gebhart/patrepeval huggingface dataset:
There is Wisdom in Harnessing the Strengths of your Enemy: Customized Encoding to Thwart Side-Channel Attacks (2016)

Side-channel attacks are an important concern for the security of cryptographic algorithms. To counteract it, a recent line of research has investigated the use of software encoding functions such as dual-rail rather than the well known masking countermeasure. The core idea consists in encoding the sensitive data with a fixed Hamming weight value and perform all operations following this fashion. This new set of countermeasures applies to all devices that leak a function of the Hamming weight of the internal variables. However when the leakage model deviates from this idealized model, the claimed security guarantee vanishes. In this work, we introduce a framework that aims at building customized encoding functions according to the precise leakage model based on stochastic profiling. We specifically investigate how to take advantage of adversary’s knowledge of the physical leakage to select the corresponding optimal encoding. Our solution has been evaluated within several security metrics, proving its efficiency against side-channel attacks in realistic scenarios. A concrete experimentation of our proposal to protect the PRESENT Sbox confirms its practicability. In a realistic scenario, our new custom encoding achieves a hundredfold reduction in leakage compared to the dual-rail, although using the same code length.
Extraction of Fowler-Nordheim parameters of thin SiO/sub 2/ oxide film including polysilicon gate depletion: validation with an EEPROM memory cell (2002)

The simulation of EEPROM memory characteristics is fundamental to the design and optimization of low-power non-volatile memory products. This paper presents a new method for extraction of Fowler-Nordheim parameters in a thin (polysilicon-gate) SiO/sub 2/ oxide. It consists of extraction of the oxide thickness from MOS capacitance characteristics including polysilicon-gate depletion. Then, we use the oxide thickness to estimate the electric field for the extraction of the FN current parameters.
Optical signal-to-noise ratio measurement by optical homodyne tomography (2006)

An all-fiber optical homodyne tomography setup is introduced that measures the optical signal-to-noise ratio through reconstruction of the photon statistics. The scheme described has been conceived for applications to optical communications. In particular, the signal-to-noise ratio has been evaluated at lambda= 1.55 microm as a function of the received power. From the experimental data, in the case of optically amplified signals, the amplifier noise figure can be estimated.
Point-NeRF: Point-based Neural Radiance Fields (2022)

Volumetric neural rendering methods like NeRF [34] generate high-quality view synthesis results but are optimized per-scene leading to prohibitive reconstruction time. On the other hand, deep multi-view stereo methods can quickly reconstruct scene geometry via direct network inference. Point-NeRF combines the advantages of these two approaches by using neural 3D point clouds, with associated neural features, to model a radiance field. Point-NeRF can be rendered efficiently by aggregating neural point features near scene surfaces, in a ray marching-based rendering pipeline. Moreover, Point-NeRF can be initialized via direct inference of a pre-trained deep network to produce a neural point cloud; this point cloud can be finetuned to surpass the visual quality of NeRF with 30× faster training time. Point-NeRF can be combined with other 3D re-construction methods and handles the errors and outliers in such methods via a novel pruning and growing mechanism.
Influence of Surface Cleaning on the Wettability of Quartz/Oil/Brine Systems (2023)

Wettability is the measure of a liquid’s ability to adhere to or spread on a solid surface. The contact angle is a quantitative measure of wettability but can be affected by surface cleaning processes. The systematic investigation of wettability modification caused by surface cleaning is lacking. This study employs pure quartz substrates to examine the effect of rock surface cleaning on the wettability of rock/oil/brine systems. The nonporous substrates were polished and aged in solvents and formation fluids before being cleaned with different agents. Wettability was assessed using the contact angle technique at elevated pressures (0.1–50 MPa) and temperatures (353 K). The study also examined adsorption, surface morphology, roughness, and changes in rock strength using scanning electron microscopy (SEM), scanning probe microscopy (SPM), and nanoindentation. Fourier transform infrared spectroscopy (FTIR) and X-ray fluorescence (XRF) analyses were also performed before and after exposure to fluids. The results showed that interactions between quartz–brine, quartz–oil, and quartz–solvents significantly influence the wetting behavior. Our findings suggest that cleaning agents may not completely remove all adsorbed salts and crude oil components from the rock surfaces and may also adsorb onto the surfaces themselves, altering wettability. The presence of oxygen-containing groups, such as hydroxyl groups (O–H), increased the surface energy and promoted hydrophilic behavior, making the surface more water-wet. While the presence of nonpolar functional groups, like alkyl groups (−CH3), aromatic C–H, and methylene (CH2) groups, makes the surface more oil-wet. Interestingly, an increase in pressure has little or no effect on the contact angle of the n-decane/brine/rock system, but exposure to fluids did modify rock surface roughness and strength. Overall, this study provides valuable insights into rock surface cleaning and its influence on the wettability of rock/oil/brine systems. Understanding these interactions is crucial for various applications in the oil and gas industry.
3D LayoutCRF for Multi-View Object Class Recognition and Segmentation (2007)

We introduce an approach to accurately detect and segment partially occluded objects in various viewpoints and scales. Our main contribution is a novel framework for combining object-level descriptions (such as position, shape, and color) with pixel-level appearance, boundary, and occlusion reasoning. In training, we exploit a rough 3D object model to learn physically localized part appearances. To find and segment objects in an image, we generate proposals based on the appearance and layout of local parts. The proposals are then refined after incorporating object-level information, and overlapping objects compete for pixels to produce a final description and segmentation of objects in the scene. A further contribution is a novel instance penalty, which is handled very efficiently during inference. We experimentally validate our approach on the challenging PASCAL'06 car database.
Characterization of the Intracellular Localization, Processing, and Secretion of Two Glial Cell Line-Derived Neurotrophic Factor Splice Isoforms (2010)

Endocrine and neuronal cells have highly developed secretion mechanisms, and the secretion can be either constitutive or regulated by physiological stimuli. In the constitutive pathway, intracellular transport vesicles undergo immediate fusion reactions after arrival at the target. In regulated secretion, vesicles accumulate near the target membrane until triggered to fuse, typically by a local rise in free Ca(2+). In the present study, we characterize the processing and secretion mechanisms of the glial cell line-derived neurotrophic factor (GDNF). Although the function of GDNF has been extensively studied, very little is known about the basic cell biology of GDNF and its precursor forms (alpha)pro-GDNF and (beta)pro-GDNF that have different pro-regions. Our results show that both (alpha)pro-GDNF and (beta)pro-GDNF are secreted. We demonstrate that KCl-induced depolarization increases the secretion of (beta)pro-GDNF and corresponding mature GDNF, but not (alpha)pro-GDNF and corresponding mature GDNF, to the cell medium in a Ca(2+)-dependent manner. In parallel with this, immunofluorescence analysis of cells show that (alpha)pro-GDNF/GDNF is localized mostly in the Golgi complex, whereas (beta)pro-GDNF/GDNF is localized primarily in secretogranin II and Rab3A-positive vesicles of the regulated secretory pathway. In addition, we find that matrix metalloproteinases and plasmin that cleave pro-BDNF and pro-NGF are not responsible for the cleavage of pro-GDNF, whereas furin endoproteinase, PACE4, and proprotein convertases PC5A, PC5B, and PC7 can cleave pro-GDNF into mature GDNF. Thus, the processing and secretion mechanisms of GDNF are different from those of BDNF and NGF.
Low‐Temperature and Hysteresis‐Free Electron‐Transporting Layers for Efficient, Regular, and Planar Structure Perovskite Solar Cells (2015)

With the aim of fully utilizing the low processing temperatures of perovskite solar cells, significant progress in replacing high temperature processed TiO 2 by various low‐temperature solution processed electron transporting layers (LT‐ETLs) was recently reported. Here, recent progress in the development of LT‐ETLs for regular planar structure perovskite solar cells, which is essential for achieving high efficiency in parallel to avoiding hysteresis, is reviewed. In addition, the application of a novel hysteresis‐free LT‐ETLs for regular planar perovskite solar cells in our laboratory is briefly discussed. By incorporating a low temperature processed WO x nanoparticular layer in combination with a mixed fullerene functionalized self‐assembled monolayers (SAMs), a regular, planar structure, and hysteresis‐free perovskite solar cell with a maximum efficiency of almost 15% can be fabricated.
Modulation of the Auditory Cortex during Speech: An MEG Study (2002)

Several behavioral and brain imaging studies have demonstrated a significant interaction between speech perception and speech production. In this study, auditory cortical responses to speech were examined during self-production and feedback alteration. Magnetic field recordings were obtained from both hemispheres in subjects who spoke while hearing controlled acoustic versions of their speech feedback via earphones. These responses were compared to recordings made while subjects listened to a tape playback of their production. The amplitude of tape playback was adjusted to match the amplitude of self-produced speech. Recordings of evoked responses to both self-produced and tape-recorded speech were obtained free of movement-related artifacts. Responses to self-produced speech were weaker than were responses to tape-recorded speech. Responses to tones were also weaker during speech production, when compared with responses to tones recorded in the presence of speech from tape playback. However, responses evoked by gated noise stimuli did not differ for recordings made during self-produced speech versus recordings made during tape-recorded speech playback. These data suggest that during speech production, the auditory cortex (1) attenuates its sensitivity and (2) modulates its activity as a function of the expected acoustic feedback.
Power Penalty in Multibit Differential Phase Shift Keying Demodulation (2006)

We demonstrate the power penalty associated with multi-bit delay DPSK demodulation. We observed a spectral filtering induced for multi-bit while frequency offset tolerance scales as 1/bit-delay and the delay-mismatch tolerance decreases by 20%.
Syndiospecific living polymerization of 4-methylstyrene with (trimethyl)pentamethylcyclopentadienyltitanium/tris(pentafluorophenyl)borane/trioctylaluminium catalytic system (1999)

The polymerization of 4-methylstyrene with the (trimethyl)pentamethylcyclopentadienyltitanium (Cp*TiMe3)/tris(pentafluorophenyl)borane (B(C6F5)3)/trioctylaluminium (AlOct3) catalytic system at –20°C was carried out. The number-average molecular weight (Mn) of the polymers increased linearly with increasing monomer conversion. The propagating chain ends were successfully reacted with tert-butyl isocyanate, and the Mn of the polymer determined by 1H NMR was in good agreement with the Mn determined by GPC measurement. It is concluded that this catalytic system promoted the syndiospecific living polymerization of 4-methylstyrene.
Information-Theoretic Distance Measures and a Generalization of Stochastic Resonance (1998)

We show that stochastic resonance (SR)-like phenomena in a nonlinear system can be described in terms of maximization of information-theoretic distance measures between probability distributions of the output variable or, equivalently, via a minimum probability of error in detection. This offers a new and unifying framework for SR-like phenomena in which the ``resonance'' becomes independent of the specific method used to measure it, the static or dynamic character of the nonlinear device in which it occurs, and the nature of the input signal. Our approach also provides fundamental limits of performance and yields an alternative set of design criteria for optimization of the information processing capabilities of nonlinear devices.
Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes–2 (2017)

Breakthroughs in Medicinal Chemistry: New Targets and Mechanisms, New Drugs, New Hopes is a series of Editorials, which are published on a biannual basis by the Editorial Board of the Medicinal Chemistry section of the journal Molecules [...].
Storage optimization for 3D streaming systems (2014)

Three dimensional (3D) content is becoming attractive in entertainment events such as soccer games and movies. Also, 3D displays are widespread at homes, offices, and theaters. Yet, 3D content may lack good 3D experience due to varying display technologies and sizes. In addition, 3D content providers may not be able to deliver their content to all potential subscribers, which leads to viewership reduction or dissatisfaction. In this work, we propose the design of a system for enhanced 3D content streaming. In order to support all 3D display technologies and sizes in the system, we design different 3D versions of the original videos that are optimized for various displays. Moreover, we propose a storage optimization algorithm that optimizes storage usage in our system depending on versions popularity as well as storage and processing requirements. The algorithm satisfies the limited processing resources, maximum delay, and request rate requirements. We implemented and deployed the proposed system on the cloud for live testing. We simulated the proposed algorithm to study its effect on the storage requirements in 3D streaming systems. The results of the simulations show that the algorithm can achieve storage gain up to 360x compared to storing all versions.
Ultralow Power Computing with Sub-threshold Leakage: A Comparative Study of Bulk and SOI Technologies (2006)

This paper presents a novel design methodology for ultralow power design (in bulk and double-gate SOI technology) using sub-threshold leakage as the operating current (suitable for medium frequency of operation: tens to hundreds of MHz). It has been shown that a complete co-design at all levels of hierarchy (device, circuit and architecture) is necessary to reduce the overall power consumption. Simulation results of co-design on a five-tap FIR filter shows ~2.5times (for bulk) and ~3.8times (for SOI) improvement in throughput at iso-power compared to a conventional design. It has been further demonstrated that the double-gate SOI technology is better suited for sub-threshold operation
Reverberant speech recognition: A phoneme analysis (2014)

We present a phoneme confusion analysis that models the impact of reverberation on automatic speech recognition performance by formulating the problem in a Bayesian framework. Our analysis under reverberant conditions shows the relative robustness to reverberation of each phoneme and also indicates that substitutions and deletions correspond to the most common errors in a phoneme recognition task. Finally, a model is proposed to estimate the confusability of each phoneme depending on the reverberation level which is evaluated using two independent data sets.
Multilevel and Three‐Dimensional Nanomagnetic Recording (2009)

This chapter contains sections titled: Introduction Multilevel Magnetic Recording Multilevel Data Encoding Conclusions Acknowledgments References
Remote Sensing of In-Use Heavy-Duty Diesel Trucks (2006)

On-road measurements in 2005 of carbon monoxide (CO), hydrocarbons, nitric oxide, nitrogen dioxide, and sulfur dioxide from 1641 individually identified heavy-duty diesel trucks at two locations in Colorado are reported. Carbon monoxide and nitric oxide show increasing emissions with increased altitude. Oxides of nitrogen (NOx) emissions have decreased with more recent model years over the last 10 years but are the same as vehicles that are 20 years old. At the Golden, CO site, there was a statistically significant decrease in fleet emissions of CO and NOx since a similar study in 1999. There was no emission trend for CO or NOx with gross vehicle weight or odometer in units of grams of pollutant per kilogram of fuel consumed. Data from this study suggest that on-road remote sensing can detect illegal, high sulfur fuel use from individual heavy-duty diesel trucks. Ammonia emissions from this study were below the detection limit of the instrument but will be useful as a baseline value for future comparison.
GPU-Based PET Image Reconstruction Using an Accurate Geometrical System Model (2012)

In positron emission tomography (PET), 3D iterative image reconstruction methods have a huge computational burden. In this paper, we developed a list-mode image reconstruction method using graphics processing units (GPUs). Efficiency of acceleration for GPU implementation largely depends on the method chosen, where a reduced number of conditional statements and a reduced memory size are required. On the other hand, accurate system models are required to improve the quality of reconstructed images. Various accurate system models for conventional CPU implementation have been proposed, but these models basically require many conditional statements and huge memory size. Therefore, we developed a new system model which matches GPU implementation better. In this model, the detector response functions, which vary depending on each line of response (LOR), are pre-computed in CPUs and modeled by sixth-order polynomial functions in order to reduce the memory size occupied in GPUs. Each element of a system matrix is obtained on-the-fly in GPUs by calculating the distance between an LOR and a voxel. Therefore the developed system model enables efficient GPU implementation of the accurate system modeling with a reduced number of conditional statements and a reduced memory size. We applied the developed method to a small OpenPET prototype, in which 4-layered depth-of-interaction (DOI) detectors were used. For image reconstruction, we used the dynamic row-action maximum likelihood algorithm (DRAMA). Compared with a conventional model for GPU implementation, in which DRFs are given as a Gaussian function of fixed width, we saw no remarkable difference for DOI data, but for non-DOI data the proposed model outperformed the conventional at the peripheral region of the field-of-view. The proposed model had almost the same calculation time as the conventional model did. For further acceleration, we tried parallel GPU implementation, and we obtained 3.8-fold acceleration by using 4 GPUs.
Simulator and Experimental Framework for the MAC of Power-Line Communications (2014)

INDY2
Oscillator-based ADCs: An exploration of time-mode analog-to-digital conversion (2017)

This paper introduces two novel ideas within the field of time-mode oscillator-based analog-to-digital conversion. In the form of a self-injection-locked ring-oscillator (SILRO), a method is presented to inherently linearise the voltage-to-frequency (V-F) characteristic, while an alternative proposal of an ultra-low-power (ULP), ultra-low-voltage (ULV) VCO-based analog-to-digital converter (ADC) operating in weak-inversion at a supply of 0.2 V is suitable for high power efficiency, direct energy harvesting applications. The ideas are distinctly separate in concept and physical implementation, but through the common platform of Verilog-A behavioural modelling, a unified methodology applicable to both architectures is proposed for system level exploration and performance evaluation.
Abstract 1888: Protein kinase C beta II suppresses colorectal cancer by regulating IGF1 mediated cell survival (2016)

Abstract Despite extensive efforts, cancer therapies directed at the Protein Kinase C (PKC) family of serine/threonine kinases have failed in clinical trials. These therapies have been directed at inhibiting PKC and have, in some cases, worsened disease outcome. Here we examine colon cancer patients and show not only that PKC Beta II is a tumour suppressor, but patients with low levels of this isozyme have significantly decreased disease free survival. Specifically, analysis of gene expression levels of all PKC genes in matched normal and cancer tissue samples from colon cancer patients revealed a striking down-regulation of the gene coding PKC Beta in the cancer tissue (n = 21). Tissue microarray analysis revealed a dramatic down-regulation of PKC Beta II protein levels in both the epithelial and stromal diseased tissue (n = 166). Of clinical significance, low levels of the protein in the normal tissue of patients is associated with a low (10%) 10 year survival compared with a much higher (60%) survival in patients with relatively high levels of the protein. Consistent with PKC Beta II levels protecting against colon cancer, overexpression of PKC Beta II in colon cancer cell lines reveals that PKC Beta II reverses transformation in cell based assays. Further to this, activation of PKC Beta II in an IGF-1 dependent manor showed a downregulation of AKT, indicating a role for PKCs in regulating IGF-1 mediated cell survival. Thus, PKC Beta II is a tumour suppressor in colon cancer and low levels serve as a predictor for poor survival outcome. Citation Format: Catriona M. Dowling, James Phelan, Julia A. Callender, Mary Clare Cathcart, Brian Mehigan, Paul McCormick, Tara Dalton, John C. Coffey, Alexandra C. Newton, Jacintha O’Sullivan, Patrick A. Kiely. Protein kinase C beta II suppresses colorectal cancer by regulating IGF1 mediated cell survival. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1888.
Structural genomics is the largest contributor of novel structural leverage (2009)

The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today's UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849-851, 2007) has resulted from systematic targeting of large families. PSI's per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another approximately15 years to cover most sequences in the current UniProt database.