gebhart/patrepeval huggingface dataset:
The Complexity of Estimating Systematic Risk in Networks (2014)

This risk of catastrophe from an attack is a consequence of a network's structure formed by the connected individuals, businesses and computer systems. Understanding the likelihood of extreme events, or, more generally, the probability distribution of the number of compromised nodes is an essential requirement to provide risk-mitigation or cyber-insurance. However, previous network security research has not considered features of these distributions beyond their first central moments, while previous cyber-insurance research has not considered the effect of topologies on the supply side. We provide a mathematical basis for bridging this gap: we study the complexity of computing these loss-number distributions, both generally and for special cases of common real-world networks. In the case of scale-free networks, we demonstrate that expected loss alone cannot determine the riskiness of a network, and that this riskiness cannot be naively estimated from smaller samples, which highlights the lack/importance of topological data in security incident reporting.
Need for Controllers Having Integer Coefficients in Homomorphically Encrypted Dynamic System (2018)

Encryption of feedback controller based on homomorphic encryption techniques allows control operation on encrypted sensor measurements, to protect data secrecy of networked control systems. In this paper, we first revisit the fact that an encrypted dynamic controller based on partially homomorphic cryptosystems cannot operate for infinite time horizon in general due to the problem of the size of encrypted controller state. Then, it is highlighted that an encrypted LTI controller can operate for infinite time horizon when the denominator of its transfer function is a monic polynomial with integer coefficients. In this case, it does not utilize bootstrapping techniques from fully homomorphic encryption for resizing the controller state, and it does not assume the decryption of controller state from time to time. In this respect, we discuss potential benefits of using PID controllers and FIR filters. Then, we introduce a way how to approximately convert controllers having non-integer coefficients to have integer coefficients without losing stability.
Mannan-binding lectin in human serum, cerebrospinal fluid and brain tissue and its role in Alzheimerʼs disease (1998)

Mannan-Binding lectin (MBL) is a serum lectin which can activate the classical complement pathway. Complement proteins of the classical pathway have been found in the brains of patients with Alzheimer's disease (AD) in association with AD brain pathology. To investigate the role for MBL in AD we have looked for its presence in the brain by immunohistochemistry and determined the levels of MBL in paired samples of cerebrospinal fluid and serum from AD patients and controls. MBL was detected in association with blood vessels in the brain tissue of both AD patients and control subjects. There was no apparent difference in the distribution of MBL in the brain tissue between the two groups. The mean concentration of MBL in the CSF was 44% lower in AD patients than in controls (AD 154 +/- 35 pg/ml, n = 19; non-AD 276 +/- 50 pg/ml, n = 15, p < 0.05). The levels of MBL in serum were not significantly different in the two groups. Thus, this study shows that MBL is associated with blood vessels in the brains of both AD and control subjects. Moreover, CSF levels of MBL appear to be lower in AD patients than in control subjects which may indicate a higher degree of MBL consumption connected with complement activation in the AD patients.
Kinetics of Polymer Interfacial Reactions: Polymer Brush Formation by Click Reactions of Alkyne End-Functional Polymers with Azide-Functional Substrates (2016)

Attenuated total reflectance infrared spectroscopy (ATR-IR) is used to directly measure the rates of copper-catalyzed 1,3-dipolar cycloaddition reactions between alkyne-terminated polystyrene and poly(n-butyl acrylate) and azide-functional substrates in the good solvent DMF. Four regimes of behavior are observed: initially, the reaction rate is diffusion-controlled scaling with t1/2; in the crossover regime at the onset of chain overlap, the rate scales with ln(t); the rate then accelerates briefly; and finally, in the terminal or penetration-limited regime, the logarithm of areal density scales linearly with time. Kinetic behavior in the diffusion-limited, crossover, and penetration-limited regimes corresponds well to the predictions of Ligoure and Leibler. The blob model suggests that the acceleration in rate is due to lateral chain contraction during the mushroom to brush transition. A theory is presented to predict that the areal density at saturation should scale as Σsaturation ∼ Mw–1.2 for good solvents, and experimentally we find Mw–0.93±0.04 scaling.
HER2/ErbB2-induced Breast Cancer Cell Migration and Invasion Require p120 Catenin Activation of Rac1 and Cdc42 (2010)

Breast cancers that overexpress the receptor tyrosine kinase ErbB2/HER2/Neu result in poor patient outcome because of extensive metastatic progression. Herein, we delineate a molecular mechanism that may govern this malignant phenotype. ErbB2 induction of migration requires activation of the small GTPases Rac1 and Cdc42. The ability of ErbB2 to activate these small GTPases necessitated expression of p120 catenin, which is itself up-regulated by signaling through ErbB2 and the tyrosine kinase Src. Silencing p120 in ErbB2-dependent breast cancer cell lines dramatically inhibited migration and invasion as well as activation of Rac1 and Cdc42. In contrast, overexpression of constitutively active mutants of these GTPases reversed the effects of p120 silencing. Lastly, ectopic expression of p120 promoted migration and invasion and potentiated metastatic progression of a weakly metastatic, ErbB2-dependent breast cancer cell line. These results suggest that p120 acts as an obligate intermediate between ErbB2 and Rac1/Cdc42 to modulate the metastatic potential of breast cancer cells.
Reactive Center Loop (RCL) Peptides Derived from Serpins Display Independent Coagulation and Immune Modulating Activities (2015)

Serpins regulate coagulation and inflammation, binding serine proteases in suicide-inhibitory complexes. Target proteases cleave the serpin reactive center loop scissile P1-P1' bond, resulting in serpin-protease suicide-inhibitory complexes. This inhibition requires a near full-length serpin sequence. Myxomavirus Serp-1 inhibits thrombolytic and thrombotic proteases, whereas mammalian neuroserpin (NSP) inhibits only thrombolytic proteases. Both serpins markedly reduce arterial inflammation and plaque in rodent models after single dose infusion. In contrast, Serp-1 but not NSP improves survival in a lethal murine gammaherpesvirus68 (MHV68) infection in interferon γ-receptor-deficient mice (IFNγR(-/-)). Serp-1 has also been successfully tested in a Phase 2a clinical trial. We postulated that proteolytic cleavage of the reactive center loop produces active peptide derivatives with expanded function. Eight peptides encompassing predicted protease cleavage sites for Serp-1 and NSP were synthesized and tested for inhibitory function in vitro and in vivo. In engrafted aorta, selected peptides containing Arg or Arg-Asn, not Arg-Met, with a 0 or +1 charge, significantly reduced plaque. Conversely, S-6 a hydrophobic peptide of NSP, lacking Arg or Arg-Asn with -4 charge, induced early thrombosis and mortality. S-1 and S-6 also significantly reduced CD11b(+) monocyte counts in mouse splenocytes. S-1 peptide had increased efficacy in plasminogen activator inhibitor-1 serpin-deficient transplants. Plaque reduction correlated with mononuclear cell activation. In a separate study, Serp-1 peptide S-7 improved survival in the MHV68 vasculitis model, whereas an inverse S-7 peptide was inactive. Reactive center peptides derived from Serp-1 and NSP with suitable charge and hydrophobicity have the potential to extend immunomodulatory functions of serpins.
Differential effects of dietary linoleic and α‐linolenic acid on lipid metabolism in rat tissues (1988)

Comparative effects of feeding dietary linoleic (safflower oil) and alpha-linolenic (linseed oil) acids on the cholesterol content and fatty acid composition of plasma, liver, heart and epididymal fat pads of rats were examined. Animals fed hydrogenated beef tallow were used as isocaloric controls. Plasma cholesterol concentration was lower and the cholesterol level in liver increased in animals fed the safflower oil diet. Feeding the linseed oil diet was more effective in lowering plasma cholesterol content and did not result in cholesterol accumulation in the liver. The cholesterol concentration in heart and the epididymal fat pad was not affected by the type of dietary fatty acid fed. Arachidonic acid content of plasma lipids was significantly elevated in animals fed the safflower oil diet and remained unchanged by feeding the linseed oil diet, when compared with the isocaloric control animals fed hydrogenated beef tallow. Arachidonic acid content of liver and heart lipids was lower in animals fed diets containing safflower oil or linseed oil. Replacement of 50% of the safflower oil in the diet with linseed oil increased alpha-linolenic, docosapentaenoic and docosahexaenoic acids in plasma, liver, heart and epididymal fat pad lipids. These results suggest that dietary 18:2 omega 6 shifts cholesterol from plasma to liver pools followed by redistribution of 20:4 omega 6 from tissue to plasma pools. This redistribution pattern was not apparent when 18:3 omega 3 was included in the diet.
A systematic RNAi screen for longevity genes in <i>C. elegans</i> (2005)

We report here the first genome-wide functional genomic screen for longevity genes. We systematically surveyed Caenorhabditis elegans genes using large-scale RNA interference (RNAi), and found that RNAi inactivation of 89 genes extend C. elegans lifespan. Components of the daf-2/insulin-like signaling pathway are recovered, as well as genes that regulate metabolism, signal transduction, protein turnover, and gene expression. Many of these candidate longevity genes are conserved across animal phylogeny. Genetic interaction analyses with the new longevity genes indicate that some act upstream of the daf-16/FOXO transcription factor or the sir2.1 protein deacetylase, and others function independently of daf-16/FOXO and sir2.1, and might define new pathways to regulate lifespan.
SENSOR VALIDATION AND FUSION WITH DISTRIBUTED 'SMART DUST' MOTES FOR MONITORING AND ENABLING EFFICIENT ENERGY USE (2002)

MEMS (microelectronic mechanical systems) sensors make a rich design space of distributed networked sensors viable. They can be deeply embedded in the physical world and spread throughout our environment like “smart dust”. Today, networked sensors called Smart Dust motes can be constructed using commercial components on the scale of a square inch in size and a fraction of a watt in power. High-density distributed networked sensors have recently been targeted for use in research devoted to the efficient use of energy. Such networks require a large number of sensors for control at different levels. However, in reality, sensor information is always corrupted to some degree by noise and degradation, which vary with operating conditions, environmental conditions, and other factors. To overcome
Enhanced Humification of Soil Organic Matter by Microwave Irradiation and Hyperthermal Catalysts (2014)

Soil organic matter (SOM) is derived from dead biomass of animals and plants, and its formation process in which the precursor materials of SOM are transformed into macro organic molecules through geo-chemical and geo-biological reactions in the subsurface environment is referred to as humification. Carbon content increases, but oxygen content decreases along with marked increased in molecular weight and degree of condensation of SOM during humification. It has been known that humus materials evolve in the order of biopolymer, fulvic acid, humic acid, and humin. Humification process takes place in a geological time scale, but it can be accelerated at extremely high temperatures, which can be achieved by microwave (MW) with hyperthermal catalysts (HTCs). Thus, MW was irradiated to the mixture of soil and HTCs to stimulate humification of SOM and to enhance its binding capacity for recalcitrant organic contaminants in this study. MW irradiation with HTCs was optimized, and the characteristic changes of SOMs before and after the irradiation were assessed to confirm humification. Soils were collected from 4 different forest regions in Seoul, Korea (Konkuk University, Yongma Mountain, Surak Mountain, and Bukhan Mountain), and they were screened by wet-sieving. Each component of SOM was isolated by acid-base extraction/selective exchange resin, which was proposed by the International Humic Substance Society. Total organic carbon (TOC) content, specific ultraviolet absorbance (SUVA), E4/E6 ratio, and Fourier transform-infrared spectroscopy (FT-IR) spectrum of SOM before and after MW irradiation were examined. Soil of Surak Mountain exhibited the highest organic carbon content, but Yongma Mountain contained the highest amount of fulvic acid. Soils of Yongma Mountain and Konkuk University were chosen due to their high fulvic acid content, which supported that these soils are relatively geologically-young soils. Powdered and granulated activated carbon (PAC and GAC), graphite, charcoal, and carbon nanotube (CNT) were selected and screened with regard to their hyperthermal activity under MW irradiation. The temperature changes by MW with HTCs were monitored at various MW irradiation intensity and time. Graphite-and CNT-soil mixtures exhibited the optimum heating capacity at 600 W, resulting in heating HTC-soil mixtures to approximately 1,000oC within 10 min. TOCs, SUVAs, E4/E6 ratios, and FT-IR spectra of SOM supported effective humification of SOM after MW irradiation with HTCs, and notable increase in binding capacity with hydrophobic organic contaminants. The results of this study are expected to provide the fundamental information for developing the performance-efficient and cost-effective treatment process for the removal of persistent organic contaminants based on MW and HTC.
An in-vehicle navigation and information system utilizing defined software services (2003)

It is proposed that applications software will be able to be executed properly on entire families of related but dissimilar in-vehicle systems if all software access to the hardware takes place through a defined set of software calls in the ROM BIOS. By allowing map data to be retrieved through a defined high-level retrieval service, application software can be written without requiring detailed familiarity with the data structures, and can be compatible with future map data retrieval services which, while providing the same interface, may provide improved performance. By providing pre-emptive multi-tasking in the vehicular computer environment, application software can be developed efficiently without requiring the developers to take responsibility for the unrelated real-time requirements of navigation, or other software that may also be executed. Unrelated vehicle information systems can use a common compact disk on which multiple versions of executable software are resident.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
PolyBuilding: Polygon transformer for building extraction (2023)

We present PolyBuilding, a polygon Transformer for building extraction. PolyBuilding direct predicts vector representation of buildings from remote sensing images. It builds upon an encoder–decoder transformer architecture and simultaneously predicts the bounding boxes and polygons for the building instances. Given a set of polygon queries, the model learns the relations among them and encodes context information from the image to predict the final set of building polygons with a fixed vertex number. Considering that predicting a fixed number of vertices would cause vertex redundancy and reduce polygon regularity, we design a corner classification head to distinguish the building corners. By taking advantage of the corner classification scores, a polygon refinement scheme is designed to remove the redundant vertices and produce the final polygons with regular contours and low complexity. In addition, although the PolyBuilding model is fully end-to-end trainable, we propose a two-phase training strategy to decompose the coordinate regression and corner classification into two stages to alleviate the difficulty of multi-task learning. Comprehensive experiments are conducted on the CrowdAI dataset and Inria dataset. PolyBuilding achieves a new state-of-the-art in terms of pixel-level coverage, instance-level detection performance, and geometry-level properties. Quantitative and qualitative results verify the superiority and effectiveness of our model.
Amino-acylation site mutations in amino acid-activating domains of surfactin synthetase: effects on surfactin production and competence development in Bacillus subtilis (1993)

The part of the srfA operon of Bacillus subtilis that contains the region required for competence development is composed of the first four amino acid-activating domains which are responsible for the incorporation of Glu, Leu, D-Leu, and Val into the peptide moiety of the lipopeptide surfactin. Ser-to-Ala substitutions were made in the amino-acylation site of each domain, and their effects on surfactin production and competence development were examined. All of the mutations conferred a surfactin-negative phenotype, supporting the finding that the conserved Ser in the amino-acylation site is required for peptide synthesis. However, none of the mutations affected significantly competence development or the expression of a lacZ fusion to the late competence operon comG. This, coupled with recent findings that only the fourth, Val-activating, domain is required for competence, suggests that some activity, other than amino-acylation and perhaps unrelated to peptide synthesis, possessed by the fourth domain is involved in the role of srfA in regulating competence development.
Dependence of threshold current density on quantum well composition for strained-layer InGaAs-GaAs lasers by metalorganic chemical vapor deposition (1989)

A series of separate confinement InxGa1−xAs-GaAs (0.08&lt;x&lt;0.42) strained-layer quantum well lasers with 70 Å well thickness has been grown by metalorganic chemical vapor deposition. Data are presented on emission wavelengths and threshold current densities (Jth) as a function of composition. A minimum in Jth of 140 A/cm2 was observed for devices with In0.24Ga0.76As wells. The dependence of Jth on well composition is explained by a balance between strain effects and carrier confinement in the quantum well.
Spontaneous Ruptured Hepatocellular Carcinoma; An Appraisal of Surgical Treatment (1989)

Spontaneous rupture with bleeding is not an infrequent complication of hepatocellular carcinoma (HCC). From May, 1972 to January, 1987, 56 symptomatic patients with ruptured HCC were managed by plication of the lesion (2 patients), ligation of either the common hepatic artery, CHAL, (39 patients), or selectively, the arterial branch supplying the tumor-bearing lobe of liver, SHAL, (8 patients), and hepatic resection, HR, (7 patients). Effective hemostasis was achieved in 68.1% of patients with the use of hepatic artery ligation (HAL). SHAL provides a comparable control of bleeding but no demonstrable reduction of postoperative organ failure when compared with CHAL. The operative treatment employed had no influence on either the postoperative rates of morbidity, mortality, or survival. However, the rate of hospital mortality was high among the four patients who had emergency anatomical lobectomy, despite the absence of severe cirrhosis. Hepatic artery ligation, either CHAL or SHAL, is a satisfactory definitive hemostatic measure for unresectable HCC when it ruptured. SHAL is probably preferred to routine emergency HR for patients with potentially resectable lesions. Nonetheless, for selected patients with easily accessible lesions, segmentectomy or subsegmentectomy could still be contemplated in the absence of severe cirrhosis.
Static force dependency of bone conduction transducer as sensory feedback for stump-socket based prosthesis (2018)

The dependency of a novel sensory feedback for stump-socket based prosthesis on the static force is presented using a bone conduction transducer as feedback source. The stimulation was induced onto the bony landmarks of the elbow, specifically the Ulna and presented in an interval halving method. The perception threshold in the range of tactile and auditory perception at three different force levels has been tested. The inter subject variability is bigger than the intra subject variation. The small static force variation suggests a similar approach as in bone conduction hearing aids and therefore a static force bigger than 6N should be applied to perceive a constant stimulation. A mechanical design to include such a novel feedback into a stump-socket needs to account for this requirement. The inter subject variability needs to be addressed by incorporate some kind of person to person calibration of the gain.
Role of C– Kit Receptor Tyrosine Kinase in Development of Oval Cells in the Rat 2–Acetylaminofluorene/Partial Hepatectomy Model (1999)

Oval cells that develop in the rat 2–acetylaminofluorene/partial hepatectomy (AAF/PH) model express the c– kit receptor tyrosine kinase (KIT) and its ligand, stem cell factor (SCF). We investigated the role of the SCF/KIT system in the development of oval cells using Ws/Ws rats, whose c– kit kinase activity was severely impaired owing to a small deletion in the kinase domain. On days 7, 9, and 13 after PH in the AAF/PH model, the development of oval cells was remarkably suppressed in Ws/Ws rats when compared with that of the control normal (+/+) rats. However, oval cells that developed in Ws/Ws rats expressed marker proteins of oval cells, such as α–fetoprotein (AFP), cytokeratin–19 (CK–19), and flt –3 receptor tyrosine kinase, similar to those of +/+ rats. Furthermore, labeling with [ 3 H]–thymidine and immunostaining of Ki–67 showed that the proliferative activity of oval cells that developed in Ws/Ws rats was comparable with that of +/+ rats. The present results indicate that the signal transduction of the SCF/KIT system plays a crucial role in the development of oval cells, at least, in the rat AAF/PH model, and suggest that KIT–mediated signal transduction plays only a small role in determining the phenotype and in the proliferative activity of oval cells.
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion (2006)

HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.