gebhart/patrepeval huggingface dataset:
Multi-protocol visualization (2003)

This paper describes a system for the visualization of multiple protocols. The visualizer makes possible the identification of both intra and inter-protocol behaviour. This tool has become a critical resource in the development of our multi-protocol monitoring system; allowing the verification of the monitoring system, identification of new modes of behaviour and the easy visualization of potentially overwhelming quantities of information.
Aging attacks for key extraction on permutation-based obfuscation (2016)

Permutation-based obfuscation has been exploited to protect hardware against cloning, overproduction, and reverse engineering with a secret key. In order to prevent key extraction from memory, this key is usually stored in volatile memory. Since the key is erased after the system loses power, this scheme is often considered the best way to prevent a key from being stolen since many attacks would require power. However, in this paper, we propose a new attack where the key is determined by exploring path aging within the permutation network used for obfuscation. Both the theoretical analysis and experimental results are provided. A practical procedure to achieve the proposed attack is also discussed in the context of an attacker's capabilities and knowledge. We also present an adjustment scheme to improve the accuracy of the attack. Various aging durations, process variations and measurement conditions are considered in our simulations. The experimental results show the accuracy of identifying the key is as high as 92.4% and more than enough to reduce the number of brute force combinations required by an attacker.
Characterization of the humoral immune response to glutamic acid decarboxylase in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) and/or type 1 diabetes (2005)

APECED-associated humoral autoimmunity to GAD65 does not differ markedly from that observed in type 1 diabetes; only IgG2-GAD65 antibodies may be more closely associated with the latter entity.
Alexandria: Extensible Framework for Rapid Exploration of Social Media (2015)

The Alexandria system under development at IBM Research provides an extensible framework and platform for supporting a variety of big-data analytics and visualizations. The system is currently focused on enabling rapid exploration of text-based social media data. The system provides tools to help with constructing "domain models" (i.e., Families of keywords and extractors to enable focus on tweets and other social media documents relevant to a project), to rapidly extract and segment the relevant social media and its authors, to apply further analytics (such as finding trends and anomalous terms), and visualizing the results. The system architecture is centered around a variety of REST-based service APIs to enable flexible orchestration of the system capabilities, these are especially useful to support knowledge-worker driven iterative exploration of social phenomena. The architecture also enables rapid integration of Alexandria capabilities with other social media analytics system, as has been demonstrated through an integration with IBM Research's SystemG. This paper describes a prototypical usage scenario for Alexandria, along with the architecture and key underlying analytics.
The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases (2010)

Metallopeptidases (MPs) are among virulence factors secreted by pathogenic bacteria at the site of infection. One such pathogen is Tannerella forsythia, a member of the microbial consortium that causes peridontitis, arguably the most prevalent infective chronic inflammatory disease known to mankind. The only reported MP secreted by T. forsythia is karilysin, a 52 kDa multidomain protein comprising a central 18 kDa catalytic domain (CD), termed Kly18, flanked by domains unrelated to any known protein. We analysed the 3D structure of Kly18 in the absence and presence of Mg(2+) or Ca(2+) , which are required for function and stability, and found that it evidences most of the structural features characteristic of the CDs of mammalian matrix metalloproteinases (MMPs). Unexpectedly, a peptide was bound to the active-site cleft of Kly18 mimicking a left-behind cleavage product, which revealed that the specificity pocket accommodates bulky hydrophobic side-chains of substrates as in mammalian MMPs. In addition, Kly18 displayed a unique Mg(2+) or Ca(2+) binding site and two flexible segments that could play a role in substrate binding. Phylogenetic and sequence similarity studies revealed that Kly18 is evolutionarily much closer to winged-insect and mammalian MMPs than to potential bacterial counterparts found by genomic sequencing projects. Therefore, we conclude that this first structurally characterized non-mammalian MMP is a xenologue co-opted through horizontal gene transfer during the intimate coexistence between T. forsythia and humans or other animals, in a very rare case of gene shuffling from eukaryotes to prokaryotes. Subsequently, this protein would have evolved in a bacterial environment to give rise to full-length karilysin that is furnished with unique flanking domains that do not conform to the general multidomain architecture of animal MMPs.
Monitoring Therapy Response of Experimental Arthritis with Radiolabeled Tracers Targeting Fibroblasts, Macrophages, or Integrin αvβ3 (2015)

(111)In-28H1, (111)In-anti-F4/80-A3-1, and (111)In-RGD2 can be used to specifically monitor the response to therapy in experimental arthritis at the molecular level. Further studies, however, still need to be performed.
Geometrical Modelling of Jacquard Quilted Structures Weft Knitted Fabrics (2016)

Jacquard quilted structure weft-knitted fabrics have many advantages, such as strong stereoscopic patterns, soft handling, adjustable apparel thickness, and use as home textiles. However, the final visual effects of such fabrics are difficult to predict prior to processing because of the rough surface caused by the connecting yarn and the inlay yarn of the fabric. This research applied a three-dimensional (3D) model instead of the original single-loop model to simulate knitted fabric. The 3D model is more suitable for a multilayer fabric because the simulation is quick, real, and convenient. The article includes experiments on structural parameters concerning regular dents of different samples, analysis of parameter data about the surface, and the simulation process with the objective of understanding the computer simulation of fabric. Results show good correlation between the simulation results and the actual fabric. Importantly, we can clearly see the expected effects in the fabrics without going through production and processing. This research will be useful for establishing a quick computer-generated simulation system for multilayer fabrics.
Dynamic response of 1.3-μm-wavelength InGaAs/GaAs quantum dots (2000)

The temperature-dependent dynamic response of 1.3-μm-InGaAs/GaAs quantum dots is investigated using time-resolved photoluminescence upconversion with subpicosecond temporal resolution for excitation in either the GaAs bulk region surrounding the dots or within the wetting layer. Relaxation to the quantum-dot ground state occurs on a time scale as short as 1 ps, while radiative lifetimes as short as 400 ps are measured. The influence of nonradiative recombination is observed only for temperatures above 250 K. At temperatures below 77 K, an increase in the relaxation time and lifetime is observed when carriers are injected into the bulk GaAs region versus excitation into the wetting layer, which suggests that diffusion in the bulk GaAs region influences both the relaxation rate and the recombination rate.
Selenoprotein-P Deficiency Predicts Cardiovascular Disease and Death (2019)

Selenoprotein-P (SELENOP) is the main carrier of selenium to target organs and reduces tissue oxidative stress both directly and by delivering selenium to protective selenoproteins. We tested if the plasma concentration of SELENOP predicts cardiovascular morbidity and mortality in the primary preventive setting. SELENOP was measured from the baseline exam in 2002-2006 of the Malmö Preventive Project, a population-based prospective cohort study, using a validated ELISA. Quintiles of SELENOP concentration were related to the risk of all-cause mortality, cardiovascular mortality, and a first cardiovascular event in 4366 subjects during a median (interquartile range) follow-up time of 9.3 (8.3-11) years using Cox proportional Hazards Model adjusting for cardiovascular risk factors. Compared to subjects in the lowest quintile of SELENOP, the risk of all three endpoints was significantly lower in quintiles 2-5. The risk (multivariate adjusted hazard ratio, 95% CI) decreased gradually with the lowest risk in quintile 4 for all-cause mortality (0.57, 0.48-0.69) (<i>p</i> < 0.001), cardiovascular mortality (0.52, 0.37-0.72) (<i>p</i> < 0.001), and first cardiovascular event (0.56, 0.44-0.71) (<i>p</i> < 0.001). The lower risk of a first cardiovascular event in quintiles 2-5 as compared to quintile 1 was significant for both coronary artery disease and stroke. We conclude that the 20% with lowest SELENOP concentrations in a North European population without history of cardiovascular disease have markedly increased risk of cardiovascular morbidity and mortality, and preventive selenium supplementation studies stratified for these subjects are warranted.
Alkoxo-bridged Cobalt(II) Cube and Its Radical Adduct (2007)

Abstract Tetranuclear cubic complexes of [Co4(heip)4(MeOH)4] (1) and [Co4(heip)4(nit-p-py)4] (2) (H2heip = 1,1,1,5,5,5-hexafluoro-4-[(2-hydroxyethyl)imino]-2-pentanone and nit-p-py = 2-(p-pyridyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) were prepared. Complexes 1 and 2 have alkoxo-bridged cubic core structures. Magnetic susceptibility measurements revealed the occurrence of ferromagnetic interactions among CoII ions in 1, while antiferromagnetic interactions were operative in 2.
CT of fluid collections associated with pancreatitis (1980)

Fluid collections are an important component of severe pancreatitis because they may produce a detectable mass and may be responsible for prolongation of fever and pain. Among 59 cases of clinically verified pancreatitis, 32 were shown by CT to be complicated by pancreatic and/or extrapancreatic fluid collections. Pancreatic fluid collections, diagnosed in 16 patients, were typically on the anterior or anterolateral surface of the gland and were covered only by a thin layer of fibrous connective tissue. Extrapancreatic fluid collections were detected in the lesser sac (19 cases), anterior pararenal space (15), posterior pararenal space (six), in or around the left lobe of the liver (five), in the spleen (three), and in the mediastinum (one). The potential undesirable consequences of escape of pancreatic juice are necrosis, abscess formation, or prolonged inflammation of the peripancreatic tissues. Relative preservation of pancreatic integrity as observed by CT was regularly found in patients with large extrapancreatic fluid collections, suggesting that escape of pancreatic juice produces a beneficial decompression of the pancreatic duct system.
Lithium ion migration pathways in LiTi2(PO4)3 and related materials (1999)

The diffusion pathways of Li+ ions within the frameworks of the high conductive solid electrolytes LiTi2(PO4)3 and the Al-doped one Li1.3Ti1.7Al0.3P3O12 are determined by molecular mechanics and molecular dynamics methods. From a potential energy profile for the lithium migration in LiTi2(PO4)3, the barrier height of lithium migration is estimated as 28.95 kJ/mol (0.30 eV) which is in excellent agreement with experimental data. The main influence on the activation energy of lithium diffusion is caused by changes in electrostatic interactions. Long molecular dynamics simulations for Li1.3Ti1.7Al0.3P3O12 also confirm a solid state diffusion process via rare and sporadic hopping of Li+ ions from their energy minimum site to a neighboring energy minimum site.
Incidence, risk factors and management of incisional hernia in a high volume liver transplant center (2013)

The risk factors for the development of incisional hernias in liver transplant patients are similar to patients with prior abdominal surgery for other reasons. Intraperitoneal onlay mesh implantation may lead to a decrease of hernia recurrences. The role of immunosuppression in the genesis of incisional hernias requires further elucidation.
Macrocyclic dimeric vanadium(IV) and heterodinuclear vanadium(IV)–nickel(II) complexes. Structure, magnetic, electronic and redox properties (1996)

The oxovanadium(IV) complexes [{VO(H2L1)}2(µ-SO4)][NO3]2, [(VO)L1Ni(H2O)2(SO4)]·H2O and [(VO)L1Ni(µ-SO4)(H2O)]·2H2O have been synthesized from the dinucleating tetraaminodiphenol macrocycle H2L1. The crystal structure of the first, in which two unco-ordinated amino nitrogens are protonated, has been determined. The two distorted-octahedral vanadium centres in the complex, separated by 6.741(4)Å, are bridged by sulfate and have an anti-oxo configuration. In the solid state the magnetic moment of this complex per vanadium decreases from 1.71 to 1.64 µB on lowering the temperature from 299 to 5 K, indicating very weak intra-/or inter-molecular exchange interactions. Its ESR spectra in fluid solution and glass, however, showed the absence of VO ⋯ VO electron-spin interaction. This complex undergoes stepwise oxidation to produce VOIVVOV and VOVVOV species with E1/2(1)= 0.445 V and E½(2)= 0.60 V vs. Ag–AgCl electrode; the comproportionation constant Kc= 4.2 × 102. The other two complexes have identical composition but differ in their IR and UV/VIS spectra and electrochemistry. In the first the oxovanadium(IV) and nickel(II) centres are revesibly oxidized at 0.436 and 0.756 V, respectively, while in the second irreversible oxidation of both metal centres takes place at 1.05 and 1.25 V. Both behave ferromagnetically and their exchange coupling constants J are 10(1) and 6(1) cm–1, respectively.
Processing issues for thin-film CdTe cells and modules (2002)

Among emerging thin-film PV technologies, CdTe-based modules have displayed perhaps the most flexibility with respect to their method of manufacture. Device efficiencies have reached >15% and there appears to be no inherent device instability. Nonetheless, there remain serious technical challenges which must be met if CdTe modules are to be manufactured at a commercially attractive level. This paper identifies and discusses these issues.
Antitumor Effects of Interleukin‐2 Gene‐modified Fibroblasts in an Orthotopic Colon Cancer Model (1999)

We transduced the interleukin-2 (IL-2) gene into murine fibroblasts BALBCL7 or murine colon cancer CT26 using a retroviral vector. BALBCL7 transduced with IL-2 gene secreted 748 pg/ml of IL-2, whereas IL-2 gene-modified CT26 secreted 1,167 pg/ml of IL-2 (48 h incubation, 1x10(6)/ml). Then, we inoculated gene-modified BALBCL7 and/or CT26 cells into BALB/c female mice, and observed the tumor growth. The tumor growth was inhibited in mice inoculated with parental CT26 plus IL-2 gene-modified BALBCL7, compared with that in mice given parental CT26 alone (P<0.01). Moreover, we investigated the cytotoxic activity of spleen cells derived from mice treated with gene-modified cells, and performed phenotypic analysis of the effector cells. The killer cells derived from mice inoculated with IL-2 gene-modified BALBCL7 plus parental CT26 showed higher cytotoxic activity than those from mice inoculated with CT26 alone. The cytotoxic activity was almost completely blocked by anti-CD8 antibody (Ab), and partially blocked by anti-asialo GM1 Ab. Next, we inoculated CT26 tumor tissue into murine cecum orthotopically, and treated the animals with gene-modified BALBCL7 plus parental CT26. The tumor size in the cecum was significantly decreased, compared with parental CT26 alone (P<0.01).
Tau Immunotherapies for Alzheimer’s Disease and Related Tauopathies: Progress and Potential Pitfalls (2018)

Tau immunotherapies have now advanced from proof-of-concept studies to Phase 2 clinical trials. This review briefly outlines developments in the field and discusses how these therapies may work, which involves multiple variables that are connected in complex ways. These various factors are likely to define therapeutic success in humans and have not been thoroughly investigated, at least based on published reports.
GHZ polarization dynamics in ferroelectric thin films (2000)

Abstract We present results from experiments which measure the local dielectric response of ferroelectric thin films driven by microwave-frequency electric fields. The repetition rate of a mode-locked Ti:Sapphire laser is used to generate a microwave drive signal that is phase-locked to an optical probe pulse and applied to the ferroelectric thin film. The induced polarization change in the ferroelectric film is measured stroboscopically via the electro-optic effect. Polarization images are acquired by scanning the laser beam across the sample in a confocal geometry. Time resolution is achieved by changing the delay between the electrical pump and the optical probe. Initial results show large local phase shifts in the ferroelectric response of closely separated regions of a Ba0.5Sr0.5TiO3 thin film. This new experimental technique may help to understand the physical mechanisms of dielectric loss in these materials.
Maximizing the integration of virtual and experimental screening in hit discovery (2022)

Experimental and virtual screening are complementary approaches that should be integrated in lead discovery settings. Virtual screening can access extremely large synthetically feasible chemical space that can be effectively searched on GPU clusters or cloud architectures. Experimental screening provides reliable datasets by quantitative HTS applications, and DNA-encoded libraries (DEL) have enlarged the chemical space covered by these technologies. These developments, together with the use of artificial intelligence methods, represent new options for their efficient integration. The case studies discussed here demonstrate the benefits of complementary strategies, such as focused and iterative screening.
Treating Retinoblastoma in Tissue Culture and in a Rat Model with a Novel Isoquinoline Derivative (2010)

PURPOSE. To investigate the effectiveness of a novel isoquinoline derivative, EDL-155, in killing retinoblastoma in vitro and in vivo. METHODS. Dose-response curves were generated in which Y79 retinoblastoma cells tagged with luciferase (Y79-Luc) were treated with serial concentrations of EDL-155. Electron microscopy was used to evaluate the ultrastructural morphology of EDL-155-treated Y79 cells. To determine whether autophagy was induced in EDL-155-treated Y79-Luc cells, staining with acridine orange and LC-3 immunoblot analysis was performed. To evaluate the efficacy of EDL-155 in vivo, Y79-Luc retinoblastoma cells were injected into the vitreous cavity of newborn rats, followed by periocular injections of EDL-155 (20 mg/kg/day) or an equivalent dosage of saline. RESULTS. EDL-155 appeared to destroy the retinoblastoma cells in vitro with an EC(50) of 9.1 micriM. EDL-155-treated retinoblastoma cells displayed a lack of viable mitochondria and the presence of autophagosomes wrapped in the characteristic double membranes. Acridine orange staining of EDL-155-treated retinoblastoma cells demonstrated the accumulation of vacuoles, and the immunoblots displayed a shift in molecular weight of LC-3, indicative of incorporation into autophagosome vesicles. In the retinoblastoma animal model, four doses of EDL-155 were delivered over 4 days, which was sufficient to see a significant decrease (P = 0.01) in viable intraocular tumors. Seven of the 25 rats treated with EDL-155 had no detectable living tumor. No significant decrease in viable tumor was observed in control animals. CONCLUSIONS. EDL-155 appears to eliminate retinoblastoma cells by disrupting mitochondria and inducing autophagy. Local delivery of EDL-155 may be an effective therapy for some types of ocular cancers.
Far-field control of the radiative lifetime of an individual optical nanocavity (2007)

Using a scanning metallic probe we demonstrate the first long-range control of the radiative lifetime of an optical nanocavity resonant near 1.5 microns. Changes in lifetime are observed for probe-cavity separations up to 70 microns.
Ultrahigh Sensitivity Ferromagnetic Resonance Measurement Based on Microwave Interferometer (2014)

An ultrahigh sensitivity ferromagnetic resonance (FMR) measurement technique based on a microwave interferometer was developed. A comparison between conventional and interferometer-based FMR showed a signal-to-noise ratio (SNR) improvement of as much as 42 dB. This largely improved SNR allowed clear resolution of the FMR signal of the uniform mode on a 100 nm diameter, 5 nm thick CoFeB single nanodot, and even higher order modes on a 400 nm diameter CoFeB single nanodot. A system noise measurement confirmed that the minimum noise level of this technique is set by Johnson noise at the input of the low noise amplifier, which is more than one order of magnitude smaller than the FMR signal obtained from the 100 nm CoFeB single nanodot.
Interactive multiresolution surface viewing (1996)

Multiresolution analysis has been proposed as a basic tool supporting compression, progressive transmission, and level-of-detail control of complex meshes in a unified and theoretically sound way. We extend previous work on multiresolution analysis of meshes in two ways. First, we show how to perform multiresolution analysis of colored meshes by separately analyzing shape and color. Second, we describe efficient algorithms and data structures that allow us to incrementally construct lower resolution approximations to colored meshes from the geometry and color wavelet coefficients at interactive rates. We have integrated these algorithms in a prototype mesh viewer that supports progressive transmission, dynamic display at a constant frame rate independent of machine characteristics and load, and interactive choice of tradeoff between the amount of detail in geometry and color. The viewer operates as a helper application to Netscape, and can therefore be used to rapidly browse and display complex geometric models stored on the World Wide Web. CR
Degradation of Low Molecular Weight Volatile Organic Compounds by Plants Genetically Modified with Mammalian Cytochrome P450 2E1 (2007)

Cytochrome P450 2E1 (CYP2E1) is a key enzyme in the mammalian metabolism of several low molecular weight volatile organic compounds (VOCs), such as trichloroethylene (TCE), vinyl chloride (VC), carbon tetrachloride (CT), benzene, chloroform, and bromodichloromethane (BDCM), which are all common environmental pollutants that pose risks to human health. We have developed a transgenic tobacco (Nicotiana tabacum cv. Xanthii) that expresses CYP2E1 with increased activity toward TCE and ethylene dibromide. In experiments with tobacco plant cuttings exposed to VOCs in small hydroponic vessels, the transgenic tobacco had greatly increased rates of removal of TCE, VC, CT, benzene, toluene, chloroform, and BDCM, compared to wild-type or vector control tobacco, but not of perchloroethylene or 1,1,1-trichloroethane.
Field trial to improve the fibre infrastructure towards 40Gbit/s transmission and beyond and decrease economically efficient the link PMD by exploitation of a POTDR (2009)

The accumulated PMD along several fibres in an optical network was measured in order to identify those short fibre portions exhibiting high PMD. By replacing high-PMD-portion(s) in each fibre, the overall-PMD could be reduced significantly.