gebhart/patrepeval huggingface dataset:
Abstract B34: Development of a urine microvesicle/exosome RNA biomarker panel to identify prostate cancer. (2013)

Abstract Introduction: Prostate cancer is diagnosed utilizing anywhere from 10-12 transrectal prostate needle biopsy specimens (PNB). The decision to biopsy is driven in part by the PSA test, which is known to have marginal accuracy in appropriate patient selection. As a result, between 40 to 60% of patients will have a benign biopsy with approximately 20% having false negative results. Exosomal RNA is stable in urine and can be easily extracted from a random urine sample. A novel molecular assay with an improved ability to predict the likelihood of having prostate cancer on a needle biopsy is being developed through isolation of RNA from urine exosomes and subsequent identification of an accurate prognostic gene signature. Methods: A multicenter study was designed to collect first catch random urine, without a prior digital rectal exam (DRE) from men presenting for a PNB. Urine samples were processed at Exosome Diagnostic's clinical laboratory under quality control using the EXO70 Urine Microvesicle RNA Isolation Kit. The exosomal RNA was reverse transcribed and qPCR assays for specific genes performed. The results of those assays along with collected clinical data and PNB histopathology were subjected to statistical analysis to derive ROC curves. Results: Urine samples from 258 men scheduled for a PNB were tested. Triaged gene lists previously shown to be important in prostate cancer were compiled and univariately assessed with respect to discrimination of PNB results. A series of single and multiple gene expression profiles representing anywhere from 1 to 3 gene signatures relative to a reference gene were identified. Multivariate models including several gene signatures with a ROC AUC performance &gt; 0.7 were found. Interestingly, a 3 gene signature composed of PCA3, ERG and KLK3 provided a very good performance with an AUC of 0.76 (N = 122). Conclusions: Prostate cancer cells release exosomes / microvesicles that can be isolated from a random urine sample. The exosomal RNA is stable and can be efficiently isolated and used for tumor profiling even without a prior DRE. This urine exosome platform presents a robust model for a quick and simple test that can assist in the initial biopsy decision process. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B34. Citation Format: Johan Skog, Mikkel Noerholm, Stefan Bentink, Charlotte Romain, Jillian Fishbeck, Ian Sinclair, Anna Scott, Romy Mueller, Tina Koestler, Susan Belzer. Development of a urine microvesicle/exosome RNA biomarker panel to identify prostate cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B34.
Expressing and verifying probabilistic assertions (2014)

Traditional assertions express correctness properties that must hold on every program execution. However, many applications have probabilistic outcomes and consequently their correctness properties are also probabilistic (e.g., they identify faces in images, consume sensor data, or run on unreliable hardware). Traditional assertions do not capture these correctness properties. This paper proposes that programmers express probabilistic correctness properties with probabilistic assertions and describes a new probabilistic evaluation approach to efficiently verify these assertions. Probabilistic assertions are Boolean expressions that express the probability that a property will be true in a given execution rather than asserting that the property must always be true. Given either specific inputs or distributions on the input space, probabilistic evaluation verifies probabilistic assertions by first performing distribution extraction to represent the program as a Bayesian network. Probabilistic evaluation then uses statistical properties to simplify this representation to efficiently compute assertion probabilities directly or with sampling. Our approach is a mix of both static and dynamic analysis: distribution extraction statically builds and optimizes the Bayesian network representation and sampling dynamically interprets this representation. We implement our approach in a tool called Mayhap for C and C++ programs. We evaluate expressiveness, correctness, and performance of Mayhap on programs that use sensors, perform approximate computation, and obfuscate data for privacy. Our case studies demonstrate that probabilistic assertions describe useful correctness properties and that Mayhap efficiently verifies them.
Molecular Spring Enabled High-Performance Anode for Lithium Ion Batteries (2017)

Flexible butyl interconnection segments are synthetically incorporated into an electronically conductive poly(pyrene methacrylate) homopolymer and its copolymer. The insertion of butyl segment makes the pyrene polymer more flexible, and can better accommodate deformation. This new class of flexible and conductive polymers can be used as a polymer binder and adhesive to facilitate the electrochemical performance of a silicon/graphene composite anode material for lithium ion battery application. They act like a "spring" to maintain the electrode mechanical and electrical integrity. High mass loading and high areal capacity, which are critical design requirements of high energy batteries, have been achieved in the electrodes composed of the novel binders and silicon/graphene composite material. A remarkable area capacity of over 5 mAh/cm² and volumetric capacity of over 1700 Ah/L have been reached at a high current rate of 333 mA/g.
PWC: A proactive worm containment solution for enterprise networks (2007)

We propose PWC, a proactive worm containment solution for enterprises. PWC can stop - instead of slowing down - an infected host from releasing worm scans as early as after merely 4 scans. Motivated by the observation that a worm uses a sustained outgoing packet rate, PWC gains infection awareness seconds before a signature or filter can be generated. To overcome denial-of-service possibly caused by such smoking signs of infection, PWC develops two new white detection (detecting who are uninfected) techniques: (a) the vulnerability time window lemma, and (b) the relaxation analysis. PWC is signature-free thus it is immunized from polymorphic worms and timely in containing. PWC is also resilient to containment evading. PWC is not sensitive to worm scan rate, and not protocol specific. Due to white detection, PWC causes minimal denial-of-service. Evaluation based on real traces and worm simulations demonstrates that PWC significantly outperforms Virus Throttle [1] in terms of number of released worm scans, number of hosts infected by local scans, and availability.
Gel spinning of poly(vinyl alcohol) from dimethyl sulfoxide/water mixture (1994)

Abstract Gel spinning of poly(vinyl alcohol) (PVA) was attempted from the PVA dope prepared from the mixture of dimethyl sulfoxide (DMSO) and water. The DMSO/H 2 O = 80/20 (w/w) mixture and methanol were found to be the best solvent for the spinning dope and the coagulant, respectively, to give PVA fiber with the highest drawability. PVA fiber with the highest strength and Young's modulus were obtained from the undrawn gel fibers when subjected to hot two‐stage drawing under conditions such as to produce maximum drawability. Furthermore, higher draw ratios of PVA fiber were attained at 6 wt % dope by lowering the coagulating temperature of methanol. In the present work, the highest tensile strength (2.8 GPa) and the highest Young's modulus (64 GPa) were realized, when the spinning dope was prepared from PVA with DP of 5,000 and the DMSO/H 2 O (80/20) mixed solvent to have the PVA concentration of 6 wt %, the coagulating temperature of methanol was −20°C, and the two‐stage drawing was carried out at 160 (first) and 200°C (second). The PVA fiber prepared under this gel spinning condition could be elongated to 45 times draw ratio. The very high drawability of PVA fibers obtained from the DMSO/H 2 O (80/20) mixture dope was ascribed to the ability of the DMSO/H 2 O mixture to promote gelation. © 1994 John Wiley & Sons, Inc.
Indol-3-yl-tetramethylcyclopropyl Ketones: Effects of Indole Ring Substitution on CB<sub>2</sub> Cannabinoid Receptor Activity (2008)

A series of potent indol-3-yl-tetramethylcyclopropyl ketones have been prepared as CB 2 cannabinoid receptor ligands. Two unsubstituted indoles ( 5, 32) were the starting points for an investigation of the effect of indole ring substitutions on CB 2 and CB 1 binding affinities and activity in a CB 2 in vitro functional assay. Indole ring substitutions had varying effects on CB 2 and CB 1 binding, but were generally detrimental to agonist activity. Substitution on the indole ring did lead to improved CB 2/CB 1 binding selectivity in some cases (i.e., 7- 9, 15- 20). All indoles with the morpholino-ethyl side chain ( 32- 43) exhibited weaker binding affinity and less agonist activity relative to that of their tetrahydropyranyl-methyl analogs ( 5- 31). Several agonists were active in the complete Freund's adjuvant model of chronic inflammatory thermal hyperalgesia ( 32, 15).
Distributed and dynamic monitoring of 4km/sec waves using a Brillouin fiber optic strain sensor (2013)

We report a Brillouin-based fully distributed and dynamic monitoring of a strain wave, propagating at a speed of ~4km/sec in a 6m long fiber. Using an audio speaker, a mechanical impulse was introduced to one end of a 6m long optical fiber, initiating a strain wave propagating towards the other fixed end of the fiber. Employing a simplified version of the Slope-Assisted Brillouin Optical Time Domain Analysis (SA-BOTDA) technique, the whole length of the fiber was interrogated every 1μs (before averaging). A dynamic spatially and temporally continuous map of the strain was obtained, from which the wave velocity could be deduced. With a trade-off among sampling rate, range and signal to noise ratio, kHz sampling rates and hundreds of meters of range can be covered with spatial resolutions down to a few centimeters.
Detection of antibodies to deiminated recombinant rat filaggrin by enzyme‐linked immunosorbent assay: A highly effective test for the diagnosis of rheumatoid arthritis (2002)

ArFA-ELISA appears to be the most efficient test among those available for the detection of antifilaggrin autoantibodies, in terms of diagnostic accuracy for RA. Its diagnostic performance in early RA and its prognostic value are currently under evaluation.
A Method to Identify and Isolate Pluripotent Human Stem Cells and Mouse Epiblast Stem Cells Using Lipid Body-Associated Retinyl Ester Fluorescence (2014)

We describe the use of a characteristic blue fluorescence to identify and isolate pluripotent human embryonic stem cells and human-induced pluripotent stem cells. The blue fluorescence emission (450-500 nm) is readily observed by fluorescence microscopy and correlates with the expression of pluripotency markers (OCT4, SOX2, and NANOG). It allows easy identification and isolation of undifferentiated human pluripotent stem cells, high-throughput fluorescence sorting and subsequent propagation. The fluorescence appears early during somatic reprogramming. We show that the blue fluorescence arises from the sequestration of retinyl esters in cytoplasmic lipid bodies. The retinoid-sequestering lipid bodies are specific to human and mouse pluripotent stem cells of the primed or epiblast-like state and absent in naive mouse embryonic stem cells. Retinol, present in widely used stem cell culture media, is sequestered as retinyl ester specifically by primed pluripotent cells and also can induce the formation of these lipid bodies.
Elicitation of the hypersensitive response by <i>Pseudomonas syringae</i> (1989)

The hypersensitive response (HR), a rapid local necrosis accompanied by the production of antimicrobial compounds, is a manifestation of the primary defense mechanisms through which plants prevent colonization by potentially pathogenic microorganisms. The pathogen factors that trigger HR‐associated defense mechanisms have yet to be established. Application of transposon mutagenesis and molecular cloning techniques have provided new insights into the bacterial elicitation of the HR. This review focuses on the interaction of Pseudomonas syringae with non‐host plants as a model system for the bacterial induction of the HR and discusses (a) the genetics of Pseudomonas syringae pathogenicity and HR elicitation, (b) the environmental conditions controlling expression of Pseudomonas syringae pathogenicity/HR determinants, (c) the nature of the HR elicitor and (d) early plant responses to the pathogen.
Handling label noise in video classification via multiple instance learning (2011)

In many classification tasks, the use of expert-labeled data for training is often prohibitively expensive. The use of weakly-labeled data is an attractive solution but raises the problem of label noise. Multiple instance learning, whereby training samples are “bagged” instead of treated as singletons, offers a possible approach to mitigating the effects of label noise. In this paper, we propose the use of MILBoost [28] in a large-scale video taxonomic classification system comprised of hundreds of binary classifiers to handle noisy training data. We test on data with both artificial and real-world noise and compare against the state-of-the-art classifiers based on AdaBoost. We also explore the effects of different bag sizes on different levels of noise on the final classifier performance. Experiments show that when training classifiers with noisy data, MILBoost provides an improvement in performance.
A Joint Torque Augmentation Robot (JTAR) for Ankle Gait Assistance (2014)

A Joint Torque Augmentation Robot (JTAR) was developed to aid walking in an unconstrained outdoor environment. JTAR is a unidirectional, compliant actuator based wearable robot that is designed to power an ankle joint. Since the robot is used to navigate uneven terrain, nearly full ankle range of motion is required to accomplish this goal. The device powers the forward locomotion while permitting out of plane kinematic motion to occur. Metabolic savings of 9% to 20% have been observed while using the JTAR device, when compared to an unpowered/uncoupled state.
Immobilized DNA Switches as Electronic Sensors for Picomolar Detection of Plasma Proteins (2008)

The sensing principle of a new class of DNA conformational switches (deoxyribosensors) is based on the incorporation of an aptamer as the receptor, whose altered conformation upon analyte binding switches on the conductivity of an adjacent helical conduction path, leading to an increase in the measured electrical signal through the sensor. We report herein the rational design and biochemical testing of candidate deoxyribosensors for the detection and quantitation of a plasma protein, thrombin, followed by surface immobilization of the optimized sensor and its electrochemical testing in both a near-physiological buffer solution and in diluted blood serum. The very high detection sensitivity (in the picomolar range) and specificity, as well as the adaptability of deoxyribosensors for the detection of diverse molecular analytes both small and macromolecular, make this novel sensing methodology an extremely promising one. Such synthetic and robust DNA-based electronic sensors should find broad application in the rapid, miniaturized, and automated on-chip detection of many biomedically relevant substances (such as metabolites, toxins, and disease and tumor markers) as well as of environmental contaminants.
External calibration of the spectral coverage for three‐dimensional multispectral MRI (2015)

Incorporating this calibration procedure into future 3D-MSI exams will help improve image signal-to-noise ratio, reduce scan time, and significantly improve clinical workflow when imaging near orthopedic implants. Magn Reson Med 76:1494-1503, 2016. © 2015 International Society for Magnetic Resonance in Medicine.
Preparation and characterization of protein‐free natural rubber (2011)

Abstract Protein‐free natural rubber was prepared by incubation of natural rubber latex with urea and polar organic solvent in the presence of surfactant. Effect of the polar organic solvent on the removal of the proteins was investigated with respect to chemical affinity and concentration of the solvents. Under a suitable condition, nitrogen content of the deproteinized natural rubber (DPNR) was 0.000 wt%, which was less than that of natural rubber deproteinized with proteolytic enzyme or urea in the presence of surfactant. The removal of all proteins from natural rubber was proved through FT‐IR spectroscopy. Changes in morphology of the DPNR were also investigated by transmission electron microscopy. Copyright © 2011 John Wiley & Sons, Ltd.
A fast regular expression indexing engine (2003)

In this paper; we describe the design, architecture, and lessons learned from the implementation of a fast regular-expression indexing engine FREE. FREE uses a prebuilt index to identify the text data units which may contain a matching string and only examines these further. In this way, FREE shows orders of magnitude performance improvement in certain cases over standard regular expression matching systems, such as lex, awk and grep.
Bit-Rate Scalable Intraframe Sinusoidal Audio Coding Based on Rate-Distortion Optimization (2006)

A coding methodology that aims at rate-distortion optimal sinusoid + noise coding of audio and speech signals is presented. The coder divides the input signal into variable-length time segments and ...
P1305CARDIAC OUTPUT AND ESTIMATED UPPER BODY BLOOD FLOW (2020)

Abstract Background and Aims Cardiopulmonary monitoring during hemodialysis has the potential to improve dialysis adequacy, prevent adverse events, improve quality of dialysis patients’ lives and reduce mortality risks. Under stable conditions the knowledge of upper body oxygen consumption, the difference between arterial and venous oxygen saturation (ScvO2) and hemoglobin concentrations allow the calculation of estimated UBBF (eUBBF; Rosales 2019). We studied the association between eUBBF and cardiac output during hemodialysis. Method In patients with a central venous catheter as the vascular access, we simultaneously measured intradialytic central-venous oxygen saturation and hemoglobin levels once per minute using the Crit-Line Monitor (Fresenius Medical Care North America, Waltham, USA). Concomitantly we measured cardiac output (CO) using the Task Force Monitor (CNSystems, Graz, Austria). We depicted CO and eUBBF as box-whiskers in 5 minute periods from 20 to 180 minutes, tested the minute-level time series for stationarity using the Dickey-Fuller test, employed differencing to make the time series stationary, and tested for linear associations using cross-correlations and determined if the CO time series was useful to predict the eUBBF time series using the Granger Causality test. Results We studied 13 patients (59±14 years, 5 (38%) male, 93±22 kg pre-dialysis weight 170±7 cm tall) during 34 hemodialyses. CO and UBBF was 4.7±1.0 and 1.3±0.4 L/min, and showed a small trend downward for CO during hemodialysis. Cross-correlations showed no remarkable correlations for all treatments, Granger causality index was less than 20% in 8 treatments however without clearly discernible patterns. Conclusion Despite variability in the CO the eUBBF remains stable, a dynamic which pathophysiologically appears plausible. While testing for linear associations yielded no significant relationships, based on the Granger causality test there nevertheless appears to be some form of a relationship which requires some further investigation which will need to also include aspects such as fluid overload, body temperature and total peripheral resistance. Based on this data, cardiopulmonary monitoring appears possible and yields a reliable continuous overview of the hemodynamic status of a patient.
H.263 based video codec for real-time visual communications over wireless radio networks (2002)

With the emergence of the International Telecommunication Union's (ITU) H.263 video coding standard, real-time visual communications over low-bandwidth, low-error-rate wired telephone networks is now possible. Unfortunately, because of the nature of the algorithms employed within this compression standard and due to the inherent limitations of the radio environment, the H.263 coded video performs pearly when employed over bandwidth-limited, error-prone wireless channels. We propose an intuitive, low-complexity, pre-compression scheme that improves the performance of H.263 coded video over radio channels. In our scheme video frames are spacially segmented into regions of different perceptual importance before being compressed independently with the H.263 encoder. This allows us to apply unequal error protection and prioritized transmission to achieve at least a minimum temporal resolution at the receiver. Additionally, with this technique, both spatial and temporal error propagation is limited and through intra-frame statistical multiplexing transmission bandwidth is utilized optimally. The results demonstrate that in the presence of severe error conditions and severe bandwidth constraints, our modified H.263 video codec exhibits better error concealment, better temporal resolution, and better bandwidth utilization properties than the original H.263 video codec.
Signal Processing-based Artificial Intelligence Approach for Power Quality Disturbance Identification (2022)

Power Quality (PQ) disturbance detection is thought to be a very significant service that many utilities provide for their commercial and industrial customers. PQ disturbances affect the load that is connected to the supply, which is troubling to the consumers. Detection and classification of the electrical problem are very difficult to find out which can cause PQ problems. In this paper, the key PQ issues such as voltage sag, voltage swell, voltage interruption, harmonics, and transient events have been tested. It has been demonstrated that a new approach may be used to identify, localize, and examine the probability of classifying distinct forms of PQ disturbances. The basic idea is to divide a disturbance signal into a transparent and comprehensive representation using DWT and ST. Many mathematical processes are utilized to extract features from these decomposed signals. The signal decomposition technique is integrated with the feed-forward neural network model to develop the power quality problem identifier (detection and classification). The simulation results show that the proposed method is effective. The proposed method is also feasible and promising for real-time applications.
New technology for thermoelectric cooling (2004)

Thermoelectric coolers in use today have a coefficient of performance (COP) of only about 0.5. This compares to COPS of larger scale machines, such as air conditioners and refrigerators at levels of 3.0 to 5.0. For electronic component cooling there is a new thermoelectric technology emerging for improved efficiency. This paper discusses this new technology which is multi-layer quantum well (MLQW) thermoelectrics, that should increase by four or five times the COP of present thermoelectric coolers used in electronic cooling applications. It also details and updates the experimental work in MLQW thermoelectric materials and will detail the supporting analysis of the predicted higher performance cooling. A specific example of an electronic cooling module configuration is presented.