gebhart/patrepeval huggingface dataset:
Co-Heterogeneous and Adaptive Segmentation from Multi-Source and\n Multi-Phase CT Imaging Data: A Study on Pathological Liver and Lesion\n Segmentation (2020)

In medical imaging, organ/pathology segmentation models trained on current\npublicly available and fully-annotated datasets usually do not well-represent\nthe heterogeneous modalities, phases, pathologies, and clinical scenarios\nencountered in real environments. On the other hand, there are tremendous\namounts of unlabelled patient imaging scans stored by many modern clinical\ncenters. In this work, we present a novel segmentation strategy,\nco-heterogenous and adaptive segmentation (CHASe), which only requires a small\nlabeled cohort of single phase imaging data to adapt to any unlabeled cohort of\nheterogenous multi-phase data with possibly new clinical scenarios and\npathologies. To do this, we propose a versatile framework that fuses appearance\nbased semi-supervision, mask based adversarial domain adaptation, and\npseudo-labeling. We also introduce co-heterogeneous training, which is a novel\nintegration of co-training and hetero modality learning. We have evaluated\nCHASe using a clinically comprehensive and challenging dataset of multi-phase\ncomputed tomography (CT) imaging studies (1147 patients and 4577 3D volumes).\nCompared to previous state-of-the-art baselines, CHASe can further improve\npathological liver mask Dice-Sorensen coefficients by ranges of $4.2\\% \\sim\n9.4\\%$, depending on the phase combinations: e.g., from $84.6\\%$ to $94.0\\%$ on\nnon-contrast CTs.\n
Hydrogen Release and Defect Formation During Heat Treatments of SiNx:H/a-Si: H Double Passivation Layer on C-SI Substrate (2006)

The quality and temperature stability of surface passivation of silicon by a double layer consisting of a hydrogenated amorphous silicon thin film capped by a silicon nitride anti-reflection coating are studied. It is established that the passivation effect of the double layer can be significantly enhanced after short annealing for temperatures up to about 500degC, whereas annealing at higher temperatures results in degradation of the passivation properties. It is found that the increased effective recombination lifetime after annealing at temperatures below 500degC results from hydrogen redistribution in the interface region. Furthermore, presence of interfacial structural defects formed due to hydrogen release at temperatures around 600degC, is believed to be the cause of the lifetime decrease after heat treatments at higher temperatures
Irradiated fuel monitoring by Cerenkov glow intensity measurements (1979)

Attribute measurement techniques for confirmation of declared irradiated fuel inventories at nuclear installations under safeguards surveillance are being investigated. High-gain measurements of the intensity of the Cerenkov glow from exposed assemblies in water-filled storage ponds are promising for this purpose. Such measurements have been made of Materials Testing Reactor plate-type fuel assemblies and Pressurized Water Reactor pin-type fuel assemblies. The measured intensities depend on cooling times as calculations predict.
Single-Pulse Mueller Matrix Polarimeter Laboratory Demonstration (2018)

Motivated by a desire to reduce CSWAP, yet maintain high scan speed, we numerically and experimentally explore a new scanning LADAR architecture that employs temporal multiplexing to enable Mueller matrix measurement for each point in a scene with a single ns-scale illumination laser pulse.
A Comparative Analysis of Synthetic Quorum Sensing Modulators in <i>Pseudomonas aeruginosa</i>: New Insights into Mechanism, Active Efflux Susceptibility, Phenotypic Response, and Next-Generation Ligand Design (2015)

Quorum sensing (QS) is a chemical signaling mechanism that allows bacterial populations to coordinate gene expression in response to social and environmental cues. Many bacterial pathogens use QS to initiate infection at high cell densities. Over the past two decades, chemical antagonists of QS in pathogenic bacteria have attracted substantial interest for use both as tools to further elucidate QS mechanisms and, with further development, potential anti-infective agents. Considerable recent research has been devoted to the design of small molecules capable of modulating the LasR QS receptor in the opportunistic pathogen Pseudomonas aeruginosa. These molecules hold significant promise in a range of contexts; however, as most compounds have been developed independently, comparative activity data for these compounds are scarce. Moreover, the mechanisms by which the bulk of these compounds act are largely unknown. This paucity of data has stalled the choice of an optimal chemical scaffold for further advancement. Herein, we submit the best-characterized LasR modulators to standardized cell-based reporter and QS phenotypic assays in P. aeruginosa, and we report the first comprehensive set of comparative LasR activity data for these compounds. Our experiments uncovered multiple interesting mechanistic phenomena (including a potential alternative QS-modulatory ligand binding site/partner) that provide new, and unexpected, insights into the modes by which many of these LasR ligands act. The lead compounds, data trends, and mechanistic insights reported here will significantly aid the design of new small molecule QS inhibitors and activators in P. aeruginosa, and in other bacteria, with enhanced potencies and defined modes of action.
An investigation on mental stress-profiling of race car drivers during a race (2015)

Car racing is an intense sport that requires high and constant mental engagement. As the average age of race car drivers increases, it becomes more apparent that the mental aspect of the sport is becoming more important. In this work, a Body Sensor Network system was developed consisting of a Heart Rate monitor, an external GPS sensor and two smartphones. Experiments were conducted during the last race of the VLN series at the Nürburgring in Germany. The Heart Rate of the driver was combined with the 3D accelerometer of the mobile phone using an existing algorithm that is calculating the stress level of the driver in real-time. The stress level, along with GPS information is subsequently transmitted via the mobile phone network and the crew is able to see the position and the stress level of the driver in real-time. Post analysis of the data indicates that there is a correlation between the stress level of the driver and specific events. Weak correlations exist (between 22% and 53%) between the stress level of the driver during an event and their performance. Finally, the difference of the stress profiles among the drivers is shown.
Optoelectronic Tweezers for Particle and Cell Manipulation (2006)

Optoelectronic tweezers is a new tool for parallel optical manipulation of colloids and cells. Using a digital projector to pattern dynamic virtual electrodes on a photoconductive surface, we demonstrate parallel trapping, transporting, and sorting of micro/bio-particles.
Abstract B127: NT219, a novel dual inhibitor of STAT3 and IRS1/2, converts immuno-oncology resistant tumors to responders (2019)

Abstract Feedback activation of STAT3 and IGF1R/IRS plays a prominent role in mediating drug resistance to a broad spectrum of targeted cancer therapies and chemotherapies. Both the IRS1/2 and STAT3 are major signaling junctions regulated by various oncogenes, and altered during EMT and drug resistance. STAT3 has also been known to play an active role in immune-evasion of tumors and inhibition of STAT3, both in the tumor, as well as in the tumor’s microenvironment, may therefore potentiate immune attack on the tumor. NT219 is a dual inhibitor of STAT3 and IRS1/2 developed by TyrNovo Ltd. to overcome cancer drug resistance. NT219 inhibits STAT3 phosphorylation and eliminates IRS1/2 in a unique 3-step mechanism: dissociation of IRS1/2 from the IGF1 receptor, induction of IRS1/2 serine phosphorylation, and subsequent degradation by the proteasome. We recently demonstrated that the inhibition of both IRS and STAT3 are required and essential for overcoming drug resistance. NT219 efficacy was demonstrated in patient-derived tumor xenograft (PDX) models of multiple cancer types: melanoma, sarcoma, pancreatic, colon, lung, and head and neck when added on to the approved therapies. In these models, NT219 overcame acquired resistance to several oncology drug families: inhibitors of EGFR (Tarceva®, Erbitux®, Tagrisso®), MEK (Mekinist®), mutated-BRAF (Zelboraf®), mTOR (Afinitor®) as well as with chemotherapy agents (Gemzar®, 5FU, oxaliplatin). We recently demonstrated that NT219 works in synergy also with immune-oncology therapies. By using double autologous PDX models we demonstrated that NT219 converted non-responding tumors to responders to Keytruda®. It also enhanced the immunotherapeutic potential of cetuximab. FACS analysis showed increased tumor infiltrated lymphocyte population following treatment with NT219 and the combination of NT219 and the immuno-oncology drug.The unique mode of action of NT219 may open a new avenue of combined targeted therapies in a wide range of malignancies, and has the potential to expand response duration and target patient population to the applicable drugs. Citation Format: Hadas Reuveni, Izhak Haviv, Lana Kupershmidt. NT219, a novel dual inhibitor of STAT3 and IRS1/2, converts immuno-oncology resistant tumors to responders [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B127.
Multiplex systems for the amplification of short tandem repeat loci: evaluation of laser fluorescence detection. (1997)

Short tandem repeat (STR) loci are ideal markers for personal identification and for genomic mapping. Two fluorescent multiplex systems, each designed for simultaneous PCR amplification of four polymorphic STR loci (HUMCSF1PO, HUMTPOX, HUMTH01 and HUMVWFA31, and HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL), were evaluated on three laser fluorescence detection instruments. Concordant DNA typing results were obtained with all three detection methods. These fluorescent multiplex STR systems offer an accurate, reproducible and versatile method of DNA profiling that is well-suited for forensic identity testing and other genetic analyses.
Microstructure and Hardness of Friction Stir Weld Bead on Steel Plate Using W-25%Re Pin Tool (2014)

One of the challenges that impede the use of the relatively new friction stir welding (FSW) process in joining steels and high temperature alloys, as well as dissimilar materials, is the development of the right pin tool material that can stand the severe welding conditions of these alloys. Recent developments in FSW tool materials include tungsten rhenium (W-Re) alloys. The ductile to brittle transition temperature of pure tungsten is reduced by the addition of rhenium (Re).. The addition of Re also improve fracture toughness of the alloy. The major focus of this paper is studying the process of making a friction stir welding bead on mild steel using a proprietary W-25%Re alloy pin tool and investigating the effects of process parameters (i.e. tool rotational and welding speeds) on microstructure, microhardness as well as tool reaction loads. Grain refining of the steel microstructure was observed in all beads. Certain process conditions produced a bead with needle like microstructure with the highest values of hardness. Reaction forces were found to increase with the increase in the tool welding speed and to decrease with the increase of the tool rotational speed. Although the spectroscopic analysis of the beads confirmed the diffusion wear of the tool, the overall tool has shown excellent resistance to mechanical wear.
Edit Machines for Robust Multimodal Language Processing (2006)

Multimodal grammars provide an expressive formalism for multimodal integration and understanding. However, handcrafted multimodal grammars can be brittle with respect to unexpected, erroneous, or disfluent inputs. Spoken language (speech-only) understanding systems have addressed this issue of lack of robustness of hand-crafted grammars by exploiting classification techniques to extract fillers of a frame representation. In this paper, we illustrate the limitations of such classification approaches for multimodal integration and understanding and present an approach based on edit machines that combine the expressiveness of multimodal grammars with the robustness of stochastic language models of speech recognition. We also present an approach where the edit operations are trained from data using a noisy channel model paradigm. We evaluate and compare the performance of the hand-crafted and learned edit machines in the context of a multimodal conversational system (MATCH). 1
De novo designed positively charged tape-forming peptides: self-assembly and gelation in physiological solutions and their evaluation as 3D matrices for cell growth (2011)

Learning to control self-assembling nanostructures is currently one of the biggest challenges and promises in nanoscale science and nanotechnology. Nanostructured 3D matrices in particular are considered essential components in tissue engineering and regenerative medicine, e.g. as multifunctional scaffolds for cell encapsulation, growth and differentiation. Self-assembling peptide gels are a promising novel class of matrices for tissue engineering. Recently a new versatile family of negatively or positively charged tape-forming peptides have been de novo designed. These peptides were all found to self-assemble into nanostructured networks and gel cell transport medium in a simple, consistent and reproducible manner. Here we focus on the positively charged peptides of this family. We systematically changed the peptide to be amphiphilic or completely polar, or to be based on different polar uncharged amino acids (glutamine, serine, asparagine or threonine). The peptides were sterilised by γ-irradiation and were all found to be biocompatible using the contact cytotoxicity test. L929 murine fibroblast cells were encapsulated in 3D cell cultures inside 2% w/v gels and their proliferation was measured after 14 days using the ATP Lite assay. In this way a structure–function activity was established. Trifluoroacetic acid present in the peptide from the purification step was found to have a negative effect on cell proliferation. Peptide self-assembly in physiological conditions was studied extensively using spectroscopic and microscopic techniques, allowing rationalization of the observed biological structure–function activity. This detailed and systematic study enables us to develop refined criteria for the design of positively charged tape forming peptides and gels for biological and medical applications.
Ultrasonic characterization of soft tissue vibrations based on the two-dimensional Fourier transform (2005)

It has recently been demonstrated that soft tissue vibrations in the body, traditionally associated with vascular bruits and cardiac murmurs, can potentially be used for the ultrasonic diagnosis of coronary artery disease and vascular trauma. In this paper, the ultrasonic spectrum of soft tissue vibrations is formulated using the two-dimensional Fourier transform, making full use of the information present in the backscattered ultrasound echoes from vibrating tissue. Parametric simulation studies show that vibrations with amplitude 1 μm may be detected even with tissue velocity of 20 cm/s and acceleration of 5 m/s2, e.g., during peak cardiac motion. Vibrations with amplitude as low as 0.1 μm may be detected when the tissue acceleration is negligible, e.g., during mid-diastole. Also, it was found that tissue vibrations in a direction transverse to the ultrasound beam can be detected. In vivo examples of cardiac wall vibrations in patients with coronary artery disease are presented. Tissue vibrations can provide improved sensitivity over conventional duplex ultrasound since the scattering strength from tissue is significantly higher than that from blood. In addition, detection of tissue vibrations has reduced angle dependency and does not require visualization of the vessel lumen, making the exam less dependent on operator skill.
Abstract 556: Structural Characterization of Distinct Subparticles of Human High-density Lipoproteins Isolated from Plasma (2018)

High-density lipoproteins (HDL) play a critical role in lipid transport and the maintenance of vascular homeostasis. HDL consists of a heterogeneous population of particles that vary in size, composition, and functionality. HDL is proteomically diverse; it can host at least 95 different proteins and structure-function studies suggest that specific protein complements on the surface of the particles are responsible for the broad spectrum of HDL function. The goal of this study was to isolate and fully characterize specific subspecies of HDL based on their protein complement and particle size. We built upon our previous studies where we segregated lipoproteins using immunoaffinity chromatography using antibodies specific to the two major scaffold proteins of HDL; apolipoprotein (apo)A-I and apoA-II. Two populations were obtained directly from plasma that either had both apoA-I and apoA-II (LpA-I/A-II) or just apoA-I with no apoA-II (LpA-I). These subpopulations were further fractionated using size exclusion chromatography using four superdex columns in series. We observed at least three distinctly sized particles within the LpA-I/A-II subfraction and two distinctly sized particles in the LpA-I subfraction which all elute in the size range of HDL. We successfully isolated the “large” and “small” subpopulations observed in the LpA-I subfraction and compositional analysis revealed profound proteomic differences between the two populations. Particles in the larger fraction were enriched in more common apolipoprotiens important for lipid metabolic processes such as apoL-I, apoD, apoM and apoE. Conversely, the smaller LpA-I particles were enriched in proteins important for immune response and complement activation. Using multiple cross-linking reagents, we have mapped the protein-protein interactions on each of these subpopulations to begin generating detailed structural models of these particles in silico .
Wafer Sojourn Time Fluctuation Analysis of Time-Constrained Dual-Arm Cluster Tools With Wafer Revisiting and Activity Time Variation (2016)

A robotic cluster tool involves many activities whose time is subject to some disturbance, thus leading to the activity time variation. It results in wafer sojourn time fluctuation in a process module, which may in turn violate wafer residency time constraints. Some wafer fabrication requires a revisiting process. With wafer revisiting, the effect of activity time variation on wafer sojourn time fluctuation is so complicated that no analysis was reported to the best knowledge of the authors. It is vitally important to accurately analyze it. To do so, this paper adopts a Petri net model to describe the dynamical behavior of cluster tools. With this model, a real-time control policy is proposed to offset the effect of the activity time variation on wafer sojourn time fluctuation as much as possible. Then, the wafer sojourn time delay is analyzed and algorithms are developed to calculate its exact upper bound. With the proposed method, one can check if a given schedule is feasible under bounded activity time variation. Some practical examples are given to show the application of the proposed approach.
HIGH POWER, DRIFT-FREE <font>4H</font>-<font>SiC</font> PIN DIODES (2004)

The path to commercializing a 4H - SiC power PiN diode has faced many difficult challenges. In this work, we report a 50 A, 10 kV 4H - SiC PiN diode technology where good crystalline quality and high carrier lifetime of the material has enabled a high yielding process with V F as low as 3.9 V @ 100 A/cm 2 . These 10 kV diodes demonstrate pulsed current handling capability up to 328 A which represents over 3 MW of pulsed power. Furthermore, incorporation of two independent basal plane dislocation reduction reduction processes (LBPD 1 and LBPD 2) have produced a large number of devices that exhibit a high degree of forward voltage stability. The more benign LBPD 2 process yields wafers with better reverse blocking capability resulting in a total yield (forward, 10 kV blocking, and drift) of >20% for 8.7 mm × 8.7 mm power PiN diode chips—the largest SiC chip reported to date.
An Example‐based Procedural System for Element Arrangement (2008)

Abstract We present a method for synthesizing two dimensional (2D) element arrangements from an example. The main idea is to combine texture synthesis techniques based‐on a local neighborhood comparison and procedural modeling systems based‐on local growth. Given a user‐specified reference pattern, our system analyzes neigh‐borhood information of each element by constructing connectivity. Our synthesis process starts with a single seed and progressively places elements one by one by searching a reference element which has local features that are the most similar to the target place of the synthesized pattern. To support creative design activities, we introduce three types of interaction for controlling global features of the resulting pattern, namely a spray tool, a flow field tool, and a boundary tool. We also introduce a global optimization process that helps to avoid local error concentrations. We illustrate the feasibility of our method by creating several types of 2D patterns.
Anti-viral RNAi nanoparticles protect shrimp against white spot disease (2017)

Nearly 20% of cultured shrimp die every year due to viral diseases. In this study, we evaluated the capacity of nanoparticulate RNA interference (RNAi) to down-regulate genes in <italic>Penaeus vannamei</italic> shrimp and protect shrimp against white spot syndrome virus (WSSV, <italic>i.e.</italic> white spot disease).
Thermal neutron detection with the lithium borate scintillator (2000)

Single crystals of /sup 6/Li/sup 158/Gd(/sup 11/B/sub 3/O)/sub 3/ were grown, then powdered and mixed with powdered Schott glass and epoxy. The dough was solidified in a Teflon mold to a scintillator foil of 3 mm thickness and size 50 mm/spl times/50 mm. By attaching the /sup 6/Li borate foil to a conventional RCA photo multiplier (PM) and to a position sensitive Hamamatsu PM the properties as a scintillator for neutron detection were investigated with neutrons, and rays of high energy betas and gammas. The neutron absorption probability is sufficient large (36% for 0.1 nm wave length neutrons). Practically all neutron events yield sufficiently large pulses. The averaged neutron pulse is 4.8 times larger than that of a /sup 6/Li glass and 0.55 times smaller than that of a /sup 6/Li iodide. The photon energy equivalent to an average neutron pulse is 2.5 MeV (for /sup 6/Li glass and /sup 6/Li iodide the energies are 1.5 and 2.4 MeV, respectively). The spatial resolution obtained with the 45 mm/spl times/55 mm Hamamatsu PM is 0.54 mm FWHM.