant proportion of human prostate cancers carry a chromosomal rearrangement resulting in the overexpression of the ETS transcription factor, ERG; however, the functional significance of this event is poorly understood. We report here that up-regulation of ERG transcript is sufficient for the initiation of prostate neoplasia. In agreement with measurements of ERG transcripts, we found that ERG protein is expressed in neoplastic human prostate epithelium. Overexpression of ERG in prostate cell lines increased cell invasion. Moreover, targeted expression of this transcript in vivo in luminal prostate epithelial cells of transgenic mice results in initiation of prostate neoplasia observed as the development of focal precancerous prostatic intraepithelial neoplasia (PIN). Similar to human cancers, luminal epithelial cells in these PIN lesions displace diminishing in numbers basal epithelial cells and establish direct contact with the stromal cell compartment. Loss of basal cells is considered to be one of the critical hallmarks of human prostate cancer; however, the mechanisms responsible for this event were unknown. We propose that up-regulation of ERG in human prostate cancer activates cell invasion programs that subsequently displace basal cells by neoplastic epithelium. Our data demonstrate that ERG plays an important causal role in the transformation of prostate epithelium and should be considered as a target for prevention or early therapeutic intervention.
The Gene-Finder computer tools for analysis of human and model organisms genome sequences. (1997)

We present a complex of new programs for promoter, 3'-processing, splice sites, coding exons and gene structure identification in genomic DNA of several model species. The human gene structure prediction program FGENEH, exon prediction-FEXH and splice site prediction-HSPL have been modified for sequence analysis of Drosophila (FGENED, FEXD and DSPL), C.elegance (FGENEN, FEXN and NSPL), Yeast (FEXY and YSPL) and Plant (FGENEA, FEXA and ASPL) genomic sequences. We recomputed all frequency and discriminant function parameters for these organisms and adjusted organism specific minimal intron lengths. An accuracy of coding region prediction for these programs is similar with the observed accuracy of FEXH and FGENEH. We have developed FEXHB and FGENEHB programs combining pattern recognition features and information about similarity of predicted exons with known sequences in protein databases. These programs have approximately 10% higher average accuracy of coding region recognition. Two new programs for human promoter site prediction (TSSG and TSSW) have been developed which use Gosh (1993) and Wingender (1994) data bases of functional motifs, respectively. POLYAH program was designed for prediction of 3'-processing regions in human genes and CDSB program was developed for bacterial gene prediction. We have developed a new approach to predict multiple genes based on double dynamic programming, that is very important for analysis of long genomic DNA fragments generated by genome sequencing projects. Analysis of uncharacterized sequences based on our methods is available through the University of Houston, Weizmann Institute of Science email servers and several Web pages at Baylor College of Medicine.
Surface Finish Effects on High-Speed Signal Degradation (2008)

In high-speed circuits, skin effects and dielectric properties are important factors for signal degradation considerations, especially in the microwave frequency region. When surface finishes are applied to prevent traces from oxidation, the electrical properties of traces are affected. In this work, experimental study and finite element method (FEM) based full wave simulation are used to investigate the effects of hot air solder leveling (HASL) and its alternatives on signal integrity. Classical interconnect structures, microstrip line, and differential mode coupled microstrip lines subjected to different finishes are investigated. Our work reveals that the net conductor loss that results from surface finishes is the dominant factor in signal degradation when the clock frequency is within the microwave frequency region. For microstrip line, the influence of surface finishes on signal distortion is negligible; for differential mode coupled microstrip lines, however, the surface finish effects, especially those with high resistivity, can lead to significant signal distortions. These findings are expected to have strong implications when designing high-speed circuits that meet strict timing requirements.
Intestinal Macrophage/Epithelial Cell-Derived CCL11/Eotaxin-1 Mediates Eosinophil Recruitment and Function in Pediatric Ulcerative Colitis (2008)

Clinical studies have demonstrated a link between the eosinophil-selective chemokines, eotaxins (eotaxin-1/CCL11 and eotaxin-2/CCL24), eosinophils, and the inflammatory bowel diseases, Crohn's disease and ulcerative colitis (UC). However, the cellular source and individual contribution of the eotaxins to colonic eosinophilic accumulation in inflammatory bowel diseases remain unclear. In this study we demonstrate, by gene array and quantitative PCR, elevated levels of eotaxin-1 mRNA in the rectosigmoid colon of pediatric UC patients. We show that elevated levels of eotaxin-1 mRNA positively correlated with rectosigmoid eosinophil numbers. Further, colonic eosinophils appeared to be degranulating, and the levels positively correlated with disease severity. Using the dextran sodium sulfate (DSS)-induced intestinal epithelial injury model, we show that DSS treatment of mice strongly induced colonic eotaxin-1 and eotaxin-2 expression and eosinophil levels. Analysis of eosinophil-deficient mice defined an effector role for eosinophils in disease pathology. DSS treatment of eotaxin-2(-/-) and eotaxin-1/2(-/-) mice demonstrated that eosinophil recruitment was dependent on eotaxin-1. In situ and immunofluorescence analysis-identified eotaxin-1 expression was restricted to intestinal F4/80(+)CD11b(+) macrophages in DSS-induced epithelial injury and to CD68(+) intestinal macrophages and the basolateral compartment of intestinal epithelial cells in pediatric UC. These data demonstrate that intestinal macrophage and epithelial cell-derived eotaxin-1 plays a critical role in the regulation of eosinophil recruitment in colonic eosinophilic disease such as pediatric UC and provides a basis for targeting the eosinophil/eotaxin-1 axis in UC.
Studies on polymer latex films: I. A study of latex film morphology (1991)

Abstract Polymer films have been formed from poly (butyl methacrylate) latices prepared by surfactant‐free emulsion polymerisation. The latices having also been cleaned by microfiltration constitute model colloid particles and hence form ‘model’ films. A novel freeze fracture replication and transmission electron microscopy technique was employed to study film morphology. It demonstrated the presence of interparticle boundaries between latex particles deformed into dodecahedra and the particle packing order without the need for a staining technique. The time and temperature of film formation and storage was shown to affect the degree of particle coalescence. Solvent cast films were also studied for comparison purposes.
Formal specification and verification of a dataflow processor array (1999)

We describe the formal specification and verification of the VGI parallel DSP chip (V. Srini et al., 1998), which contains 64 compute processors with /spl sim/30 K gates in each processor. Our effort coincided with the informal verification stage of the chip. By interacting with the designers, we produced an abstract but executable specification of the design which embodies the programmer's view of the system. Given the size of the design, an automatic check that even one of the 64 processors satisfies its specification is well beyond the scope of current verification tools. However, the check can be decomposed using assume-guarantee reasoning. For VGI, the implementation and specification operate at different time scales: several steps of the implementation correspond to a single step in the specification. We generalized both the assume-guarantee method and our model checker MOCHA to allow compositional verification for such applications. We used our proof rule to decompose the verification problem of the VGI chip into smaller proof obligations that were discharged automatically by MOCHA. Using our formal approach, we uncovered and fixed subtle bugs that were unknown to the designers.
The Antitumor Drug Aclacinomycin A, Which Inhibits the Degradation of Ubiquitinated Proteins, Shows Selectivity for the Chymotrypsin-like Activity of the Bovine Pituitary 20 S Proteasome (1996)

The antitumor drug aclacinomycin A was previously shown to inhibit the degradation of ubiquitinated proteins in rabbit reticulocyte lysates with an IC50 of 52 microM (Isoe, T., Naito, M., Shirai, A., Hirai, R., and Tsuruo, T.(1992) Biochim. Biophys. Acta 1117, 131-135). We report here that from all the catalytic activities of the 20 S proteasome tested, the chymotrypsin-like activity was the only one affected by the antitumor drug. An important requirement for inhibition of the chymotrypsin-like activity seemed to be the presence of hydrophobic nonpolar residues in positions P1 to P3. Degradation of Z-E(OtBu)AL-pNA and Z-LLL-AMC at pH 7.5 was dramatically (87-98%) inhibited by 50 microM of the drug, while that of Z-GGL-pNA (containing uncharged polar residues in positions P2 and P3) and succinyl-LLVY-AMC (containing an uncharged polar residue in the P1 position) was inhibited only 11 and 24%, respectively. Aclacinomycin A had no effect on cathepsin B, stimulated trypsin, and inhibited chymotrypsin and, to a lesser extent, calpain. The aglycone and sugar moieties of the cytotoxic drug are essential for inhibition. The results presented here support a major role for the chymotrypsin-like activity in the degradation of ubiquitinated proteins. Aclacinomycin A is the first described non-peptidic inhibitor showing discrete selectivity for the chymotrypsin-like activity of the 20 S proteasome.
Prediction of chronic allograft damage index of renal allografts using serum level of plasminogen activator inhibitor‐1 (2009)

Serum PAI-1 level has the potential to be a marker to predict CADI score, the quantitative score of CAN.