gebhart/patrepeval huggingface dataset:
ATAVE: A framework for automatic timing attack vulnerability evaluation (2017)

Timing leakage can be exploited to break a cryptographic system. Even though timing attacks have been well-researched for the past decade, recent system implementations remain highly vulnerable to these attacks. There is a critical need to develop a framework for automatic evaluation of vulnerability of a design against these attacks, so that integrated circuit designers can understand the vulnerability and take appropriate actions to counter them. In this paper, we proposed a novel CAD tool framework for automatic timing attack vulnerability evaluation, referred to as ATAVE, with associated algorithms and metrics. RSA implementation using Montgomery multiplication with square-and-multiply algorithm is efficiently analyzed using ATAVE.
Digital nonlinear compensation techniques for high-speed DWDM transmission systems (2011)

Nonlinear distortion is one of the major obstacles in DWDM systems with enhanced spectral efficiencies. In this paper several approaches to address the issue of nonlinear impairments by means of digital signal processing are discussed. Firstly, implementation-efficient and novel intra-channel nonlinear compensation schemes are proposed; one is based on digital pre-distortion at the transmitter end and the other is based on digital back-propagation at the receiver end. The virtues of the two approaches and implications to various applications are discussed; the pre-distortion technique is in particular advantageous with QPSK modulation format; on the other hand, the improved version of digital back-propagation is attractive in transceivers with adaptive or variable modulation/demodulation. Second, digital signal processing algorithms to counteract inter-channel nonlinearities, namely cross-phase modulation, are discussed; nonlinear polarization crosstalk canceller (NPCC) is proposed for mitigating the impact of nonlinear-induced fast polarization crosstalk in dual-polarization systems (in the speed beyond MHz), which is too fast to be tracked by ordinary polarization demultiplexing algorithms; improvement to the carrier phase recovery circuit and its combination with NPCC are even more useful for further performance improvement. Numerical and experimental data are introduced to support the above discussions.
Transgenic Glutathione Peroxidase Mouse Models for Neuroprotection Studiesa (1994)

Seleno-glutathione peroxidase (GSHPx) is considered to be the major enzymatic activity in charge of removing excess cytosolic and mitochondrial H2O2 in most tissues including brain. Intracellular GSHPx activity is therefore hypothesized to be one important factor that contributes to minimize hydroxyl radical formation via Fenton-type reactions. An animal model was developed to challenge this hypothesis in vivo and evaluate the role of GSHPx in hydroperoxide metabolism and oxidative stress homeostasis. Three lines of transgenic mice, homozygous for the integration of 1 to 3 GSHPx transgene copies, have been generated. The transgene was placed under transcriptional control of a metallothionein promoter (hMT-IIA). This promoter was chosen because metallothionein expression, normally low in most tissues, can be induced by several inflammatory cytokines, protein kinase C activators, and stress agents including heavy metals. The data reported here provide information on the constitutive expression of GSHPx mRNA and enzyme in various brain regions of healthy untreated adult tg-MT-GPx mice. Northern and/or Western analysis indicated that transgenic GSHPx was expressed constitutively in all brain regions investigated in tg-MT-GPx-6 mice, including the cerebral cortex, brainstem, hippothalamus, cerebellum, substantia nigra, and striatum. Similar results were obtained with the two other transgenic lines, tg-MT-GPx-11 and -13. Depending on the brain region, the GSHPx immunoreactivity detected in tissue extracts with an immunoaffinity-purified polyclonal antibody was about 2- to 5-fold stronger in transgenic extracts than in their non-tg counterparts (western blots). In contrast, the corresponding increase in GSHPx activity measured in these extracts was smaller, for example, about 1.5-fold in transgenic mesencephalon. Immunocytochemical data indicated that GSHPx-like staining was distinctly more intense in transgenic midbrain brain sections than in corresponding non-tg sections. Interestingly, only a subset of the cells displayed higher density staining that most likely reflects increased amounts of GSHPx protein. This observation suggests that the stained cells, not yet identified, may have larger GSHPx activity increments than the cell-average increments measured in tissue extracts. Current work is in progress to determine whether transgenic GSHPx expression may be induced by inflammatory processes or perturbations of heavy metal metabolism.
Metathesis Reactions between Heavy d-8 Fluorides and I(III)–Pyridine Complexes (2020)

The reaction between <i>trans</i>-[AuF<sub>2</sub>(pyridine)<sub>2</sub>]<sup>+</sup> and [PhI(pyridine)<sub>2</sub>]<sup>2+</sup> results in the formation of PhIF<sub>2</sub> and [Au(pyridine)<sub>4</sub>]<sup>3+</sup>. Investigation of the reaction pathway using model Pd and Pt analogues of the gold complex indicate that the most likely mechanism is attack by the Au-F onto the I(III), rather than a redox process. This demonstrates that the Au(III)-F fragment can behave in a nucleophilic manner even in a relatively electron-poor cationic complex.
Thymic Medullary Epithelium and Thymocyte Self-Tolerance Require Cooperation between CD28–CD80/86 and CD40–CD40L Costimulatory Pathways (2013)

A critical process during thymic development of the T cell repertoire is the induction of self-tolerance. Tolerance in developing T cells is highly dependent on medullary thymic epithelial cells (mTEC), and mTEC development in turn requires signals from mature single-positive thymocytes, a bidirectional relationship termed thymus crosstalk. We show that CD28-CD80/86 and CD40-CD40L costimulatory interactions, which mediate negative selection and self-tolerance, upregulate expression of LTα, LTβ, and receptor activator for NF-κB in the thymus and are necessary for medullary development. Combined absence of CD28-CD80/86 and CD40-CD40L results in profound deficiency in mTEC development comparable to that observed in the absence of single-positive thymocytes. This requirement for costimulatory signaling is maintained even in a TCR transgenic model of high-affinity TCR-ligand interactions. CD4 thymocytes maturing in the altered thymic epithelial environment of CD40/CD80/86 knockout mice are highly autoreactive in vitro and are lethal in congenic adoptive transfer in vivo, demonstrating a critical role for these costimulatory pathways in self-tolerance as well as thymic epithelial development. These findings demonstrate that cooperativity between CD28-CD80/86 and CD40-CD40L pathways is required for normal medullary epithelium and for maintenance of self-tolerance in thymocyte development.
The Roles of Streptozotocin Neurotoxicity and Neutral Endopeptidase in Murine Experimental Diabetic Neuropathy (2009)

We demonstrated that inhibition of neutral endopeptidase (NEP), a protease that degrades vaso- and neuroactive peptides, improves vascular and neural function in diabetic animal models. In this study we explored the role of NEP in neuropathy related to either insulin-deficient diabetes or diet-induced obesity using NEP deficient (-/-) mice. Initial studies showed that streptozotocin, in the absence of subsequent hyperglycemia, did not induce nerve conduction slowing or paw thermal hypoalgesia. Glucose disposal was impaired in both C57Bl/6 and NEP -/- mice fed a high fat diet. Thermal hypoalgesia and nerve conduction slowing were present in both streptozotocin-diabetic and high fat fed C57Bl/6 mice but not in NEP -/- mice exposed to either streptozotocin-induced diabetes or a high fat diet. These studies suggest that streptozotocin does not induce neurotoxicity in mice and that NEP plays a role in regulating nerve function in insulin-deficient diabetes and diet-induced obesity.
The Schizophrenia Variant V1282F in SCN2A Causes Functional Impairment of NaV1.2 (2021)

Neuropsychiatric disorders such as schizophrenia are challenging to treat due to the biological complexity of the disease and the lack of knowledge of the underlying pathophysiology. Whole exome and genome sequencing studies have identified disease-linked rare variants in patients with large effect size. Here, we functionally characterize the schizophrenia linked variant V1282F in SCN2A, encoding the sodium channel Nav1.2. This variant was introduced into isogenic lines of hiPSCs using CRISPR/CAS9 genome editing tools. hiPSCs were then differentiated into cortical neurons to understand how the variant and gene may be contributing to disease. We observed a significant (~25%) decrease in sodium current in the V1282F neurons compared to control neurons, suggesting the mutation is causing a loss-of-channel function. These results were supported by recordings in recombinant cells overexpressing either the mutant or wildtype Nav1.2, with the mutant channel having significantly (~75%) lower current amplitude than wildtype. We hypothesize that this phenotype may contribute to disease either through the direct loss of neuronal activity or through subsequent abnormal neurodevelopment.
One-dimensional dense disparity estimation for three-dimensional reconstruction (2003)

We present a method for fully automatic three-dimensional (3D) reconstruction from a pair of weakly calibrated images in order to deal with the modeling of complex rigid scenes. A two-dimensional (2D) triangular mesh model of the scene is calculated using a two-step algorithm mixing sparse matching and dense motion estimation approaches. The 2D mesh is iteratively refined to fit any arbitrary 3D surface. At convergence, each triangular patch corresponds to the projection of a 3D plane. The proposed algorithm relies first on a dense disparity field. The dense field estimation modelized within a robust framework is constrained by the epipolar geometry. The resulting field is then segmented according to homographic models using iterative Delaunay triangulation. In association with a weak calibration and camera motion estimation algorithm, this 2D planar model is used to obtain a VRML-compatible 3D model of the scene.
Functional connectivity between Bötzinger complex glycinergic neurons and parafacial late‐expiratory neurons for expiratory and sympathetic control (712.17) (2014)

Our computational model predicts that post‐inspiratory (post‐I) neurons expressing the glycine transporter 2 (GLYT2) located in the Bötzinger Complex (BötC) suppress generation of abdominal and sympathetic late‐expiratory (late‐E) activities in eucapnia. Hypercapnia allows parafacial late‐E neurons to escape this inhibition. To test functional connectivity between glycinergic BötC and late‐E neurons, we used cell‐type specific viral vector expression of channelrhodopsin (ChETA) or hallorhodopsin (eNpHR3.0) to excite/inhibit GLTY2 neurons in the BötC of rats. Intracellular recordings of parafacial late‐E neurons (n=9) confirmed that inhibition during post‐I prevents generation of late‐E activity under eucapnia. eNpHR3.0‐mediated inhibition of GLYT2 neurons in the BötC evoked abdominal and sympathetic late‐E activities and increased arterial pressure (n=4).In contrast, ChETA‐mediated excitation of GLYT2 neurons in the BötC abolished the CO2‐induced abdominal and sympathetic late‐E activities (n=4), due to inhibition of parafacial late‐E neurons (n=3). These results indicate an emergence of parafacial late‐E activity with hypercapnia which is normally suppressed by BötC glycinergic neurons. Grant Funding Source : Supported by NIH R01 NS069220 and FAPESP
Relationship between Corneal Temperature and Intraocular Pressure in Healthy Individuals: A Clinical Thermographic Analysis (2016)

Purpose. To study the geographical distribution of corneal temperature (CT) and its influence on the intraocular pressure (IOP) of healthy human volunteers. Materials and Methods. Fifteen subjects (7 M, 8 F), 33.8 ± 17.4 years old, were enrolled in this pilot, cross-sectional study. Measurements of CT were taken after one hour with closed eyelids (CET) or closed eyelids with a cooling mask (cm-CET) and compared to baseline. Results. If compared to baseline, after CET, average CT significantly increased by 0.56°C in the RE and by 0.48°C in the LE (p < 0.001) and IOP concomitantly significantly increased by 1.13 mmHg and 1.46 mmHg, respectively, in each eye (p < 0.001). After cm-CET, average CT significantly decreased by 0.11°C and 0.20°C, respectively, in the RE and LE (RE p = 0.04; LE p = 0.024), followed by a significant IOP decrease of 2.19 mmHg and 1.54 mmHg, respectively, in each eye (RE p < 0.001; LE p = 0.0019). Conclusion. Significant variations of CT occurred after CET and cm-CET and were directly correlated with significant differences of IOP. It can be speculated that both oxidative stress and sympathetic nerve fiber stimulation by temperature oscillations may affect the regulation of AH vortex flow and turnover, thus influencing IOP values.
Generating 3D People in Scenes without People (2019)

We present a fully automatic system that takes a 3D scene and generates plausible 3D human bodies that are posed naturally in that 3D scene. Given a 3D scene without people, humans can easily imagine how people could interact with the scene and the objects in it. However, this is a challenging task for a computer as solving it requires that (1) the generated human bodies to be semantically plausible within the 3D environment (e.g. people sitting on the sofa or cooking near the stove), and (2) the generated human-scene interaction to be physically feasible such that the human body and scene do not interpenetrate while, at the same time, body-scene contact supports physical interactions. To that end, we make use of the surface-based 3D human model SMPL-X. We first train a conditional variational autoencoder to predict semantically plausible 3D human poses conditioned on latent scene representations, then we further refine the generated 3D bodies using scene constraints to enforce feasible physical interaction. We show that our approach is able to synthesize realistic and expressive 3D human bodies that naturally interact with 3D environment. We perform extensive experiments demonstrating that our generative framework compares favorably with existing methods, both qualitatively and quantitatively. We believe that our scene-conditioned 3D human generation pipeline will be useful for numerous applications; e.g. to generate training data for human pose estimation, in video games and in VR/AR. Our project page for data and code can be seen at: \url{https://vlg.inf.ethz.ch/projects/PSI/}.
Development of Low-Cost Alloy Supported SOFCs (2003)

The LBNL group has been developing ferritic steel supported solid oxide fuel cells. The use of ferritic steel as a support for electrode supported solid oxide fuel cells greatly reduces the raw materials cost and improves the strength of the thin-film cells. The basic design includes the use of a high-strength FeCr support, a thin interlayer electrode (Ni-YSZ or other), and a thin electrolyte film. The entire structure is fabricated through co-firing of the three layers in a reducing environment. This paper describes the preliminary performance of the metal supported cells, as well as a variety of possible interlayer electrodes.
Combined dose and geometry correction (DMG) for low energy multi electron beam lithography (5kV): application to the 16nm node (2012)

Lithography faces today many challenges to meet the ITRS road-map. 193nm is still today the only existing industrial option to address high volume production for the 22nm node. Nevertheless to achieve such a resolution, double exposure is mandatory for critical level patterning. EUV lithography is still challenged by the availability of high power source and mask defectivity and suffers from a high cost of ownership perspective. Its introduction is now not foreseen before 2015. Parallel to these mask-based technologies, maskless lithography regularly makes significant progress in terms of potential and maturity. The massively parallel e-beam solution appears as a real candidate for high volume manufacturing. Several industrial projects are under development, one in the US, with the KLA REBL project and two in Europe driven by IMS Nanofabrication (Austria) and MAPPER (The Netherlands). Among the developments to be performed to secure the takeoff of the multi-beam technology, the availability of a rapid and robust data treatment solution will be one of the major challenges. Within this data preparation flow, advanced proximity effect corrections must be implemented to address the 16nm node and below. This paper will detail this process and compare correction strategies in terms of robustness and accuracy. It will be based on results obtained using a MAPPER tool within the IMAGINE program driven by CEA-LETI, in Grenoble, France. All proximity effects corrections and the dithering step were performed using the software platform Inscale® from Aselta Nanographics. One important advantage of Inscale® is the ability to combine both model based dose and geometry adjustment to accurately pattern critical features. The paper will focus on the advantage of combining those two corrections at the 16nm node instead of using only geometry corrections. Thanks to the simulation capability of Inscale®, pattern fidelity and correction robustness will be evaluated and compared between the correction strategies. This work will be lead on the most critical layers of the 16nm integrate circuits layouts which are contact and metal 1. Finally the aim of this paper is to demonstrate that a complete data preparation flow including advanced proximity effects corrections, simulation and verification capabilities is available for the maskless lithography at the 16nm node and below, through the direct write version of Inscale®. This data preparation platform is already in use in several laboratories for direct write processes.
Erythropoietin or Darbepoetin for patients with cancer - meta-analysis based on individual patient data (2008)

BackgroundErythropoiesis-stimulating agents (ESAs) reduce anemia in cancer patients and may improve quality of life, but there are concerns that ESAs might increase mortality. ObjectivesOur objectives were to examine the effect of ESAs and identify factors that modify the effects of ESAs on overall survival, progression free survival, thromboembolic and cardiovascular events as well as need for transfusions and other important safety and efficacy outcomes in cancer patients. Search strategyWe searched the Cochrane Library, Medline, Embase and conference proceedings for eligible trials.Manufacturers of ESAs were contacted to identify additional trials. Selection criteria1 Erythropoietin or Darbepoetin for patients with cancer -meta-analysis based on individual patient data (Review) Copyright © 2009 The Cochrane Collaboration.Published by
Bringing Onco-Innovation to Europe’s Healthcare Systems: The Potential of Biomarker Testing, Real World Evidence, Tumour Agnostic Therapies to Empower Personalised Medicine (2021)

Rapid and continuing advances in biomarker testing are not being matched by uptake in health systems, and this is hampering both patient care and innovation. It also risks costing health systems the opportunity to make their services more efficient and, over time, more economical. The potential that genomics has brought to biomarker testing in diagnosis, prediction and research is being realised, pre-eminently in many cancers, but also in an ever-wider range of conditions-notably <i>BRCA1/2</i> testing in ovarian, breast, pancreatic and prostate cancers. Nevertheless, the implementation of genetic testing in clinical routine setting is still challenging. Development is impeded by country-related heterogeneity, data deficiencies, and lack of policy alignment on standards, approval-and the role of real-world evidence in the process-and reimbursement. The acute nature of the problem is compellingly illustrated by the particular challenges facing the development and use of tumour agnostic therapies, where the gaps in preparedness for taking advantage of this innovative approach to cancer therapy are sharply exposed. Europe should already have in place a guarantee of universal access to a minimum suite of biomarker tests and should be planning for an optimum testing scenario with a wider range of biomarker tests integrated into a more sophisticated health system articulated around personalised medicine. Improving healthcare and winning advantages for Europe's industrial competitiveness and innovation require an appropriate policy framework-starting with an update to outdated recommendations. We show herein the main issues and proposals that emerged during the previous advisory boards organised by the European Alliance for Personalized Medicine which mainly focus on possible scenarios of harmonisation of both oncogenetic testing and management of cancer patients.
Development of new Si-contained hardmask for tri-layer process (2011)

In the advanced semiconductor lithography process, the tri-layer process have been used for the essential technique{photoresist/ silicon contained hard mask (Si-HM) / spin on carbon hard mask (SOC)}(Figure 1). Tri-layer process was introduced and applied to the L/S and C/H patterning in the ArF dry and ArF immersion lithography process. Therefore, Si-HM should have the wider compatibility with different photoresist. In this paper, we investigate the interface behavior between photoresist and Si-HM in detail and get the new Si-HM to have the wider compatibility with different photoresist.
Calsequestrin, Myosin, and the Components of the Protein‐Glycogen Complex in Rabbit Skeletal Muscle (1978)

The protein‐glycogen particle preparation isolated from rabbit skeletal muscle extracts by mild acidification and differential centrifugation shows eight major protein‐staining bands when examined by polyacrylamide gel electrophoresis, five of which have previously been identified as the glycogen debranching enzyme, the α and β subunits of phosphorylase kinase, glycogen phosphorylase and glycogen synthase [Taylor, C., Cox, A. J., Kernohan, J. C. &amp; Cohen, P. (1975) Eur. J. Biochem. 51 , 105–115]. The other three major proteins in this preparation have now been identified. Two of the proteins were identified as the heavy chain of myosin and actin respectively, based on their electrophoretic migration, their insolubility in buffers of low ionic strength, and their solubility in buffers containing 0.6 M KCl. The third protein has been found to be calsequestrin, a major calcium‐binding protein of the sarcoplasmic reticulum. This conclusion was based on the unusual chromatographic behaviour of the protein on DEAE‐cellulose at pH 7.5, its electrophoretic mobility, amino acid composition, and immunological cross reactivity. A simple method for the isolation of calsequestrin as a by‐product of the purification of glycogen synthase has been developed, by which 70–80 mg of the protein were routinely isolated from 5000 g of muscle (6 rabbits) within five days. The protein was homogeneous by the criterion of polyacrylamide gel electrophoresis and sedimentation equilibrium centrifugation. The molecular weight determined by the latter technique was 41000 and the absorbance index A 280 nm 1% , was 11.7. The protein had a very low sedimentation coefficient of 1.97 S indicating that it is either very asymmetric or a largely unfolded protein, in the buffers used in these experiments, a conclusion supported by its abnormal gel filtration behaviour. Since the three hitherto unidentified components of the protein‐glycogen particle preparation are not enzymes of glycogen metabolism and merely constituents of particulate material (actomyosin and fragments of the sarcoplasmic reticulum) which have coprecipitated with the protein‐glycogen complex, over 95% of the protein attached to glycogen is accounted for by just four enzymes.