gebhart/patrepeval huggingface dataset:
Trojan detection via delay measurements: a new approach to select paths and vectors to maximize effectiveness and minimize cost (2013)

One of the growing issues in IC design is how to establish trustworthiness of chips fabricated by untrusted vendors. Such process, often called Trojan detection, is challenging since the specifics of hardware Trojans inserted by intelligent adversaries are difficult to predict and most Trojans do not affect the logic behavior of the circuit unless they are activated. Also, Trojan detection via parametric measurements becomes increasingly difficult with increasing levels of process variations. In this paper we propose a method that maximizes the resolution of each path delay measurement, in terms of its ability to detect the targeted Trojan. In particular, for each Trojan, our approach accentuates the Trojan's impact by generating a vector that sensitizes the shortest path passing via the Trojan's site. We estimate the minimum number of chips to which each vector must be applied to detect the Trojan with sufficient confidence for a given level of process variations. Finally, we demonstrate the significant improvements in effectiveness and cost provided by our approach under high levels of process variations. Experimental results on several benchmark circuits show that we can achieve dramatic reduction in test cost using our approach compared to classical path delay testing.
A Candidate High Density Lipoprotein (HDL) Receptor, HB2, with Possible Multiple Functions Shows Sequence Homology with Adhesion Molecules (1998)

High density lipoprotein (HDL), an antiatherogenic lipoprotein comprises several subclasses differing in composition and metabolic function. This physiological complexity appears to be matched with the growing number of candidate HDL receptors, since several HDL binding proteins have recently been identified in various tissues. Because these putative receptors may signal different pathways it is important to identify their structure and potential role in HDL metabolism. We review recent progress in the cloning and characterization of HB2, one of a pair of HDL binding proteins (HB1 and HB2) first purified from rat liver. The structure of HB2 is consistent with a receptor role for this membrane protein and when expressed in cells, increases HDL binding 2 fold. HB2, minimally present in THP-1 cells, is substantially upregulated in macrophages and appears sensitive to cholesterol loading of these cells. The protein shows high homology with adhesion molecules ALCAM and BEN and the possibility that HDL by binding to HB2, reduces adhesion induced arterial wall injury, is discussed in the context of the known protective role of HDL against atherosclerosis. The possible functions of HB2 are also compared with other recently cloned HDL receptors.
Dominant-negative TLR5 polymorphism reduces adaptive immune response to flagellin and negatively associates with Crohn's disease (2006)

Crohn's disease (CD) is associated with elevated adaptive immunity to commensal microbes, with flagellin being a dominant antigen. In light of heightened awareness of the importance of innate immunity in regulating adaptive immunity and ambiguity as to the role of CD-associated immune responses in CD pathophysiology, we sought to determine whether natural acquisition of immune responses to flagellin were regulated by the innate immune flagellin receptor toll-like receptor 5 (TLR5) and determine whether persons carrying a recently defined common dominant-negative TLR5 polymorphism (TLR5-stop) might be protected from developing CD. Carriage rates of a recently defined dominant-negative TLR5 polymorphism (TLR5-stop) and levels of serum immunoreactivity to bacterial products were measured in inflammatory bowel disease patients, first-degree relatives, and unrelated controls. We observed that, in healthy subjects, persons carrying TLR5-stop had significantly lower levels of flagellin-specific IgG and IgA but had similar levels of total and LPS-specific Ig. Moreover, we observed that, among Jewish subjects, the carriage rate of TLR5-stop (in heterozygous state) was significantly less in CD patients, but not ulcerative colitis (UC) patients, compared with unaffected relatives and unrelated controls (5.4, 0.9, 6.0, and 6.5% for unaffected relatives, CD, UC, and unrelated Jewish controls, respectively, n = 296, 215, 185, and 416, respectively; P = 0.037 by likelihood calculation for CD vs. controls), indicating that TLR5-stop can protect persons of Jewish ethnicity against CD. We did not observe a significant association of TLR5-stop with CD in a non-Jewish cohort (11.1, 10.4, and 11.7% for unaffected relatives, CD, and UC, respectively; n = 841, 543, and 300 for unaffected relatives, respectively). These results demonstrate that natural acquisition of immune responses to flagellin are regulated by TLR5 and suggest that immune responses to flagellin are not merely associated with CD but rather promote the pathogenic response.
Electrical and optical properties of gold-doped n-type silicon (1989)

Different measurement techniques, both electrical and optical, were utilized in this work to characterize gold diffusion in n-type, float-zoned silicon in the temperature range 600–1150 °C. In the lower temperature region (≤750 °C), the gold diffusion is observed by the introduction of the Au acceptor state at 0.53 eV below the conduction band, and is correlated to the electrical behavior of the samples deduced from Hall effect and resistivity data. Also, the effects of Au diffusion on the free-carrier concentration and mobilities are discussed. It was shown that high temperatures and long times for gold diffusion change the conductivity type in the samples from n to p. In the samples that converted to p type, a limiting room-temperature resistivity of 2.0×103 Ω cm was attained, when the conduction is mainly influenced by the Au-related deep electronic states in the band gap. In this case, the diffusion mechanism is also investigated by secondary ion mass spectroscopy data determining the equilibrium Au solubility, which is close to the equilibrium solubility of interstitial gold. Low-temperature photoluminescence measurements have shown that the intensity of the lines often attributed to dislocations, increases significantly by gold diffusion in the lower temperature region. At higher diffusion temperatures, a decrease of the dislocation-related lines was found, associated with formation of gold-related precipitates. Introducing an inhomogeneous internal stress distribution in the Si matrix, these precipitates cause line shifts as well as line broadenings of the free exciton, the phosphorus bound exciton, and the electron-hole droplet photoluminescence emissions. The concentration of substitutional phosphorus is found to decrease with increasing diffusion temperatures.
ShapeNet: An Information-Rich 3D Model Repository (2023)

We present ShapeNet: a richly-annotated, large-scale repository of shapes represented by 3D CAD models of objects. ShapeNet contains 3D models from a multitude of semantic categories and organizes them under the WordNet taxonomy. It is a collection of datasets providing many semantic annotations for each 3D model such as consistent rigid alignments, parts and bilateral symmetry planes, physical sizes, keywords, as well as other planned annotations. Annotations are made available through a public web-based interface to enable data visualization of object attributes, promote data-driven geometric analysis, and provide a large-scale quantitative benchmark for research in computer graphics and vision. At the time of this technical report, ShapeNet has indexed more than 3,000,000 models, 220,000 models out of which are classified into 3,135 categories (WordNet synsets). In this report we describe the ShapeNet effort as a whole, provide details for all currently available datasets, and summarize future plans.
Hybrid Capillary/Microfluidic System for Comprehensive Online Liquid Chromatography-Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry (2013)

A hybrid multidimensional separation system was made by coupling capillary liquid chromatography (LC) to a microfluidic device. The microfluidic device integrated flow splitting, capillary electrophoresis (CE), electroosmotic pumping, and electrospray ionization (ESI) emitter functional elements. The system was used with a time-of-flight mass spectrometer for comprehensive online LC-CE-MS of proteolytic digests. Analysis of a complex mixture of peptides yielded a peak capacity of approximately 1400 in 50 min. Three replicate runs demonstrated mean reproducibility for LC retention and CE migration times of 0.32% and 0.75% relative standard deviation (RSD), respectively. The same LC-CE-MS method was also used to characterize the N-linked glycosylation of a monoclonal antibody. Glycopeptides from two different N-linked glycosylation sites were separated from all other tryptic peptides and identified using MS data. The relative amounts of each glycoform and total site occupancy were quantified using LC-CE-MS data.
Modeling Chromosomes in Mouse to Explore the Function of Genes, Genomic Disorders, and Chromosomal Organization (2006)

One of the challenges of genomic research after the completion of the human genome project is to assign a function to all the genes and to understand their interactions and organizations. Among the various techniques, the emergence of chromosome engineering tools with the aim to manipulate large genomic regions in the mouse model offers a powerful way to accelerate the discovery of gene functions and provides more mouse models to study normal and pathological developmental processes associated with aneuploidy. The combination of gene targeting in ES cells, recombinase technology, and other techniques makes it possible to generate new chromosomes carrying specific and defined deletions, duplications, inversions, and translocations that are accelerating functional analysis. This review presents the current status of chromosome engineering techniques and discusses the different applications as well as the implication of these new techniques in future research to better understand the function of chromosomal organization and structures.
Instrumenting gait with an accelerometer: A system and algorithm examination (2015)

Gait is an important clinical assessment tool since changes in gait may reflect changes in general health. Measurement of gait is a complex process which has been restricted to the laboratory until relatively recently. The application of an inexpensive body worn sensor with appropriate gait algorithms (BWM) is an attractive alternative and offers the potential to assess gait in any setting. In this study we investigated the use of a low-cost BWM, compared to laboratory reference using a robust testing protocol in both younger and older adults. We observed that the BWM is a valid tool for estimating total step count and mean spatio-temporal gait characteristics however agreement for variability and asymmetry results was poor. We conducted a detailed investigation to explain the poor agreement between systems and determined it was due to inherent differences between the systems rather than inability of the sensor to measure the gait characteristics. The results highlight caution in the choice of reference system for validation studies. The BWM used in this study has the potential to gather longitudinal (real-world) spatio-temporal gait data that could be readily used in large lifestyle-based intervention studies, but further refinement of the algorithm(s) is required.
Evidence of an energy transfer reaction between atomic hydrogen and argon II or helium II as the source of excessively hot H atoms in radio-frequency plasmas (2005)

From the width of the emitted 656.3 nm Balmer $\alpha$ line, it was found that low-pressure (0.5 torr) capacitively coupled radio-frequency (RF) ${\rm He}/{\rm H}_2$ (95/5%) as well as ${\rm Ar}/{\rm H}_2$ (95/5%) plasmas showed excess broadening throughout the volume (13.5 cm ID $\times$ 38 cm length) of a General Electronics Conference (GEC)-type cell; not merely in the vicinity of the electrodes of ${\rm Ar}/{\rm H}_2$ plasmas as reported by several groups. About 50% of the hydrogen of the ${\rm He}/{\rm H}_2$ was 'hot' with an average hydrogen atom energy of 40–50 eV, compared to $\sim$1 eV for pure hydrogen, whereas ${\rm Ar}/{\rm H}_2$ showed a single fast or 'hot' 40–50 eV population. The broadening was undiminished at 15 cm from the powered electrode, independent of power over a substantial range, but dependent on the hydrogen concentration. In contrast to the atomic hydrogen lines, no broadening was observed in helium or argon lines. Also, in 'control' ${\rm Xe}/{\rm H}_2$ plasmas run in the same cell at similar pressures and absorbed power, no significant broadening of atomic hydrogen, ${\rm Xe}$, or any other lines was observed. Stark broadening or acceleration of charged species due to high electric fields cannot explain the results since: (i) the electron density was insufficient by orders of magnitude, (ii) the RF field was essentially confined to the cathode fall region in contrast to the broadening that was independent of position, and (iii) only the atomic hydrogen lines were broadened. Rather, the data are consistent with a model wherein ${\rm He}^+$ and ${\rm Ar}^+$ act catalytically through a resonant energy transfer mechanism to create 'hot' hydrogen atoms in plasmas.
The Nuclear Dot Protein Sp100, Characterization of Domains Necessary for Dimerization, Subcellular Localization, and Modification by Small Ubiquitin-like Modifiers (1999)

The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs) or PML bodies, and are both covalently modified by the small ubiquitin-related protein SUMO-1. NDs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia. To date, little is known about the function of the Sp100 protein. Here we analyzed Sp100 domains that determine its subcellular localization, dimerization, and SUMOylation. A functional nuclear localization signal and an ND-targeting region that coincides with an Sp100 homodimerization domain were mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain. The lysine residue of the Sp100 protein, to which SUMO-1 is covalently linked, was mapped within and may therefore modulate the previously described HP1 protein-binding site. A consensus sequence for SUMOylation of proteins in general is suggested. SUMOylation strictly depended on a functional nuclear localization signal but was not necessary for nuclear import or ND targeting. A three-dimensional structure of Sp100, which supports the mapping data and provides additional information on Sp100 structure/function relationships, was generated by computer modeling. Taken together, our studies indicate the existence of well defined Sp100 domains with functions in ND targeting, nuclear import, nuclear SUMOylation, and protein-protein interaction.
Analysis of the Paired TCR α- and β-chains of Single Human T Cells (2012)

Analysis of the paired i.e. matching TCR α- and β-chain rearrangements of single human T cells is required for a precise investigation of clonal diversity, tissue distribution and specificity of protective and pathologic T-cell mediated immune responses. Here we describe a multiplex RT-PCR based technology, which for the first time allows for an unbiased analysis of the complete sequences of both α- and β-chains of TCR from single T cells. We validated our technology by the analysis of the pathologic T-cell infiltrates from tissue lesions of two T-cell mediated autoimmune diseases, psoriasis vulgaris (PV) and multiple sclerosis (MS). In both disorders we could detect various T cell clones as defined by multiple T cells with identical α- and β-chain rearrangements distributed across the tissue lesions. In PV, single cell TCR analysis of lesional T cells identified clonal CD8(+) T cell expansions that predominated in the epidermis of psoriatic plaques. An MS brain lesion contained two dominant CD8(+) T-cell clones that extended over the white and grey matter and meninges. In both diseases several clonally expanded T cells carried dual TCRs composed of one Vβ and two different Vα-chain rearrangements. These results show that our technology is an efficient instrument to analyse αβ-T cell responses with single cell resolution in man. It should facilitate essential new insights into the mechanisms of protective and pathologic immunity in many human T-cell mediated conditions and allow for resurrecting functional TCRs from any αβ-T cell of choice that can be used for investigating their specificity.
Adenoviral Gene Transfer of Connective Tissue Growth Factor in the Lung Induces Transient Fibrosis (2003)

Connective tissue growth factor (CTGF) is felt to be one of the key profibrotic factors and is a downstream effector molecule mediating the action of transforming growth factor (TGF)-beta1, a cytokine known to induce severe and progressive fibrosis. However, the in vivo fibrogenic effect of isolated CTGF expression is not well described. We used adenoviral gene transfer to transiently overexpress CTGF in rat lungs after intratracheal administration and compared it with transient overexpression of active TGF-beta1 delivered by a similar adenovirus vector. This high expression of CTGF over 6-10 days induced a moderate but reversible fibrosis. We observed an increase of fibronectin, procollagen 1a2, and endogenous CTGF gene expression at 14 days, which suggested an indirect activation by CTGF. Tissue inhibitor of metalloproteinase-1 was weakly and transiently upregulated after CTGF exposure. These same genes were robustly and persistently stimulated by TGF-beta1 from Day 3 to Day 21. This data suggested that CTGF may act as a TGF-beta1 cofactor rather than a direct fibrogenic factor. We demonstrate that CTGF overexpression can initiate fibrogenic activity but likely requires the presence of additional factors, such as tissue inhibitor of metalloproteinase-1, to maintain a nonfibrolytic environment and to cause progression of fibrosis.
Salmonella typhimurium mutants lacking flagella or motility remain virulent in BALB/c mice (1990)

Nonmotile flagellated (mot) and nonflagellated (fla) mutants of Salmonella typhimurium LT-2 were isolated from a collection of mutants with random Tn10-insertion mutations. Both classes of mutants were resistant to infection by the flagellotropic bacteriophage chi. The nonflagellated (fla::Tn10) mutants did not react with H antigen-specific antisera and did not possess flagella when examined by electron microscopy, and sheared-cell extracts were devoid of flagellin. The nonmotile (mot::Tn10) mutants reacted with H-specific antisera and expressed paralyzed flagella that were indistinguishable from wild-type flagella. The Tn10 insertions in strain LT-2 were mapped to loci in regions II (flh and mot) and III (fli) of the flagellar genes, and the mutations were transduced into the mouse-virulent S. typhimurium strains SR-11 and SL1344. Lack of motility reduced the ability of S. typhimurium to invade Henle cells in vitro, yet the virulence in mice of the nonmotile mutants of SR-11 and SL1344 was unaffected by the inactivity or loss of flagella. Wild-type SR-11 had a 50% lethal dose (LD50) in BALB/c mice following oral (p.o.) challenge of 2.4 x 10(4) CFU. The p.o. LD50 of the SR-11 fli-8007::Tn10 mutant was 4.5 x 10(4) CFU. The mot-8008::Tn10 mutation in SR-11 conferred paralyzed flagella and increased the p.o. LD50 in mice to 2.2 x 10(5) CFU, but this was not statistically significant. A similar increase in the p.o. LD50 was observed when the SL1344 mot-8008::Tn10 mutant was tested in mice. Wild-type SR-11 and the isogenic nonflagellated and nonmotile mutants were equally virulent in mice challenged via intraperitoneal injection.
Human Immunoglobulin G and Immunoglobulin G Subclasses: Biochemical, Genetic, and Clinical Aspects (1989)

Human IgG consists of two identical heavy (H) chains and two identical light (L) chains joined by interchain disulfide bridges. Heterogeneity in the amino acid sequences of the H and L polypeptides results in at least three types of IgG variants at the structural and genetic levels. The four isotypic forms are IgG1, IgG2, IgG3, and IgG4, which share extensive homologies in the primary structure of their H chains. As a result, the subclasses cross-react antigenically, but they can be differentiated on the basis of subtle architectural dissimilarities. The biological and effector properties of the IgG isotypes have been associated, in part, with their structural differences. Genes determining the synthesis of human IgG heavy chains are located on chromosome 14. In several clinical situations the isotypes appear to be regulated or expressed in patterns reflecting the gene arrangement. The numeric designations of the subclasses correspond to the order of their proportional amounts in healthy adult serum: IgGl> IgG2 > IgG3 > IgG4.Awareness of the importance of the roles of the four IgG isotypes in human health has steadily increased since they were first described in the 1960s. The recognition that deficits or increases in selected IgG subclasses may have clinical consequences has prompted considerable interest in quantifying the four isotypes in clinical specimens. In particular, deficiencies of IgG2, IgG3, and IgG4, singly or combined, are associated with chronic infections which may not be readily recognized in otherwise healthy people with normal serum total IgG concentrations. Different assay methods using polyclonal or monoclonal antisera with various calibrants have been applied; however, no standardized method exists at the present. IgG deficits are associated with gene defects and are acquired in secondary immunodeficiencies in conjunction with other disorders. IgG isotype selectivity has been recognized in autoimmune diseases and in response to carbohydrate and protein antigens derived from pathogenic microorganisms and ommon allergens.
Efficient synthesis of hydroxyethylidene and (E)-alkene dipeptide isosteres (2016)

which was hampered by the lack ofStereoselectivity in the vinylmagnesium halide addition toamino aldehydes, long reaction steps, and low overall yields.As a solution to the synthetic problem in preparing hy-droxyethylidene dipeptide isosteres, we have developed anefficient route from ketovinyl dipeptide isostere.
Uniform Resource Locators (1994)

&amp;quot;. To refer to several attributes, clients send the server the attribute names seperated by spaces so it is neccesary to seperate the attribute names with coded spaces. To retrieve a collection of item attributes specified with a gopher+ string of &amp;quot;!+ABSTRACT%20+SMELL&amp;quot; a gopher client would send a_gopher_selector&amp;lt;tab&amp;gt;!+ABSTRACT +SMELL&amp;lt;cr&amp;gt;&amp;lt;lf&amp;gt; to the gopher server. Gopher+ allows for optional alternate data representations (alternate views) of items. To retrieve a Gopher+ alternate view, the gopher+ client sends the appropriate view and language identifier (found in the item&amp;apos;s +VIEW attribute). To refer to a specific Gopher+ alternate view, the URL&amp;apos;s Gopher+ string would be in the form &amp;quot;+view name%20language name&amp;quot;. For example, a gopher+ string of &amp;quot;+application/postscript%20Es ES&amp;quot; refers to the spanish language postscript alternate view of a gopher+ item. To retrieve this alternate view the client would send a_gopher_selector&amp;lt;tab&amp;gt;+application/postscript Es_ES&amp;lt;cr&amp;gt;&amp;lt;lf&amp;gt; to the gopher ...