gebhart/patrepeval huggingface dataset:
Experimental Characterization of the Near-Wall Plasma in a 6-kW Hall Thruster and Comparison to Simulation (2011)

In order to better understand interactions between the plasma and channel walls of a Hall thruster, the near-wall plasma was characterized within the H6 Hall thruster using five flush-mounted Langmuir probes. These probes were placed within the last 15% of the discharge channel and were used to measure plasma potential, electron temperature, and ion number density near the inner and outer channel walls. These data were then compared to prior internal measurements inside the channel using a High-speed Axial Reciprocating Probe stage. Comparison of these data has shown that, at the nominal operating condition of 300 V and 20 mg/s anode flow rate, the plasma near the wall begins to accelerate further upstream than plasma closer to centerline. This shift in acceleration zone creates large radial electric fields (~ 40-50 V/mm) that tend to defocus ions and drive them towards the walls. The shift is likely caused by large plasma density gradients between centerline and the channel walls, creating a significant deviation of equipotentials from magnetic field lines near the walls. Electron temperature axial profiles were found to be largely consistent across the channel, supporting the isothermal assumption along magnetic field lines. The experimental results were also compared to simulation results from the hybrid-PIC program HPHall-2. General agreement was found between simulation and experiment for axial profiles of plasma potential, electron temperature, and ion number density, with minor differences occurring in peak locations. Slight asymmetries in properties were found between the inner and outer channel walls despite the use of a symmetric magnetic field topology. This asymmetry was caused by a difference in the location of the maximum radial magnetic field, resulting in axial shifts of acceleration zone and peak electron temperature. This result is supported by asymmetric erosion profiles after 334 hours of operation, showing increased erosion along the outer wall where acceleration began further upstream.
Task-Oriented Data Compression for Multi-Agent Communications Over Bit-Budgeted Channels (2020)

Various applications for inter-machine communications are on the rise. Whether it is for autonomous driving vehicles or the internet of everything, machines are more connected than ever to improve their performance in fulfilling a given task. While in traditional communications the goal has often been to reconstruct the underlying message, under the emerging task-oriented paradigm, the goal of communication is to enable the receiving end to make more informed decisions or more precise estimates/computations. Motivated by these recent developments, in this paper, we perform an indirect design of the communications in a multi-agent system (MAS) in which agents cooperate to maximize the averaged sum of discounted one-stage rewards of a collaborative task. Due to the bit-budgeted communications between the agents, each agent should efficiently represent its local observation and communicate an abstracted version of the observations to improve the collaborative task performance. We first show that this problem can be approximated as a form of data-quantization problem which we call task-oriented data compression (TODC). We then introduce the state-aggregation for information compression algorithm (SAIC) to solve the formulated TODC problem. It is shown that SAIC is able to achieve near-optimal performance in terms of the achieved sum of discounted rewards. The proposed algorithm is applied to a geometric consensus problem and its performance is compared with several benchmarks. Numerical experiments confirm the promise of this indirect design approach for task-oriented multi-agent communications.
<title>Parallel environment for parallel image processing on top of PVM</title> (1997)

This paper presents the implementation of virtual topologies on top of PVM for developing parallel portable image processing on coarse grained machines. It allows the user to define a high level logical numbering to make easy the management and the interaction between tasks. A template convolution primitive has been implemented on 2D mesh topology.
Contextual multi-armed bandit algorithms for personalized learning action selection (2017)

Optimizing the selection of learning resources and practice questions to address each individual student's needs has the potential to improve students' learning efficiency. In this paper, we study the problem of selecting a personalized learning action for each student (e.g. watching a lecture video, working on a practice question, etc.), based on their prior performance, in order to maximize their learning outcome. We formulate this problem using the contextual multi-armed bandits framework, where students' prior concept knowledge states (estimated from their responses to questions in previous assessments) correspond to contexts, the personalized learning actions correspond to arms, and their performance on future assessments correspond to rewards. We propose three new Bayesian policies to select personalized learning actions for students that each exhibits advantages over prior work, and experimentally validate them using real-world datasets.
The 5-Hydroxymethylcytosine Landscape of Prostate Cancer (2022)

In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
Synthetic and computer-assisted analysis of the structural requirements for selective, high-affinity ligand binding to diazepam-insensitive benzodiazepine receptors (1993)

Several 1,4-diazepines were recently reported to bind with high affinities to the "diazepam-insensitive" (DI) isoform of the benzodiazepine receptor (BzR) (Korpi, E.R.; Uusi-Oukari, M.; Wegelius, K. Eur. J. Pharm. 1992, 213, 323-329. Wong, G.; Skolnick, P. Eur. J. Pharmacol. Mol. Pharm. Sec. 1992, 225, 63-68). However, only the putative ethanol antagonist 1 (Ro 15-4513) displayed modest selectivity for the DI site compared to other "diazepam-sensitive" (DS) BzR isoforms. In order to probe the requirements for selective, high-affinity binding to the DI site, the affinities of 47 benzodiazepines have been determined at both DI and DS BzR sites. In addition, single X-ray crystallographic analyses for three of these derivatives, 5 (Ro 17-1812), 6 (Ro 16-6028), and 42 (Ro 14-5974), are reported. The radioligand binding studies reveal that modifications to the 3-, 7-, and 8-positions of 6-oxoimidazo[1,5-alpha] [1,4]benzodiazepines have a marked influence on the Ki(DI)/Ki(DS) ratios. In order to more precisely determine the structural requirements for both high affinity and selectivity at DI BzR relative to DS, 3D-QSAR analyses were carried out on ligand affinities at both of these BzR isoforms. This analysis was based, in part, on the new X-ray crystallographic data. Satisfactory cross-validated regression equations were obtained individually for the logarithms of ligand affinities at DI and DS as well as for the differences of the logarithms of their affinities at these two isoforms (cross-validated R2 > 0.70 for all three regression equations). The steric and electrostatic 3D-QSAR DI and DS maps are in qualitative accord with the structure-activity relationship (SAR) data. Furthermore, the DI and DI/DS maps may be useful in the design of ligands with enhanced DI affinity and DI/DS selectivity, respectively.
Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli (2013)

Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities.
Feasibility of cardiac output measurements in critically ill patients by medical students (2020)

Medical students seem capable of obtaining sufficient quality CCUS images for CO measurement in the majority of critically ill patients. Measurements of CO by medical students, however, had poor agreement with expert measurements. Experts remain indispensable for reliable CO measurements. Trial registration Clinicaltrials.gov; http://www.clinicaltrials.gov; registration number NCT02912624.
Recruitment of a SAP18-HDAC1 Complex into HIV-1 Virions and Its Requirement for Viral Replication (2009)

HIV-1 integrase (IN) is a virally encoded protein required for integration of viral cDNA into host chromosomes. INI1/hSNF5 is a component of the SWI/SNF complex that interacts with HIV-1 IN, is selectively incorporated into HIV-1 (but not other retroviral) virions, and modulates multiple steps, including particle production and infectivity. To gain further insight into the role of INI1 in HIV-1 replication, we screened for INI1-interacting proteins using the yeast two-hybrid system. We found that SAP18 (Sin3a associated protein 18 kD), a component of the Sin3a-HDAC1 complex, directly binds to INI1 in yeast, in vitro and in vivo. Interestingly, we found that IN also binds to SAP18 in vitro and in vivo. SAP18 and components of a Sin3A-HDAC1 complex were specifically incorporated into HIV-1 (but not SIV and HTLV-1) virions in an HIV-1 IN-dependent manner. Using a fluorescence-based assay, we found that HIV-1 (but not SIV) virion preparations harbour significant deacetylase activity, indicating the specific recruitment of catalytically active HDAC into the virions. To determine the requirement of virion-associated HDAC1 to HIV-1 replication, an inactive, transdominant negative mutant of HDAC1 (HDAC1(H141A)) was utilized. Incorporation of HDAC1(H141A) decreased the virion-associated histone deacetylase activity. Furthermore, incorporation of HDAC1(H141A) decreased the infectivity of HIV-1 (but not SIV) virions. The block in infectivity due to virion-associated HDAC1(H141A) occurred specifically at the early reverse transcription stage, while entry of the virions was unaffected. RNA-interference mediated knock-down of HDAC1 in producer cells resulted in decreased virion-associated HDAC1 activity and a reduction in infectivity of these virions. These studies indicate that HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. Furthermore, HIV-1 virion-associated HDAC1 is required for efficient early post-entry events, indicating a novel role for HDAC1 during HIV-1 replication.
3‐Hydroxybenzene 1,2,4‐Trisphosphate, a Novel Second Messenger Mimic and Unusual Substrate for Type‐I myo‐Inositol 1,4,5‐Trisphosphate 5‐Phosphatase: Synthesis and Physicochemistry. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Morphology-Based Prediction of Osteogenic Differentiation Potential of Human Mesenchymal Stem Cells (2013)

Human bone marrow mesenchymal stem cells (hBMSCs) are widely used cell source for clinical bone regeneration. Achieving the greatest therapeutic effect is dependent on the osteogenic differentiation potential of the stem cells to be implanted. However, there are still no practical methods to characterize such potential non-invasively or previously. Monitoring cellular morphology is a practical and non-invasive approach for evaluating osteogenic potential. Unfortunately, such image-based approaches had been historically qualitative and requiring experienced interpretation. By combining the non-invasive attributes of microscopy with the latest technology allowing higher throughput and quantitative imaging metrics, we studied the applicability of morphometric features to quantitatively predict cellular osteogenic potential. We applied computational machine learning, combining cell morphology features with their corresponding biochemical osteogenic assay results, to develop prediction model of osteogenic differentiation. Using a dataset of 9,990 images automatically acquired by BioStation CT during osteogenic differentiation culture of hBMSCs, 666 morphometric features were extracted as parameters. Two commonly used osteogenic markers, alkaline phosphatase (ALP) activity and calcium deposition were measured experimentally, and used as the true biological differentiation status to validate the prediction accuracy. Using time-course morphological features throughout differentiation culture, the prediction results highly correlated with the experimentally defined differentiation marker values (R>0.89 for both marker predictions). The clinical applicability of our morphology-based prediction was further examined with two scenarios: one using only historical cell images and the other using both historical images together with the patient's own cell images to predict a new patient's cellular potential. The prediction accuracy was found to be greatly enhanced by incorporation of patients' own cell features in the modeling, indicating the practical strategy for clinical usage. Consequently, our results provide strong evidence for the feasibility of using a quantitative time series of phase-contrast cellular morphology for non-invasive cell quality prediction in regenerative medicine.
An overview of the Ultra-Fast X-ray Imager (UXI) program at Sandia Labs. (2016)

Abstract not provided.
Silicon on Silicon Carbide Ring Resonators for Coupling to Color Centers (2018)

We present hybrid crystalline-silicon (c-Si) ring resonators on top of 4H silicon carbide with measured quality factor ~9600 for coupling to spin qubits like divacancies and Cr ions for future applications in quantum information networks.
On the decoding delay of encoders for input-constrained channels (1996)

Finite-state encoders that encode n-ary data into a constrained system S are considered. The anticipation, or decoding delay, of such an (S,n)-encoder is the number of symbols that a state-dependent decoder needs to look ahead in order to recover the current input symbol. Upper bounds are obtained on the smallest attainable number of states of any (S, n)-encoder with anticipation t. Those bounds can be explicitly computed from t and S, which implies that the problem of checking whether there is an (S, n)-encoder with anticipation t is decidable. It is also shown that if there is an (S,n)-encoder with anticipation t, then a version of the state-splitting algorithm can be applied to produce an (S, n) encoder with anticipation at most 2t-1. We also observe that the problem of checking whether there is an (S, n)-encoder having a sliding-block decoder with a given memory and anticipation is decidable.
Lipid-Rich Plaque Masquerading as a Coronary Thrombus (2006)

A 43-year-old woman presented with exertional chest pressure. Right coronary angiography showed a clear filling defect. Intravascular ultrasound revealed a plaque with 80% stenosis and a large lipid pool. Therefore, a stent was placed, and the patient became angina-free. Lipid-rich plaques are a cause of angiographic filling defects. Intravascular ultrasound is an integral part of coronary artery evaluation.
Reduced Magnet Designs and Position Self-Sensing Control Methods of Flux-Intensifying Permanent Magnet Synchronous Machines (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper presents advanced and cost-reducing technologies of a motor drive system with reduced permanent magnets but without a position sensor. The key enabler is the integration of novel designs of flux-intensifying interior permanent magnet synchronous machines (FI-IPMSMs) and position self-sensing control technologies. In this paper, we focus on two advantages of FI-IPMSM over conventional flux-weakening interior permanent magnet synchronous machines (FW-IPMSMs). The first benefit is that thinner magnets are possible and there is less concern for demagnetization because of its significantly smaller flux-weakening current. This paper presents two design examples of FI-IPMSMs, one of which has not only smaller magnets but also similar power conversion capability. The second advantage is reduced saturation and cross-saturation effect, which leads to improved position self-sensing capability. However, even in the FI-IPMSM, non-ideal effects of both machine and inverter limit the position estimation accuracy. Therefore, this paper includes experimental evaluation of decoupling methods to improve position estimation accuracy.&lt;/div&gt;&lt;/div&gt;
Visual Cryptography for Biometric Privacy (2010)

Preserving the privacy of digital biometric data (e.g., face images) stored in a central database has become of paramount importance. This work explores the possibility of using visual cryptography for imparting privacy to biometric data such as fingerprint images, iris codes, and face images. In the case of faces, a private face image is dithered into two host face images (known as sheets) that are stored in two separate database servers such that the private image can be revealed only when both sheets are simultaneously available; at the same time, the individual sheet images do not reveal the identity of the private image. A series of experiments on the XM2VTS and IMM face databases confirm the following: 1) the possibility of hiding a private face image in two host face images; 2) the successful matching of face images reconstructed from the sheets; 3) the inability of sheets to reveal the identity of the private face image; 4) using different pairs of host images to encrypt different samples of the same private face; and 5) the difficulty of cross-database matching for determining identities. A similar process is used to de-identify fingerprint images and iris codes prior to storing them in a central database.
Ultra-widely tunable photonic microcavities through evanescent field perturbation (2006)

Evanescent perturbation is examined as a means of tuning photonic microcavities over large wavelength ranges. 27nm reversible tuning is achieved through nanometric control of a silica perturbing body in the near-field of a microring resonator.
Intra super-channel fiber nonlinearity compensation in flex-grid optical networks (2013)

We report on the nonlinear transmission limits of various super-channel configurations in a flex-grid network upgrade scenario. In particular, we consider flexible data-rates ranging from 180Gb/s to 1.2Tb/s, employing either single-carrier, dual-carrier, or penta-carrier polarization multiplexed m-state quadrature amplitude modulation (PM-8QAM/PM-16QAM) -termed as super-channels, and establish transmission performance margins for each configuration, both with and without super-channel fiber nonlinearity compensation. Our results show that the benefit of intra super-channel nonlinearity mitigation (nonlinear compensation addressing full super-channel bandwidth) reduces with increasing sub-carrier count within the super-channel, and that single-carrier super-channel achieves the maximum improvement from nonlinearity mitigation (up to ~4.5dB, in Q-factor), better than dual-carrier (up to ~3.5dB) and penta-carrier (up to ~2dB) configurations. Moreover, the maximum reach improvement, compared to linear compensation only, is found to be ~170% (180Gb/s, PM-8QAM), ~150% (240Gb/s, PM-16QAM), ~100% (360Gb/s, PM-8QAM), ~100% (480Gb/s, PM-16QAM), and ~65% (1.2Tb/s, PM-16QAM).
Room-Temperature Plasticity of a Nanosized GaN Crystal (2021)

GaN wurtzite crystal is commonly regarded as eminently brittle. However, our research demonstrates that nanodeconfined GaN compressed along the M direction begins to exhibit room-temperature plasticity, yielding a dislocation-free structure despite the occurrence of considerable, irreversible deformation. Our interest in M-oriented, strained GaN nanoobjects was sparked by the results of first-principles bandgap calculations, whereas subsequent nanomechanical tests and ultrahigh-voltage (1250 kV) transmission electron microscopy observations confirmed the authenticity of the phenomenon. Moreover, identical experiments along the C direction produced only a quasi-brittle response. Precisely how this happens is demonstrated by molecular dynamics simulations of the deformation of the C- and M-oriented GaN frustum, which mirror our nanopillar crystals.
POTHER: Patch-Voted Deep Learning-Based Chest X-ray Bias Analysis for COVID-19 Detection (2022)

A critical step in the fight against COVID-19, which continues to have a catastrophic impact on peoples lives, is the effective screening of patients presented in the clinics with severe COVID-19 symptoms. Chest radiography is one of the promising screening approaches. Many studies reported detecting COVID-19 in chest X-rays accurately using deep learning. A serious limitation of many published approaches is insufficient attention paid to explaining decisions made by deep learning models. Using explainable artificial intelligence methods, we demonstrate that model decisions may rely on confounding factors rather than medical pathology. After an analysis of potential confounding factors found on chest X-ray images, we propose a novel method to minimise their negative impact. We show that our proposed method is more robust than previous attempts to counter confounding factors such as ECG leads in chest X-rays that often influence model classification decisions. In addition to being robust, our method achieves results comparable to the state-of-the-art. The source code and pre-trained weights are publicly available at (https://github.com/tomek1911/POTHER).
Sensor-based controller tuning of indirect drive trains (2008)

This paper presents a sensor-based controller tuning method for indirect-drive trains. In the standard control practice of the indirect-drive trains, the variable for control feedback (motor position) is different from the variable for performance evaluation (load position). In order to improve the performance of such standard controllers, it is suggested to use additional load-side sensor measurements in the controller tuning process. The load-side acceleration is utilized in this paper due to the easy installation of MEMS accelerometers. The additional load-side acceleration measurement is included in the performance index of the controller tuning. The iterative feedback tuning (IFT) method is utilized to adjust the controller gains to minimize the performance index based on the sensor measurements. The effectiveness of the controller tuning method is demonstrated by experiments.