gebhart/patrepeval huggingface dataset:
Detection and Mitigation of Byzantine Attacks in Distributed Training (2022)

A plethora of modern machine learning tasks require the utilization of large-scale distributed clusters as a critical component of the training pipeline. However, abnormal Byzantine behavior of the worker nodes can derail the training and compromise the quality of the inference. Such behavior can be attributed to unintentional system malfunctions or orchestrated attacks; as a result, some nodes may return arbitrary results to the parameter server (PS) that coordinates the training. Recent work considers a wide range of attack models and has explored robust aggregation and/or computational redundancy to correct the distorted gradients. In this work, we consider attack models ranging from strong ones: $q$ omniscient adversaries with full knowledge of the defense protocol that can change from iteration to iteration to weak ones: $q$ randomly chosen adversaries with limited collusion abilities which only change every few iterations at a time. Our algorithms rely on redundant task assignments coupled with detection of adversarial behavior. We also show the convergence of our method to the optimal point under common assumptions and settings considered in literature. For strong attacks, we demonstrate a reduction in the fraction of distorted gradients ranging from 16%-99% as compared to the prior state-of-the-art. Our top-1 classification accuracy results on the CIFAR-10 data set demonstrate 25% advantage in accuracy (averaged over strong and weak scenarios) under the most sophisticated attacks compared to state-of-the-art methods.
Purkinje tissue modification and ventricular fibrillation (2019)

Dr. Asirvatham:
Effects of a Phase Rotation Scheme on the DTX Detection Performance for the E-UTRA Uplink ACK/NACK Signals (2011)

Hybrid automatic repeat request (HARQ) is employed for the Evolved Universal Terrestrial Radio Access (E-UTRA) downlink. The base station not only decodes the ACK/NACK signals from the user equipment (UE), but also detects a termination of the transmission (DTX) of the ACK/NACK signals caused by the mis-detection of the downlink control information (DCI) at the UE side. Since ACK/NACK signals from UEs are multiplexed by CDMA, there are sometimes severe inter-code interference (ICI) effects, which significantly degrade the performance of ACK/NACK signals. In order to mitigate such ICI effects, in [1],[2], we proposed a novel phase rotation scheme on the constellations of the uplink ACK/NACK signals, and confirmed the effects on the ACK/NACK bit error rate performance; however, the previous paper did not analyze the effects of the phase rotation on the DTX detection performance. Hence, in this paper, we further analyze the effects of the phase rotation for the ACK/NACK signals in conjunction with a new DTX detection scheme which utilizes equalizer outputs, and investigate the performance of the proposed scheme by means of computer simulations.
Generalized Semiparametric Regression with Covariates Measured with Error (2009)

We develop generalized semiparametric regression models for exponential family and hazard regression where multiple covariates are measured with error and the functional form of their effects remains unspecified. The main building blocks in our approach are Bayesian penalized splines and Markov chain Monte Carlo simulation techniques. These enable a modular and numerically efficient implementation of Bayesian measurement error correction based on the imputation of true, unobserved covariate values. We investigate the performance of the proposed correction in simulations and an epidemiological study where the duration time to detection of heart failure is related to kidney function and systolic blood pressure.
Development of the Wireless Vibration Sensor Module with the Anomaly Detection Function Calculated by the Variational Auto-Encoder (VAE) (2021)

An ultra-low power consumption wireless vibration sensor module system equipped with an abnormality determination function using a variable automatic encoder (VAE) has been developed as a new method of anomaly prediction solution for rotating equipment such as motors, pumps, and fans, which are widely used in factories. This system uses a cloud service to learn the vibration conditions of rotating equipment during normal operation, and after wirelessly transmitting the learning parameters to the sensor module, the sensor module itself calculates the abnormality score. In order to be able to transmit the learning parameters wirelessly via LPWA, a compression method using branch pruning and quantization has been established. In addition, it was confirmed that the monitoring by the anomaly score by VAE can detect the anomaly of the equipment more quickly than the conventional monitoring by the vibration characteristic evaluation index value, and this method was confirmed to be extremely useful.
Chromosomal periodicity of evolutionarily conserved gene pairs (2007)

Chromosomes are compacted hundreds of times to fit in the cell, packaged into dynamic folds whose structures are largely unknown. Here, we examine patterns in gene locations to infer large-scale features of bacterial chromosomes. Specifically, we analyzed >100 genomes and identified thousands of gene pairs that display two types of evolutionary correlations: a tendency to co-occur and a tendency to be located close together in many genomes. We then analyzed the detailed distribution of these pairs in Escherichia coli and found that genes in a pair tend to be separated by integral multiples of 117 kb along the genome and to be positioned in a 117-kb grid of genomic locations. In addition, the most pair-dense locations coincide with regions of intense transcriptional activity and the positions of top transcribed and conserved genes. These patterns suggest that the E. coli chromosome may be organized into a 117-kb helix-like topology that localizes a subset of the most essential and highly transcribed genes along a specific face of this structure. Our approach indicates an evolutionarily maintained preference in the spacing of genes along the chromosome and offers a general comparative genomics framework for studying chromosome structure, broadly applicable to other organisms.
Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism (2019)

Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach.
Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand (2019)

The double-stranded RNA-binding domain (dsRBD) is a broadly distributed domain among RNA-maturing enzymes. Although this domain recognizes dsRNA's structures via a conserved canonical structure adopting an α<sub>1</sub>-β<sub>1</sub>β<sub>2</sub>β<sub>3</sub>-α<sub>2</sub> topology, several dsRBDs can accommodate discrete structural extensions expanding further their functional repertoire. How these structural elements engage cooperative communications with the canonical structure and how they contribute to the dsRBD's overall folding are poorly understood. Here, we addressed these issues using the dsRBD of human dihydrouridine synthase-2 (hDus2) (hDus2-dsRBD) as a model. This dsRBD harbors N- and C-terminal extensions, the former being directly involved in the recognition of tRNA substrate of hDus2. These extensions engage residues that form a long-range hydrophobic network (LHN) outside the RNA-binding interface. We show by coarse-grain Brownian dynamics that the Nt-extension and its residues F359 and Y364 rigidify the major folding nucleus of the canonical structure via an indirect effect. hDus2-dsRBD unfolds following a two-state cooperative model, whereas both F359A and Y364A mutants, designed to destabilize this LHN, unfold irreversibly. Structural and computational analyses show that these mutants are unstable due to an increase in the dynamics of the two extensions favoring solvent exposure of α2-helix and weakening the main folding nucleus rigidity. This LHN appears essential for maintaining a thermodynamic stability of the overall system and eventually a functional conformation for tRNA recognition. Altogether, our findings suggest that functional adaptability of extended dsRBDs is promoted by a cooperative hydrophobic coupling between the extensions acting as effectors and the folding nucleus of the canonical structure.
Optical leaky wave antennas integrated with resonator topologies (2014)

Summary form only given. In this work, we study the theory and design of an optical leaky wave antenna (OLWA) integrated with resonator topologies such as Fabry-Pérot resonator and ring resonator tuned to the telecommunication wavelength of 1550 nm (193.4 THz). The presented OLWA design is compatible with CMOS fabrication technologies. It comprises silicon (Si), silica glass (SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) domains forming a dielectric waveguide that hosts numerous periodic perturbations. The radiation from an isolated OLWA takes place due to the leaky wave which decays slowly as it propagates along the perturbed waveguide. The design is tuned by purposely using perturbations of very small filling fraction in a unit cell, thus resulting in a leaky wave harmonic with very small attenuation and phase constants. This in turn leads to a very directive radiated beam almost in the direction normal to the axis of leaky wave propagation. In [Campione et al., Opt. Exp., 20, pp. 21305-21317, (2012)], for a similar isolated OLWA design, the tunability of radiation levels by modifying the optical properties of the Si domain through electron-hole excess carrier generation (thus the leaky wave's propagation constant) is proven to be limited, and an analytic model of OLWA in FPR is provided for the first time with a significant radiation level control. Therefore, in this research we turn our attention to utilizing the OLWA design integrated with resonator schemes such as ring resonators in order to achieve significant radiation control through the control of carrier densities in Si domains. We demonstrate effective control of radiation level alongside engineering a desired beam direction and directivity. Depending on the scheme of OLWA placement inside the resonator topology, the design procedure involves the construction of far-field as an interference beam radiated by different OLWA regions. Such a design allows for forming a stable radiated beam with frequency as well as achieving a high quality factor of resonance and hence an effective control of radiation level. Moreover the minimization of Si regions' sizes can lead to fast electronic operation through control of Si carrier density. The OLWA integrated with resonators are promising for improving the performances of optical switches.
Morphological effects of coronary balloon angioplasty in vivo assessed by intravascular ultrasound imaging. (1992)

Intravascular ultrasound provides a more complete quantitative and qualitative description of plaque geometry and composition than angiography after balloon angioplasty. In addition, intravascular ultrasound identified a subset of atherosclerotic plaque that has a higher incidence of restenosis. This information could be used prospectively to consider other therapeutic options in this subset. Intravascular ultrasound provides a method to describe the effects of angioplasty that will be useful in comparing future coronary intervention studies.
A Laboratory Photomask Production Facility (1972)

A simple, rapid procedure is described for making photomasks consisting of reduced and repeated microelectronic patterns. This process utilizes two compact and economically constructed cameras. The first camera, using a pinhole array, produces the initial reduction and repeat of the circuit pattern, while the second camera, using a conventional camera lens, accomplishes the final reduction.
A 7T SRAM bit-cell for low-power embedded memories (2011)

With CMOS technology scaling, data stability and yield have become key concerns of low power embedded memories, which are realized using the static random access memory (SRAM). In this paper, we propose a seven transistor (7T) SRAM bit-cell to address these concerns. The cell decouples the read bit line from the write bit lines and uses the latter as the cell power lines. The cell exhibits a much higher static noise margin than the conventional 6T SRAM cell as the storage node is not perturbed during the read operation. Consequently, the proposed cell shows higher data stability and yield under varying process, voltage, and temperature (PVT) conditions. In addition, a unique write mechanism of the cell reduces the write power to less than one third of the write power consumed by the 6T cell when laid out and simulated using a commercial 65-nm CMOS technology. The soft error critical charge of the proposed cell is 30% larger and hence the soft error rate (SER) is approximately less than half of that of the 6T cell. It takes same silicon area as 6T cell while other recently reported SRAM cells incur 30-37% area overhead.
A rational approach to identifying effective combined anticoronaviral therapies against feline coronavirus (2020)

Abstract Feline infectious peritonitis (FIP), caused by a genetic mutant of feline enteric coronavirus known as FIPV, is a highly fatal disease of cats with no currently available vaccine or FDA-approved cure. Dissemination of FIPV in affected cats results in a range of clinical signs including cavitary effusions, anorexia, fever and lesions of pyogranulomatous vasculitis and peri-vasculitis with or without central nervous system and/or ocular involvement. There is a critical need for effective and approved antiviral therapies against coronaviruses including FIPV and zoonotic coronaviruses such as SARS-CoV-2, the cause of COVID-19. With regards to SARS-CoV-2, preliminary evidence suggests that there may be potential clinical and pathological overlap with feline coronaviral disease including enteric and neurological involvement in some cases. We have screened 89 putative antiviral compounds and have identified 25 compounds with antiviral activity against FIPV, representing a variety of drug classes and mechanisms of antiviral action. Based upon successful combination treatment strategies for human patients with HIV or hepatitis C virus infections, we have identified combinations of drugs targeting different steps of the FIPV life cycle resulting in synergistic antiviral effect. Translationally, we suggest that a combined anticoronaviral therapy (cACT) with multiple mechanisms of action and penetration of all potential anatomic sites of viral infection should be applied towards other challenging to treat coronaviruses, like SARS-CoV-2. Author summary We have screened 89 compounds in vitro for antiviral activity against FIPV. The putative antiviral activity of these compounds was either purported to be a direct effect on viral proteins involved in viral replication or an indirect inhibitory effect on normal cellular pathways usurped by FIPV to aid viral replication. Twenty-five of these compounds were found to have significant antiviral activity. Certain combinations of these compounds were determined to be superior to monotherapy alone.
Modeling of a Urea SCR Catalyst With Automotive Applications (2002)

A zero order lumped parameter control oriented model of a Selective Catalytic Reduction (SCR) catalyst is presented. The lumped parameter model is developed using two approaches. in the first approach it was assumed that the catalyst behaves as an Isothermal Continuously Stirred Tank Reactor (ICSTR). The second approach involved deriving the lumped parameter model from a 1D model using the method of weighted residuals. Both approaches led to a three state model, with the gas phase concentrations of NOx and NH3 and the surface coverage fraction as the states. The model depends on chemical properties specific to the SCR catalyst; consequently model validation requires knowledge of these parameters, either via laboratory-based experiments or as supplied by the catalyst supplier. We present an alternate approach that allows estimation of the essential parameters through a minimization of the l2 errors between measured and simulated results.
T Cell-Receptor V Gene Use by CD4+ Melanoma-Reactive Clonal and Oligoclonal T-Cell Lines (1998)

Tumor-reactive CD4+ T cells can be isolated and expanded from the peripheral blood and tumor lesions of patients with melanoma. In contrast to CD8+ T cells, little is known about the antigens recognized by these CD4+ T cells. As a consequence, little is known about the diversity of the T-cell receptor (TcR) use by melanoma-reactive CD4+ T cells. To address these questions, a panel of clonal or highly oligoclonal CD4+ T-cell lines was established from a patient with metastatic melanoma. A CD4+ tumor-infiltrating lymphocyte (TIL) line was established that was highly oligoclonal and recognized only autologous melanoma cells but not allogeneic melanomas, suggesting the expression of a mutated or uniquely expressed antigen by this melanoma. The antigen recognized by the CD4+ TILs could be presented by intact melanoma cells or by autologous Epstein-Barr virus (EBV) B cells pulsed with melanoma cell lysates. A panel of CD4+ clonal and highly oligoclonal T-cell lines was isolated from peripheral blood mononuclear cells (PBMC) from this patient; these were also reactive with autologous melanoma cells or tumor extracts pulsed on autologous EBV B cells. Despite their reactivity with the autologous melanoma, we found no evidence of restricted TcR V gene use, because all six T-cell lines recognized antigen via different TcR α/β rearrangements. Furthermore, there were no conserved amino acids in the CDR3 regions of these TcRs, indicating that multiple TcR clono-types could mediate recognition of a single unique major histocompatibility (MHC) complex class II restricted melanoma antigen or that multiple MHC class II restricted melanoma antigens are expressed by the melanoma.
BRDF-dependent accuracy of array-projection-based 3D sensors (2017)

In order to perform high-speed three-dimensional (3D) shape measurements with structured light systems, high-speed projectors are required. One possibility is an array projector, which allows pattern projection at several tens of kilohertz by switching on and off the LEDs of various slide projectors. The different projection centers require a separate analysis, as the intensity received by the cameras depends on the projection direction and the object's bidirectional reflectance distribution function (BRDF). In this contribution, we investigate the BRDF-dependent errors of array-projection-based 3D sensors and propose an error compensation process.
Evolution of selenocysteine‐containing proteins: Significance of identification and functional characterization of selenoproteins (2001)

In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec). Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid. Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence. Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere. In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates. The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions. Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins.
The Mediating Role of Radical Innovation in the Relationship Between Knowledge Management and Competitive Advantage in Sudanese Manufacturing Firms (2014)

For hyperspectral imaging, diffraction gratings based spectrometers exhibit high spectral resolution and optical performance. Among those spectrometers, the Offner type (which consists of an entrance slit, two concave mirrors and convex grating) offers a lot of advantages. In this paper, we propose the design and modelization of a convex grating which covers a spectral band ranging from 0.7 I¼m to 5 I¼m with a minimum diffraction efficiency of 20% at 800 nm, 50% at 3000 nm and 25% at 5000 nm. For a so wide band, a grating with a single blaze cannot satisfy these requirements. We will therefore propose an approach of multi-blaze grating which is subdivided into different sections each with its own blaze angle. On April 30, 2016 we published a similar article in your journal and the optimization process resulted in a grating design of 9 blaze wavelengths. We have continued to work on this and currently we propose a better optimization method which allows to obtain the same results but only with 3 blaze wavelengths. Meanwhile, we perform the diffraction efficiency prediction using the scalar and rigorous theories to prove the compliance of this design with the technical specifications. The rigorous theory will also allow us to study the polarization sensitivity of this grating and the calculation of the diffraction efficiency of a grating with a profile degraded by manufacturing errors to assess the impact on the diffraction efficiency and the sensitivity to polarization.