gebhart/patrepeval huggingface dataset:
ERG protein expression in prostate and vascular tumors: A potential for ERG-based stratification. (2011)

e15171 Background: Frequent overexpression of ERG in prostate tumors is a result of prevalent gene fusions involving upstream sequences of androgen regulated genes (predominantly TMPRSS2) and downstream coding sequences of nuclear transcription factors within the ETS gene family (primarily ERG). Despite numerous reports of ERG alterations at the transcript and genome levels, the ERG oncoprotein remains to be defined. Using a highly specific ERG monoclonal antibody, we have recently developed a comprehensive insight into ERG expression in various cell types of benign and malignant prostate glands. Further, we have analyzed ERG protein expression in human tumors of diverse origins. Methods: Using whole-mount prostate sections from 150 prostatectomy specimens, ERG protein expression was analyzed in PIN, tumor foci, benign glands and other cell types in prostate. In randomly selected cases ERG protein expression was correlated with ERG fusion status. A broad range of vascular endothelial (n=250), other mesenchymal (n=973), and epithelial tumors (n=657) were examined. Results: CPDR ERG-MAb showed striking specificity for detecting prostate tumor cells (>99.9%). Specimens from 65% patients had one or more ERG positive tumor focus. Examination of ERG positive PINs and ERG positive tumors within the same whole-mount sections revealed a 97% concordance. In normal adult tissues, including human and mouse prostate, ERG was restricted to endothelial cells and a subset of bone marrow precursors. ERG was expressed in virtually all vascular tumors and absent in all epithelial tumors except prostate tumors. Conclusions: Taken together, the homogeneous and strong ERG expression in individual tumors and the remarkable correlation between ERG positive PIN lesions and tumors suggests a role for ERG in the pre-invasive to invasive transition of prostate cancer cells. The demonstrated high specificity of CPDR ERG-MAb has potential to provide new opportunities in prostate cancer diagnosis and stratification. Further, ERG is a highly specific new marker for benign and malignant vascular tumors.
Inosine reduces inflammation and improves survival in a murine model of colitis (2003)

Inosine, a naturally occurring purine formed from the breakdown of adenosine, has recently been shown to exert powerful anti-inflammatory effects both in vivo and in vitro. This study evaluated inosine as a potential therapy for colitis. Colitis was induced in mice by the administration of dextran sulfate sodium (DSS). Oral treatment with inosine was begun either before the onset of colitis or as a posttreatment once colitis was established. Evaluation of colon damage and inflammation was determined grossly (body wt, rectal bleeding), histologically, and biochemically (colon levels of MPO, MDA, and cytokines). DSS-induced colitis significantly increased inflammatory cell infiltration into the colon. DSS-induced colitis also increased colon levels of lipid peroxidation, cytokines, and chemokines. Inosine protected the colon from DSS-induced inflammatory cell infiltration and lipid peroxidation. Inosine also partially reduced these parameters in an experimental model of established colitis. Thus inosine treatment may be a potential therapy in colitis.
Protection-against-collision optical packet network (1992)

An optically transparent packet network controlled by a simple medium access circuit is presented. The system, based on frequency division multiplexing and tunable transmitters, has no internal blocking and is optically self-routing. It provides internal collision-free traffic by allowing access to the network only if the addressed channel (output port) is available. A packet denied access to the network is reflected back to its input port, which is thus informed of the packet status. Therefore, the traffic is not bogged down by acknowledgments between input and output ports. To achieve this result, each input of the network is controlled by a protection-against-collision (PAC) circuit located at a central hub. The PAC circuit uses the packet for probing the energy present in the addressed channel. The resulting signal controls an optical switch connecting the input port to the network. Thus, full optical connectivity is provided between ports controlled by electrical signals derived from simple optical power measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Propioxatins A and B, new enkephalinase B inhibitors. III Total synthesis of propioxatin A. (1986)

Propioxatin A, a potent enkephalinase B inhibitor produced by Kitasatosporia setae SANK 60684, was synthesized. The synthetic route involved a regio-selective synthesis of O-benzyl-alpha-propylsuccinic acid monohydroxamic acid via the acid chloride of alpha-propylsuccinic acid. The stereoisomer of the N-acyl moiety of natural propioxatin A was analyzed by X-ray crystallography in the form of the di-O-benzyl ester and was determined as S. Devalyl propioxatin A synthesized by the same method showed a higher Ki value for enkephalinase B than propioxatin A.
Raman fiber laser at 1.45 mm: comparison of different schemes (2000)

Various configurations of 1.45-µm Raman fiber laser pumped by double-clad Yb-doped fiber laser have been experimentally investigated and compared with respect to their power conversion efficiency. An output power of 1.9 W with 10 W power at 978 nm was achieved for four-step Raman conversion in a DSF fiber.
Assist feature placement analysis using focus sensitivity models (2006)

Sub-Resolution Assist Features (SRAFs) are placed into patterns to enhance the through process imaging performance of critical features. SRAFs are typically placed using complex rules to achieve optimal configurations for a pattern. However, as manufacturing process nodes are growing increasingly complex, the SRAF placement rules will most likely be unable to produce optimal performance on some critical features. A primary impediment to resolving these problems is identifying poorly performing features in an efficient manner. A new process model form referred to as a Focus Sensitivity Model (FSM) is capable of rapidly analyzing SRAF placement for through process pattern performance. This study will demonstrate that an FSM is capable of finding suboptimal SRAF placements as well as missing SRAFs. In addition, the study suggests that the FSM does not need to comprehend the entire photolithography process to analyze SRAF placement. This results in simpler models that can be generated before a manufacturing process enters its development phase.
332. Dual Gene Transfer and Transgenesis by Novel Lentiviral Vectors Carrying Synthetic Bi-Directional Promoters (2004)

Expression of more than one transgene within the same cell allows combining genetic correction with marking, selection, amplification, and conditional elimination of transduced cells. In addition, it is required when gene therapy depends on multiple or synergic genes. Unfortunately, reaching coordinate, high-level dual gene expression in the majority of transduced cells poses significant challenges to current gene transfer technologies. We showed that IRES-based bicistronic lentiviral vectors co-express two transgenes in only a fraction of transduced cells, and that transgene expression was significantly lower when IRES-dependent than when it was cap-dependent. Thus, selection of transduced cells was required to ensure coordinate expression of both transgenes in all target cells. To overcome these limitations, we developed a novel vector design in which a minimal core promoter was fused upstream and close to an efficient promoter, but in the opposite orientation. The resulting bi-directional promoter mediated coordinate transcription of two divergent mRNA's. We tested several constructs by changing the trailer core promoter and the driver enhancer/promoter, and found that the bi-directional design significantly enhanced transcription from the trailer core promoter, did not affect downstream expression from the driver promoter, and allowed stable co-expression of two genes from a single vector genome. Strikingly, this new type of vector enabled efficient dual gene transfer and expression in primary hematopoietic progenitors, both of human and mouse origin, tested as immature cells, and after transplantation and differentiation, and in primary T lymphocytes, transduced when proliferating and when non proliferating, after cytokine exposure. Importantly, the new vectors allowed proficient in vivo dual gene transfer and transgenesis. After perivitelline injection of bi-directional vector, we observed robust pan-cellular co-expression of two marker genes in all tissues analyzed of founder and progeny transgenic mice, including brain, liver, kidney, gut, spleen, heart and muscle. Intriguingly, a recent survey of the human genome indicated an abundance of divergently transcribed gene pairs, whose transcription start sites are separated by less than 1 kb. It is likely that many of the promoter elements found between these gene pairs can initiate transcription in both directions, and contain shared elements that regulate both genes. Thus, the synthetic bi-directional promoters that we developed may mimic a well-represented and evolutionary conserved feature of eukaryotic transcription, providing a structural basis for their robust performance. The new lentiviral vectors built around these bi-directional promoters will advance the reach of gene therapy and increase the power of gene-function and target validation studies.
Assessing the elasticity change of cataract lens with OCE (2016)

Cataract is one of the most common degenerative diseases that causes blindness. Careful quantification of lens biomechanical properties can greatly assist in early detection of the disease as well as personalization of treatment procedures. In this study, we utilize a phase-sensitive optical coherence elastography (OCE) system to assess the effects of the cold cataract on the biomechanical properties of porcine crystalline lens <i>in vitro</i>. Relaxation rates of air puff induced elastic waves were measured on the same crystalline lens with and without cold cataract. Results demonstrate that the relaxation rate and, thus, associated elasticity of the porcine lens, increased due to the presence of cold cataract.
<title>No-reference quality metric for degraded and enhanced video</title> (2003)

In this paper we present a no-reference objective quality metric (NROQM) that has resulted from extensive research on impairment metrics, image feature metrics, and subjective image quality in several projects in Philips Research, and participation in the ITU Video Quality Experts Group. The NROQM is aimed at requirements including video algorithm development, embedded monitoring and control of image quality, and evaluation of different types of display systems. NROQM is built from metrics for desirable and non-desirable image features (sharpness, contrast, noise, clipping, ringing, and blocking artifacts), and accounts for their individual and combined contributions to perceived image quality. We describe our heuristic, incremental approach to modeling quality and training the NROQM, and its advantages to deal with imperfect data and imperfect metrics. The results of training the NROQM using a large set of video sequences, which include degraded and enhanced video, show high correlation between objective and subjective scores, and the results of the first performance test show good objective-subjective correlations as well. We also discuss issues that require further research such as fully content-independent metrics, measuring over-enhanced video quality, and the role of temporal impairment metrics.
Toward Real-Time Estimation of Driver Situation Awareness: An Eye-tracking Approach based on Moving Objects of Interest. (2020)

Eye-tracking techniques have the potential for estimating driver awareness of road hazards. However, traditional eye-movement measures based on static areas of interest may not capture the unique characteristics of driver eyeglance behavior and challenge the real-time application of the technology on the road. This article proposes a novel method to operationalize driver eye-movement data analysis based on moving objects of interest. A human-subject experiment conducted in a driving simulator demonstrated the potential of the proposed method. Correlation and regression analyses between indirect (i.e., eye-tracking) and direct measures of driver awareness identified some promising variables that feature both spatial and temporal aspects of driver eye-glance behavior relative to objects of interest. Results also suggest that eye-glance behavior might be a promising but insufficient predictor of driver awareness. This work is a preliminary step toward real-time, on-road estimation of driver awareness of road hazards. The proposed method could be further combined with computer-vision techniques such as object recognition to fully automate eye-movement data processing as well as machine learning approaches to improve the accuracy of driver awareness estimation.
Extreme Nonlinear Optics: Attosecond Photonics at Short Wavelengths (2004)

We discuss coherent up-conversion of near-infrared femtosecond laser light into the extreme ultraviolet and soft-X-ray regions of the spectrum using the process of high-harmonic generation. We show that by using concepts from visible wavelength photonics, it is now possible to extend nonlinear optics well into the X-ray region of the spectrum. By manipulating the dynamics of the high harmonic process using optimized waveguide structures and pulse shapes, and on attosecond timescales, we can control the energy of the emitted photons, as well as increase the efficiency of the up-conversion process. Use of these optimized waveguide structures and pulse shapes can also improve the spatial and temporal coherence of the light. This work demonstrates that sophisticated concepts from nonlinear-optical photonics and coherent control can be applied to "extreme" nonlinear optics.
Multicenter clinical validation of an on-line monitor of dialysis adequacy. (1996)

Quantitation of hemodialysis by measuring changes in blood solute concentration requires careful timing when taking the postdialysis blood sample to avoid errors from postdialysis rebound and from recirculation of blood through the access device. It also requires complex mathematical interpretation to account for solute disequilibrium in the patient. To circumvent these problems, hemodialysis can be quantified and its adequacy assessed by direct measurement of the urea removed in the dialysate. Because total dialysate collection is impractical, an automated method was developed for measuring dialysate urea-nitrogen concentrations at frequent intervals during treatment. A multicenter clinical trial of the dialysate monitoring device, the Biostat 1000 (Baxter Healthcare Corporation, McGaw Park, IL) was conducted to validate the measurements of urea removed, the delivered dialysis dose (Kt/V), and net protein catabolism (PCR). The results were compared with a total dialysate collection in each patient. During 29 dialyses in 29 patients from three centers, the paired analysis of urea removed, as estimated by the dialysate monitor compared with the total dialysate collection, showed no significant difference (14.7 +/- 4.7 g versus 14.8 +/- 5.1 g). Similarly, measurements of Kt/V and PCR showed no significant difference (1.30 +/- 0.18 versus 1.28 +/- 0.19, respectively, for Kt/V and 42.3 +/- 15.7 g/day versus 52.2 +/- 17.4 g/day for PCR). When blood-side measurements during the same dialyses were analyzed with a single-compartment, variable-volume model of urea kinetics, Kt/V was consistently overestimated (1.49 +/- 0.29/dialysis, P < 0.001), most likely because of failure to consider urea disequilibrium. Because urea disequilibrium is difficult to quantitate during each treatment, dialysate measurements have obvious advantages. The dialysate monitor eliminated errors from dialysate bacterial contamination, simplified dialysate measurements, and proved to be a reliable method for quantifying and assuring dialysis adequacy.
Prophylactic use of flagellin to reduce Graft-vs-Host Disease in allogeneic HSCT recipients: a novel therapeutic approach (145.21) (2010)

Abstract To control Graft-vs-Host Disease (GvHD) in allogeneic hematopoietic stem cell transplant (HSCT) recipients, we tested whether flagellin, a bacterial protein that agonistically binds with TLR5 can modulate allo-reactivity of donor T-cells in murine HSCT. Administration of flagellin (50μg/mouse i.p.) 3 hrs before 11Gy irradiation and 24 hrs after allogeneic HSCT {5 million splenocytes and 5 million T cell depleted bone marrow (BM) cells} in H-2K → H-2b model significantly reduced GvHD and had 33% death by 132 days post transplant versus severe acute GvHD and 100% early mortality among control HSCT recipients that received PBS. Flagellin-treated recipients had 100% donor chimerism with both naïve and memory T cells in their blood and BM and the cell numbers were similar to a normal B6 mice. The numbers of B, NK and stem cells per BM were also found similar with that of normal B6 mouse. Flagellin-treated CB6F1 recipients in allogeneic parent to F1 model also showed similar immune reconstitution without GvHD within 70 days post transplant and had higher levels CMV specific CD8+ T cells in spleen on day 10 after i.p. MCMV infection compared to control recipients and survived. Generation of new donor BM- and spleen-derived T cells and regulatory T cells were maintained through functional thymus. Thus, flagellin protected allogeneic HSCT recipients from lethal GvHD, established central and peripheral immune reconstitution, and protected recipients from opportunistic CMV infection.
Integrated Differential-Mode and Common-Mode Filter to Mitigate the Effects of Long Motor Leads on AC Drives (2011)

Pulsewidth-modulated (PWM) ac drives generate high differential-mode (DM) motor voltages due to the reflected wave phenomenon. The common-mode (CM) voltage produced by a PWM inverter also has fast transitions that result in high peak currents to ground. For low-power ac drives, this can present several issues, such as pump-up of the dc bus and failure of the power module due to high instantaneous currents that are often undetected because of the typical sampling algorithm used. In this paper, existing drive output filter solutions are reviewed, and a new filter design is presented, which has integrated DM and CM impedance with damping matched to typical cable surge impedance. This eliminates reflections of both DM and CM traveling waves and also reduces peak cable charging currents. Experimental results are provided to demonstrate that the new filter has improved performance to reduce motor DM and CM voltages and drive output CM current, thus mitigating the issues specifically seen with low-power ac drives. Complete design details for the filter and a particular implementation of the integrated DM and CM reactor are also presented.
An adaptive statistical time-frequency method for detection of broken bars and bearing faults in motors using stator current (1999)

It is well known that motor current is a nonstationary signal, the properties of which vary with respect to the time-varying normal operating conditions of the motor. As a result, Fourier analysis makes it difficult to recognize fault conditions from the normal operating conditions of the motor. Time-frequency analysis, on the other hand, unambiguously represents the motor current which makes signal properties related to fault detection more evident in the transform domain. In this paper, the authors present an adaptive, statistical, time-frequency method for the detection of broken bars and bearing faults. Due to the time-varying normal operating conditions of the motor and the effect of motor geometry on the current, they employ a training-based approach in which the algorithm is trained to recognize the normal operating modes of the motor before the actual testing starts. During the training stage, features which are relevant to fault detection are estimated using the torque and mechanical speed estimation. These features are then statistically analyzed and segmented into normal operating modes of the motor. For each mode, a representative and a threshold are computed and stored in a database to be used as a baseline during the testing stage. In the testing stage, the distance of the test features to the mode representatives are computed and compared with the thresholds. If it is larger than all the thresholds, the measurement is tagged as a potential fault signal. In the postprocessing stage, the testing is repeated for multiple measurements to improve the accuracy of the detection. The experimental results from their study suggest that the proposed method provides a powerful and a general approach to the motor-current-based fault detection.
A State Observer For The Permanent-Magnet Synchronous Motor (1987)

An identity state observer for the smooth-rotor permanent-magnet synchronous motor is derived which reconstructs the electrical and mechanical states of the motor from current and voltage measurements. The observer operates in the rotor frame and estimates direct and quadrature stator currents, rotor velocity, and rotor position. Since the rotor position is estimated, the rotor reference frame is approximated using the latest rotor position estimate. The motor dynamics and the transformation into the estimated rotor frame are nonlinear and thus the observer and observer error dynamics are nonlinear. Therefore, small signal stability is analyzed from a linearized model. Simulations including realis-tic measurement disturbances are used to investigate the global stability and accuracy of the observer.
A cationic fluorescent polymeric thermometer for the ratiometric sensing of intracellular temperature (2015)

We developed new cationic fluorescent polymeric thermometers containing both benzothiadiazole and BODIPY units as an environment-sensitive fluorophore and as a reference fluorophore, respectively. The temperature-dependent fluorescence spectra of the thermometers enabled us to perform highly sensitive and practical ratiometric temperature sensing inside living mammalian cells. Intracellular temperatures of non-adherent MOLT-4 (human acute lymphoblastic leukaemia) and adherent HEK293T (human embryonic kidney) cells could be monitored with high temperature resolutions (0.01-1.0 °C) using the new cationic fluorescent polymeric thermometer.
Sub-wavelength Plasmonic Graphene-based Slot Electro-optic Modulator (2017)

We proposed a novel structure for plasmonic graphene modulator. Extinction ratio (ER) larger than 1 dB/um is shown using single layer graphene. Also, by engineering more layers of graphene, an even higher ER is demonstrated.
Counter-Selectable Marker for Bacterial-Based Interaction Trap Systems (2006)

Counter-selectable markers can be used in two-hybrid systems to search libraries for a protein or compound that interferes with a macromolecular interaction or to identify macromolecules from a population that cannot mediate a particular interaction. In this report, we describe the adaptation of the yeast URA3/5-FOA counter-selection system for use in bacterial interaction trap experiments. Two different URA3 reporter systems were developed that allow robust counter-selection: (i) a single copy F' episome reporter and (ii) a co-cistronic HIS3-URA3 reporter vector. The HIS3-URA3 reporter can be used for either positive or negative selections in appropriate bacterial strains. These reagents extend the utility of the bacterial two-hybrid system as an alternative to its yeast-based counterpart.