gebhart/patrepeval huggingface dataset:
Semiautomatic three-dimensional segmentation of the prostate using two-dimensional ultrasound images (2003)

In this paper, we report on two methods for semiautomatic three-dimensional (3-D) prostate boundary segmentation using 2-D ultrasound images. For each method, a 3-D ultrasound prostate image was sliced into the series of contiguous 2-D images, either in a parallel manner, with a uniform slice spacing of 1 mm, or in a rotational manner, about an axis approximately through the center of the prostate, with a uniform angular spacing of 5 degrees. The segmentation process was initiated by manually placing four points on the boundary of a selected slice, from which an initial prostate boundary was determined. This initial boundary was refined using the Discrete Dynamic Contour until it fit the actual prostate boundary. The remaining slices were then segmented by iteratively propagating this result to an adjacent slice and repeating the refinement, pausing the process when necessary to manually edit the boundary. The two methods were tested with six 3-D prostate images. The results showed that the parallel and rotational methods had mean editing rates of 20% and 14%, and mean (mean absolute) volume errors of -5.4% (6.5%) and -1.7% (3.1%), respectively. Based on these results, as well as the relative difficulty in editing, we conclude that the rotational segmentation method is superior.
Forecasting bacterial survival-success and adaptive evolution through multi-omics stress-response mapping, network analyses and machine learning (2018)

ABSTRACT Whether a bacterial pathogen establishes an infection and/or evolves antibiotic resistance depends on successful survival while experiencing stress from for instance the host immune system and/or antibiotics. Predictions on bacterial survival and adaptive outcomes could thus have great prognostic value. However, it is unknown what information is required to enable such predictions. By developing a novel network-based analysis method, a bacterium's phenotypic and transcriptional response can be objectively quantified in temporal 3D-feature space. The resulting trajectories can be interpreted as a degree of coordination, where a focused and coordinated response predicts bacterial survival-success, and a random uncoordinated response predicts survival-failure. These predictions extend to both antibiotic resistance and in vivo infection conditions and are applicable to both Gram-positive and Gram-negative bacteria. Moreover, through experimental evolution we show that the degree of coordination is an adaptive outcome - an uncoordinated response evolves into a coordinated response when a bacterium adapts to its environment. Most surprisingly, it turns out that phenotypic and transcriptional response data, network features and genome plasticity data can be used to train a machine learning model that is able to predict which genes in the genome will adapt under nutrient or antibiotic selection. Importantly, this suggests that deterministic factors help drive adaptation and that evolution is, at least partially, predictable. This work demonstrates that with the right information predictions on bacterial short-term survival and long-term adaptive outcomes are feasible, which underscores that personalized infectious disease diagnostics and treatments are possible, and should be developed.
Electrically Tunable Liquid Crystal Lenses and Applications (2014)

Electrically tunable liquid crystal (LC) lenses have been studied for over 30 years. Three main problems of LC lenses hinder the applications: 1) the paradox between the response time and tunable focusing range, 2) polarization dependency, and 3) large aperture size for ophthalmic lenses. In this paper, we introduce the two mode switching method of the LC lenses to solve the paradox of the LC lenses. The basic optical principles for designing polarization independent LC lenses are discussed and several polarizer-free LC lenses we developed are reviewed. Several applications of LC lenses are also introduced, including auto-focusing imaging systems, auto-focusing projection systems, optical zoom systems, endoscopic systems, solar cells, ophthalmic lenses for myopia-presbyopia.
Optimal scheduling of time-constrained single-arm cluster tools with wafer revisiting (2016)

It is very difficult to schedule a single-arm cluster tool with wafer revisiting such that wafer residency time constraints are satisfied. This paper conducts a study on this challenging problem for a single-arm cluster tool with atomic layer deposition (ALD) process. With a so called p-backward strategy being applied, a Petri net model is developed to describe the dynamic behavior of the system. Based on the model, existence of a feasible schedule is analyzed, schedulability conditions are derived, and a scheduling algorithm is presented if there is a schedule. A schedule is obtained by simply setting the robot waiting time and it is very computationally efficient. The obtained schedule is shown to be optimal. Illustrative examples are given to demonstrate the proposed approach.
Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo (2015)

Human intestinal organoids (HIOs) are a tissue culture model in which small intestine-like tissue is generated from pluripotent stem cells. By carrying out unsupervised hierarchical clustering of RNA-sequencing data, we demonstrate that HIOs most closely resemble human fetal intestine. We observed that genes involved in digestive tract development are enriched in both fetal intestine and HIOs compared to adult tissue, whereas genes related to digestive function and Paneth cell host defense are expressed at higher levels in adult intestine. Our study also revealed that the intestinal stem cell marker OLFM4 is expressed at very low levels in fetal intestine and in HIOs, but is robust in adult crypts. We validated our findings using in vivo transplantation to show that HIOs become more adult-like after transplantation. Our study emphasizes important maturation events that occur in the intestine during human development and demonstrates that HIOs can be used to model fetal-to-adult maturation.
Compact and Blinking-Suppressed Quantum Dots for Single-Particle Tracking in Live Cells (2014)

Quantum dots (QDs) offer distinct advantages over organic dyes and fluorescent proteins for biological imaging applications because of their brightness, photostability, and tunability. However, a major limitation is that single QDs emit fluorescent light in an intermittent on-and-off fashion called "blinking". Here we report the development of blinking-suppressed, relatively compact QDs that are able to maintain their favorable optical properties in aqueous solution. Specifically, we show that a linearly graded alloy shell can be grown on a small CdSe core via a precisely controlled layer-by-layer process, and that this graded shell leads to a dramatic suppression of QD blinking in both organic solvents and water. A substantial portion (>25%) of the resulting QDs does not blink (more than 99% of the time in the bright or "on" state). Theoretical modeling studies indicate that this type of linearly graded shell not only can minimize charge carrier access to surface traps but also can reduce lattice defects, both of which are believed to be responsible for carrier trapping and QD blinking. Further, we have evaluated the biological utility of blinking-suppressed QDs coated with polyethylene glycol (PEG)-based ligands and multidentate ligands. The results demonstrate that their optical properties are largely independent of surface coatings and solvating media, and that the blinking-suppressed QDs can provide continuous trajectories in live-cell receptor tracking studies.
In vitro and animal studies of sodium thiosulfate as a potential chemoprotectant against carboplatin-induced ototoxicity. (1996)

When carboplatin (cis-diammine-1,1-cyclobutane-dicarboxylato-platinum) delivery to brain tumors is optimized with osmotic blood-brain barrier disruption (BBBD), high frequency hearing loss can result. Treatment with sodium thiosulfate (STS) blocked carboplatin cytotoxicity against the LX-1 human small cell lung carcinoma cell line in vitro. STS decreased carboplatin-induced ototoxicity in a guinea pig model, as determined by electrophysiological measurements and analysis of inner ear outer hair cell numbers. Protection was found when STS was administered up to 8 h subsequent to carboplatin but not 24 h after carboplatin. In a rat model of osmotic BBBD, STS was neurotoxic when given immediately after BBBD but not when given 60 min after BBBD, when the barrier is reestablished. Thus, delayed administration of STS may provide a mechanism to reduce the cochlear toxicity caused by BBBD-enhanced carboplatin delivery to the brain.
317 Development of non-catalytic hydrogen generator from molecular ammonia (2013)

Non-catalytic hydrogen production from ammonia gas using a pulsed atmospheric plasma have been developed to solve the problems of hydrogen transportation and storages. Ammonia is easily decomposed by electron energy generated by plasma, which is converted to molecular hydrogen and nitrogen by global reaction; NH_3 + e → 0.5 N_2 + 1.5 H_2. A hydrogen yield attained 100% at an applied voltage of 15 kV and an ammonia flow rate of 0.2 L/min. T o improve the energy efficiency of hydrogen production, a plasma reactor with a hydrogen separator was proposed. As the hydrogen separator was inhibited the reverse reaction for ammonia formation (N + 3H→NH_3), the hydrogen yield attained 100% at an applied voltage of9kV and an ammonia flow rate of0.8L/min..
Parenteral nutrition and oral intake: effect of branched-chain amino acids. (1992)

The effect of peripheral parenteral nutrition (PPN) on voluntary food intake was examined in healthy male subjects. Each study (lasting 17 to 19 days) was divided into three phases: Ringer's lactate (RL); PPN administered as a combination of glucose, fat, and amino acids; and finally RL. During the middle phase, some of the subjects received a parenteral formula in which half of the amino acids had been replaced with the branched-chain amino acids (BCPPN). When PPN was infused, subjects reduced their food intake within 48 hours by approximately 80% of the infused calories (p less than 0.001) within 48 hours, whereas intake was reduced by less than 40% of the infused calories when BCPPN was infused. Use of branched-chain amino acid-enriched parenteral nutrition may minimize the reduction in food intake seen during intravenous nutrition, possibly hastening a return to normal eating.
Equivalence Checking of Arithmetic Circuits on the Arithmetic Bit Level (2004)

One of the most severe shortcomings of currently available equivalence checkers is their inability to verify arithmetic circuits and multipliers, in particular. In this paper, we present a bit-level reverse-engineering technique that complements standard equivalence checking frameworks. We propose a Boolean mapping algorithm that extracts a network of half adders from the gate netlist of an addition circuit. Once the arithmetic bit-level representation of the circuit is obtained, equivalence checking can be performed using simple arithmetic operations. We have successfully applied the technique for the verification of a large number of multipliers of different architectures as well as more general arithmetic circuits, such as multiply/add units. The experimental results show the great promise of our approach.
Enhanced microbial electrosynthesis by using defined co-cultures (2016)

Microbial uptake of free cathodic electrons presents a poorly understood aspect of microbial physiology. Uptake of cathodic electrons is particularly important in microbial electrosynthesis of sustainable fuel and chemical precursors using only CO<sub>2</sub> and electricity as carbon, electron and energy source. Typically, large overpotentials (200 to 400 mV) were reported to be required for cathodic electron uptake during electrosynthesis of, for example, methane and acetate, or low electrosynthesis rates were observed. To address these limitations and to explore conceptual alternatives, we studied defined co-cultures metabolizing cathodic electrons. The Fe(0)-corroding strain IS4 was used to catalyze the electron uptake reaction from the cathode forming molecular hydrogen as intermediate, and Methanococcus maripaludis and Acetobacterium woodii were used as model microorganisms for hydrogenotrophic synthesis of methane and acetate, respectively. The IS4-M. maripaludis co-cultures achieved electromethanogenesis rates of 0.1-0.14 μmol cm<sup>-2</sup> h<sup>-1</sup> at -400 mV vs standard hydrogen electrode and 0.6-0.9 μmol cm<sup>-2</sup> h<sup>-1</sup> at -500 mV. Co-cultures of strain IS4 and A. woodii formed acetate at rates of 0.21-0.23 μmol cm<sup>-2</sup> h<sup>-1</sup> at -400 mV and 0.57-0.74 μmol cm<sup>-2</sup> h<sup>-1</sup> at -500 mV. These data show that defined co-cultures coupling cathodic electron uptake with synthesis reactions via interspecies hydrogen transfer may lay the foundation for an engineering strategy for microbial electrosynthesis.
Generation and clinical application of human T cell-derived induced pluripotent stem cells (2011)

Pluripotent stem (iPS) cells are a very promising cell source for models of human genetic diseases and revolutionary new therapies. Successful reprogramming of human blood cells has been reported and is likely to advance the clinical application of iPS cells. In terms of a patient's own somatic cells, generating iPS cells from peripheral blood cells has advantages for clinical applications because these cells are an easily accessible cell source. Of the human peripheral blood cells, T cells can be readily cultured in vitro and proliferate rapidly. Furthermore, only a small amount of peripheral blood is needed to generate iPS cells from T cells, thus increasing the number of patients in whom the technique can be used. iPS cells that contain T-cell receptor (TCR) rearrangements in their genome also have the potential to be traceable markers when establishing novel transplantation therapies. The present review summarizes recent progress in the methods used to generate iPS cells and the future potential of human T cell-derived iPS cells.
An optical fibre sensor for the measurement of pressure (1988)

Abstract This paper describes the design, construction and testing of a fibre optic pressure sensor based on a reflecting Fabry-Perot etalon. The etalon comprised one fixed mirror and a second mirror designed to flex under the action of the pressure being monitored. A single multimode fibre was used to connect the passive, remote sensor to the transmitter/receiver section, and dual wavelength referencing was used to eliminate the effects of bending-induced attenuation in the fibre.
Addressee and Response Selection in Multi-Party Conversations with Speaker Interaction RNNs (2017)

In this paper, we study the problem of addressee and response selection in multi-party conversations. Understanding multi-party conversations is challenging because of complex speaker interactions: multiple speakers exchange messages with each other, playing different roles (sender, addressee, observer), and these roles vary across turns. To tackle this challenge, we propose the Speaker Interaction Recurrent Neural Network (SI-RNN). Whereas the previous state-of-the-art system updated speaker embeddings only for the sender, SI-RNN uses a novel dialog encoder to update speaker embeddings in a role-sensitive way. Additionally, unlike the previous work that selected the addressee and response separately, SI-RNN selects them jointly by viewing the task as a sequence prediction problem. Experimental results show that SI-RNN significantly improves the accuracy of addressee and response selection, particularly in complex conversations with many speakers and responses to distant messages many turns in the past.
Design of a soft upper body robot for physical human-robot interaction (2015)

To physically interact with children, a robot should be safe and durable. We have developed a small toy sized robot with a soft skin that is robust to playful physical interaction. The upper body, including the arms, pelvis, chest and back has soft, 3D printed air-filled modules connected to pressure sensors to sense contact and provide protection to the child and robot while interacting. These soft skin modules cover the underlying actuators and the rigid 3D printed frame with printed bearings. In this paper, we present the design process of these modules and demonstrate their efficacy by implementing a "grab and move" user interface for posing the robot link by link.
Multi-model robust error correction for face recognition (2016)

In this work we present a general framework for robust error estimation in face recognition. The proposed formulation allows the simultaneous use of various loss functions for modeling the residual in face images, which usually follows non-standard distributions, depending on the image capturing conditions. Our method extends the current vast literature offering flexibility in the selection of the residual modeling characteristics but, at the same time, considering many existing algorithms as special cases. As such, it proves robust for a range of error inducing factors, such as, varying illumination, occlusion, pixel corruption, disguise or their combinations. Extensive simulations document the superiority of selecting multiple models for representing the noise term in face recognition problems, allowing the algorithm to achieve near-optimal performance in most of the tested face databases. Finally, the multi-model residual representation offers useful insights into understanding how different noise types affect face recognition rates.
Robust speech recognition using dynamic noise adaptation (2011)

Dynamic noise adaptation (DNA) is a model-based technique for improving automatic speech recognition (ASR) performance in noise. DNA has shown promise on artificially mixed data such as the Aurora II and DNA+Aurora II tasks - significantly outperforming well-known techniques like the ETSI AFE and fMLLR - but has never been tried on real data. In this paper, we present new results generated by commercial-grade ASR systems trained on large amounts of data. We show that DNA improves upon the performance of the spectral subtraction (SS) and stochastic fMLLR algorithms of our embedded recognizers, particularly in unseen noise conditions, and describe how DNA has been evolved to become suitable for deployment in low-latency ASR systems. DNA improves our best embedded system, which utilizes SS, fMLLR, and fMPE by over 22% relative at SNRs below 6 dB, reducing the word error rate in these adverse conditions from 4.24% to 3.29%.
Hsp90: A Novel Target for Cancer Therapy (2006)

Hsp90 is a molecular chaperone required for the stress-survival response, protein refolding, and the conformational maturation of a variety of signaling proteins. Natural products that bind selectively to Hsp90 and inhibit its function have been used to determine its biologic role. Experiments with these drugs have shown that Hsp90 is required for maintaining the malignant phenotype of cancer cells. Studies in vivo show that Hsp90 inhibitors have antitumor activity when given alone and in combination with cytotoxics. The basis for the therapeutic index (selective toxicity to cancer cells) of Hsp90 inhibitors is complex and may have to do with induction of degradation of mutant oncoproteins and other proteins necessary for their proliferation and survival as well as to an enhanced requirement of these cells for Hsp90 stress-survival functions. Based on these data, 17-AAG, an ansamycin antibiotic inhibitor of Hsp90, is being tested extensively in clinical trials in patients with advanced cancer. These trials demonstrate that the biologic function of Hsp90 can be inhibited in patients and antitumor activity has been noted in patients with breast cancer, multiple myeloma and other cancers. These data and the physicochemical properties of 17-AAG that limit its use as a drug, have led to broad efforts to develop improved and novel Hsp90 inhibitors. This article will review the preclinical data which supports the testing of Hsp90 inhibitors as cancer drugs and update the reader on the current status of the ongoing clinical trials of Hsp90 inhibitors.
Technology Independent Large Signal Non Quasi-Static FET Models by Direct Construction from Automatically Characterized Device Data (1991)

This paper describes a new, general and accurate, large signal GaAs FET model for nonlinear (e.g. harmonic balance) circuit simulation, its fast and unambiguous construction (model generation) by explicit calculations applied to the raw device data, and the adaptive, automated data acquisition system used to characterize the device. The model implementation in a harmonic balance simulator, the model generation procedure, and the automated data acquisition system form an efficient, practical, commercially available package. for state-of-the-art nonlinear circuit design.
Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS (2018)

Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.
Progress toward development of an inhalation vaccine against botulinum toxin (2004)

The looming threat of bioterrorism has enhanced interest in the development of vaccines against agents such as botulinum toxin. This in turn has stimulated efforts to create vaccines that are effective by the oral and inhalation routes. Recently, considerable progress has been made in creating an inhalation vaccine against botulism. This work stems from the discovery that a polypeptide that represents a third of the toxin molecule retains the ability to be adsorbed from the airway and to evoke an immune response but retains none of the adverse effects of the native toxin. Interestingly, this polypeptide can also serve as a carrier molecule in the creation of inhalation vaccines against other pathogens.
Differential distribution of intravenous curcumin formulations in the rat brain. (2011)

These data indicate that curcumin does localize in putative damaged brain tissues and suggest therapeutic trials be explored with all three formulations in animal models with pre- and post traumatic states.
A Computational Study of the Performance and Robustness Properties of Retrospective Cost Adaptive Control (2010)

We present a computational study of a discrete-time adaptive control algorithm that is eective for multi-input, multi-output systems that are either minimum phase or nonminimum phase. The adaptive control algorithm requires limited model information, specically, the rst nonzero Markov parameter and the nonminimum-phase transmission zeros of the transfer function from the control signal to the performance measurement. Furthermore, the adaptive control algorithm is eective for stabilization, command following, and disturbance rejection. For command following and disturbance rejection, the algorithm does not require knowledge of the command or disturbance spectrum. We explore computationally the algorithm’s performance and robustness in the presence of errors in the required modeling information.