gebhart/patrepeval huggingface dataset:
IL2 Inducible T-cell Kinase, a Novel Therapeutic Target in Melanoma (2015)

We conclude that ITK, formerly considered an immune cell-specific protein, is aberrantly expressed in melanoma and promotes tumor development and progression. Our finding that ITK is aberrantly expressed in most metastatic melanomas suggests that inhibitors of ITK may be efficacious for melanoma treatment. The efficacy of a small-molecule ITK inhibitor in the Tyr-Cre/Pten(null)/Braf(V600E) mouse melanoma model supports this possibility.
TMPRSS2-ERG fusion prostate cancer: An early molecular event associated with invasion. (2006)

Abstract: Prostate cancer (PCA) is one of the most prevalent cancers and a major leading cause of morbidity and mortality in the Western world. The TMPRSS2-ERG fusion was recently identified as a common recurrent chromosomal aberration in this malignancy. In our study, we interrogated a broad spectrum of benign, precursor, and malignant prostatic lesions to assess the TMPRSS2-ERG fusion status using a multicolor interphase fluorescence in situ hybridization assay. Samples from hospital-based cohorts consisted of 237 clinically localized PCA, 34 hormone naive metastases, 9 hormone refractory metastases, 26 high grade prostatic intraepithelial neoplasia lesions, 15 samples of benign prostatic hyperplasia, 38 of proliferative inflammatory atrophy, and 47 of benign prostatic tissue. The TMPRSS2-ERG fusion was present in 48.5 % of clinically localized PCA, 30 % of hormone naive metastases, 33 % of hormone refractory meta-stases, and in 19 % of high grade prostatic intraepithelial neoplasia lesions in intermingling to cancer foci. Almost all these fusion positive cases show a homogenous distribution of the fusion pattern. In contrast, none of the other samples harbored this genetic aberration. If we consider the high incidence of PCA and the high frequency of this gene fusion, TMPRSS2-ERG is the most common genetic aberration so far described in human malignancies. Furthermore, its clinical application as a biomarker and ancillary diagnostic test is promising given its high specificity. Key Words: prostate cancer, TMPRSS2-ERG gene rearrange-ment, fluorescence in situ hybridization, PIN
Ethylene-Triggered Formation of Ruthenium Alkylidene from Decomposed Catalyst (2020)

Ethylene is known to readily decompose ruthenium-based olefin metathesis catalysts, such as Grubbs second-generation catalyst (GII), by forming the unsubstituted ruthenacyclobutane (Ru-2) that may undergo a 1,2-H shift and liberate propene. The resulting alkylidene loss has been assumed to be irreversible. Yet, by reacting (SIMes)(η6-p-cymene)RuCl2 (1), the p-cymene-stabilized alkylidene-free fragment resulting from loss of propene from Ru-2, with ethylene, we show that the methylidene analogue of GII (GIIm) and other Ru alkylidenes are formed, along with catalytic amounts of propene and butenes, and can be stabilized by tricyclohexylphosphine (PCy3) at 50 °C in C6D6. An almost 20-fold increase in activity for ring-closing metathesis of diethyl diallylmalonate (DEDAM) on pretreatment of 1 with ethylene suggests that the reversibility of the alkylidene loss may be used to develop longer-lived metathesis catalysts and processes. Mechanistic density functional theory (DFT) calculations suggest that the connection between 1 and GIIm involves oxidative coupling of two ethylene molecules to form a key metallacyclopentane intermediate (M49). A 1,2-H shift in M49 gives the methyl-substituted ruthenacyclobutane M303, which, on cycloreversion, liberates propene and GIIm. Alternatively, successive H-shifts starting in M49 may give 1-butene (fast reaction) and 2-butene (slower) with a lower barrier than that of Ru alkylidene. The lower predicted barrier is consistent with butene, especially 1-butene, being the dominating product at the start of the experiments, in particular at lower temperature.
Equine Protozoal Myeloencephalitis: Antigen Analysis of Cultured <i>Sarcocystis Neurona</i> Merozoites (1993)

Antigens of cultured Sarcocystis neurona merozoites were examined using immunoblot analysis. Blotted proteins were probed with S. cruzi, S. muris, and S. neurona antisera produced in rabbits, S. fayeri (pre- and post-infection) and S. neurona (pre- and post-inoculation) sera produced in horses, immune sera from 7 histologically confirmed cases of equine protozoal myeloencephalitis (EPM), and pre-suckle serum from a newborn foal. Eight proteins, 70, 24, 23.5, 22.5, 13, 11, 10.5, and 10 Kd, were detected only by S. neurona antiserum and/or immune serum from EPM-affected horses. Equine sera were titered by the indirect immunofluorescent antibody (IFA) method using air-dried, cultured S. neurona merozoites. Anti-Sarcocystis IFA titers were found in horses with or without EPM. Serum titers did not correspond to the number of specific bands recognized on immunoblots.
Optimization of an enzyme linked DNA aptamer assay for cardiac troponin I detection: synchronous multiple sample analysis on an integrated microfluidic platform (2019)

In this study, an enzyme linked DNA aptamer based assay was optimized for human cardiac troponin I (cTnI) detection which is a prominent biomarker for acute myocardial infarction (AMI), on an integrated microfluidic platform. This platform allowed for the multiplex detection of six samples (5 μL per sample), and only 30 min were required for detection. First, cTnI-specific aptamers were surface-coated on magnetic beads. Bead-captured proteins were allowed to bind to a primary cTnI antibody and then to a secondary antibody labelled with horseradish peroxidase. Finally, chemiluminescence intensities were detected for quantification of cTnI. Purified proteins, serum from AMI patients and unknown serum samples were used to test the efficacy of the on-chip system. The limit of detection was measured to be only 12 ng L-1, and off-target effects from other proteins were minimal. This sensitive, cTnI-specific aptamer-based assay could consequently be used for reliable diagnosis of AMI.
Saliency Detection Using Region-Based Incremental Center-Surround Distance (2011)

A new method to detect salient region(s) in images is proposed in this paper. The proposed approach, which is inspired by object-based visual attention theory, segments the input image into coherent regions and measures region-based center-surround distance (RBCSD), which is a distance between region attributes such as color histograms found in each region and its surrounding region. Furthermore, segmented regions are merged such that the RBCSD of the merged region is greater than the individual RBCSD of the component regions through region-based incremental center surround distance (RBCSD+I) process. Due to this RBCSD+I process, merged regions may contain incoherent color regions, which improves the robustness of the proposed approach. The key advantages of the proposed algorithm are: (1) it provides a salient region with plausible object boundaries, (2) it is robust to color incoherency present in the salient region, and (3) it is computationally efficient. Extensive qualitative and quantitative evaluation of the proposed algorithm on widely used data sets and comparison with the existing saliency detection approaches clearly indicates the feasibility and efficiency of the proposed approach.
Effective Pre-Silicon Verification of Processor Cores by Breaking the Bounds of Symbolic Quick Error Detection (2021)

We present a novel approach to pre-silicon verification of processor designs. The purpose of pre-silicon verification is to find logic bugs in a design at an early stage and thus avoid time- and cost-intensive post-silicon debugging. Our approach relies on symbolic quick error detection (Symbolic QED, or SQED). SQED is targeted at finding logic bugs in a symbolic representation of a design by combining bounded model checking (BMC) with QED tests. QED tests are powerful in generating short sequences of instructions (traces) that trigger bugs. We extend an existing SQED approach with symbolic starting states. This way, we enable the BMC tool to select starting states arbitrarily when generating a trace. To avoid false positives, (e.g., traces starting in unreachable states that may not be-have in accordance with the processor instruction-set architecture), we define constraints to restrict the set of possible starting states. We demonstrate that these constraints, togeth-er with reasonable assumptions about the system behavior, allow us to avoid false positives. Using our approach, we discovered previously unknown bugs in open-source RISC-V processor cores that existing methods cannot detect. Moreover, our novel approach out-performs existing ones in the detection of bugs having long traces and in the detection of hardware Trojans, i.e., unauthorized modifications of a design.
Controlled introduction of flux pinning centers in YBa2Cu3O7−x films during pulsed-laser deposition (2005)

To introduce controlled random inclusion of nanometer-sized nonsuperconducting particulates in YBa2Cu3O7−x films for flux pinning enhancement, a special pulsed-laser-ablation YBa2Cu3O7−x target with a Y2BaCuO5 sector was made and the films were deposited on LaAlO3 substrates. Initial results showed that the films consist of 10–20 nm-sized precipitates. In a 0.5μm thick film, a transport critical current density (Jc)&gt;3MA∕cm2 at 77 K in self-field was measured. Magnetization Jc at 77 and 65 K showed significant improvements in these films with fine precipitates as compared to regular YBa2Cu3O7−x films (&gt;10 times increase at 9 T, 65 K).
Retardation‐controlling color filter with two directly stacked retardation layers (2007)

Abstract— A polymerizable liquid crystal (PLC), the orientation of which can be frozen, is useful for making retardation layers. In this paper, a new color filter (CF) with retardation‐controlling layers made of PLC is reported. It has a positive A‐plate and a negative C‐plate, both directly stacked on a color‐filter layer. These two retardation layers exhibit good orientation ability, and function well as retarders, even when they are only 1/10 or less as thick as ordinary retardation films. The new CF also has excellent thermal stability. The change in retardation after heat treatment at 200°C for 30 min is around 5%, and there is no observable peeling. A prototype VA‐LCD made with our new CF provides good optical compensation, with the light leakage being extremely low in all azimuthal directions. This technology is very useful for making thin, highly reliable color filters for LCDs, even with other modes.
Chemical-Reaction-Inspired Metaheuristic for Optimization (2009)

We encounter optimization problems in our daily lives and in various research domains. Some of them are so hard that we can, at best, approximate the best solutions with (meta-) heuristic methods. However, the huge number of optimization problems and the small number of generally acknowledged methods mean that more metaheuristics are needed to fill the gap. We propose a new metaheuristic, called chemical reaction optimization (CRO), to solve optimization problems. It mimics the interactions of molecules in a chemical reaction to reach a low energy stable state. We tested the performance of CRO with three nondeterministic polynomial-time hard combinatorial optimization problems. Two of them were traditional benchmark problems and the other was a real-world problem. Simulation results showed that CRO is very competitive with the few existing successful metaheuristics, having outperformed them in some cases, and CRO achieved the best performance in the real-world problem. Moreover, with the No-Free-Lunch theorem, CRO must have equal performance as the others on average, but it can outperform all other metaheuristics when matched to the right problem type. Therefore, it provides a new approach for solving optimization problems. CRO may potentially solve those problems which may not be solvable with the few generally acknowledged approaches.
VISQOL: The Virtual Speech Quality Objective Listener (2021)

A model of human speech quality perception has been developed to provide an objective measure for predicting subjective quality assessments. The Virtual Speech Quality Objective Listener (ViSQOL) model is a signal based full reference metric that uses a spectro-temporal measure of similarity between a reference and a test speech signal. This paper describes the algorithm and compares the results with PESQ for common problems in VoIP: clock drift, associated time warping and jitter. The results indicate that ViSQOL is less prone to underestimation of speech quality in both scenarios than the ITU standard.
Three-dimensional gamut mapping using various color difference formulae and color spaces. (1999)

Gamut mapping is a technique to transform out-of-gamut colors to the inside of the output device's gamut. It is essential to develop effective mapping algorithms to realize WYSIWYG (What You See Is What You Get) color reproduction 1 . In this paper, three-dimensional gamut mapping using various color difference formulae and color spaces are considered Visual experiments were performed to evaluate which combination of color difference formula and color space for gamut mapping was most preferred for five images. The color difference formulae used in the experiments were ΔE * ab , ΔE * uv , ΔE 94 , ΔE CMC , ΔE and ΔE wt . The color spaces used in the experiments were CIELAB, CIELUV, CIECAM97s, IPT, and NC-IIIC. A clipping method was used that maps all out-of-gamut colors to the surface of the gamut, and no change was made to colors inside the gamut. It was found that gamut mapping using ΔE 94 , ΔE CMC , and ΔE wt were effective in CIELAB color space. For mapping images containing a large portion of blue colors, ΔE BFD and ΔE * uv were found to be more effective. ΔE * ab was least preferred for all images. With respect to color spaces, gamut mapping performed in the CIELUV color space was superior to any other color spaces for the blue region. We conclude that ΔE 94 -LUV and ΔE BFD -LAB are the most useful combinations of color difference formula and color space for gamut mapping, if we are to apply a single combination universally.
Robust Online Spike Recovery for High-Density Electrode Recordings using Convolutional Compressed Sensing (2019)

Recent high-density multi-electrode arrays pose new challenges for spike sorting in electrophysiology. In this work, we study online spike detection using concepts from sparse signal recovery. A linear convolutional model is used to describe the extracellular recording and compressed sensing is used to recover the spiking activity as a sparse signal. Error propagation in response to new measurements is characterized using results on banded matrices. We demonstrate that accurate signal recovery can be performed by processing finite buffers and derive improved buffer sizes, by introducing effective bandwidths. An adaptation of Compressive Sampling Matching Pursuit is proposed for online processing by restricting iterations to a finite buffer. Evaluation with noisy, ground-truth simulations show virtually identical performance to offline processing indicating an appropriate choice of the buffer size. Negligible errors were observed for signal-to-noise ratio larger than 7. Furthermore, the proposed online algorithm achieves spike detection comparable to manual spike sorting in high-density recordings from a behaving macaque (deviation: 6.6- 7.7%), while enabling resolution of overlapping activity. In summary we demonstrate that sparse signal recovery with limited buffer size enables accurate online spike detection. In combination with offline waveform extraction from training data, this provides a means for using single-neuron spiking activity in closed loop experiments or brain-machine interfaces.
Nonlinear beat noise in optical parametric chirped-pulse amplification (2017)

The pulse contrast of state-of-the-art petawatt lasers is limited by coherent noise. This paper reports on a new family of noise, termed nonlinear beat noise, which is generated by the nonlinear mixing of two kinds of coherent noise in optical parametric chirped-pulse amplification (OPCPA). We theoretically study the various nonlinear beat noises and reveal their intensity evolutions in an OPCPA amplifier. The results suggest that nonlinear beat noise will be destructive to the future hundred-petawatt lasers.
Cancer Cell Coating Nanoparticles for Optimal Tumor-Specific Cytokine Delivery (2020)

Although cytokine therapy is an attractive strategy to build a more robust immune response in tumors, cytokines have faced clinical failures due to toxicity. In particular, interleukin-12 has shown great clinical promise but was limited in translation because of systemic toxicity. In this study, we demonstrate an enhanced ability to reduce toxicity without affecting the efficacy of IL-12 therapy. We engineer the material properties of a NP to meet the enhanced demands for optimal cytokine delivery by using the layer-by-layer (LbL) approach. Importantly, using LbL, we demonstrate cell-level trafficking of NPs to preferentially localize to the cell's outer surface and act as a drug depot, which is required for optimal payload activity on neighboring cytokine membrane receptors. LbL-NPs showed efficacy against a tumor challenge in both colorectal and ovarian tumors at doses that were not tolerated when administered carrier-free.
Bi-State Bifurcation Control of a Shaped-Comb Parametric Resonator (2013)

This work employs behavioral modeling to develop a bi-state control technique capable of servoing at the onset of the microelectromechanical parametric resonant bifurcation setpoint. The parametric resonance features a sharp “turn-on” in oscillation amplitude at the bifurcation, enhancing sensitivity to resonance frequency change. A bi-state controller is constructed to servo at this sharp jump point. It has two states of operation: one state is within the instability tongue where the oscillation amplitude builds up exponentially; another state resides outside of the tongue where the oscillation turns off. The rapid turn on and off of the parametric resonance keeps the resonant amplitude small and circumvents the slow build-up time. Both the simulated and experimental loop transient responses are presented.
Synthesis and antitumor activity of 3'-deamino-3'-hydroxydoxorubicin. A facile procedure for the preparation of doxorubicin analogs. (1984)

Two successful routes have been developed for preparation of 3'-deamino-3'-hydroxydoxorubicin (11), based on protection of the 14-hydroxyl group of the aglycon by using tert-butylchlorodimethylsilane. The key intermediate, 14-O-tert-butyldimethylsilyl-7-O-(3,4-di-O-acetyl-2,6-dideoxy-alpha-L-ly xo -hexopyranosyl)adriamycinone (9), was successively deacetylated and desilylated in high yield to give the desired product 11. This route constitutes a general method of access to glycon-modified doxorubicin analogs. Compound 11 showed high antitumor activity in vivo in the murine P388 lymphocytic leukemia assay.
A bootstrapping training technique for obtaining demisyllable reference patterns (1982)

The process of obtaining reference patterns for syllablelike units is tedious, error prone, and time consuming. As such, speech recognition systems based on such units are usually tested on only a single talker. In this paper we describe a procedure for using demisyllable reference patterns, excised from spoken utterances for one talker and automatically creating demisyllable reference patterns for a new talker. The procedure is based on dynamic time warping alignment of the spoken utterances (each containing the relevant demisyllable), and the assumption that the optimum warping path identifies the best matching demisyllable within the utterance. The automatic procedure has been used to create demisyllable reference patterns for two new talkers, each talking over a dialed-up telephone line (the original recordings were made over a high-quality microphone). Reference patterns were made for 100 isolated words from a given lexical specification of each word in terms of demisyllables in the inventory. Word recognition accuracies greater than 90% were obtained for both talkers on the 100-word vocabulary. In a second experiment, using a 1109-word vocabulary, recognition accuracies from reference patterns based on automatically extracted demisyllables were from 2%–5% worse than accuracies from reference patterns based on hand corrections applied to the demisyllables. These results show that the automatic demisyllable extraction technique provides a very good first pass set of demisyllables, and that combined with some manual corrections, provides a set of demisyllable patterns suitable for use in a recognition system.
Epidemiology And Partial Nucleotide Sequence Of Four Novel Genital Human (1994)

Polymerase chain reaction (PCR)-based genital human papillomavirus (HPV) detection methods that use consensus primers have enabled the broad-spectrum detection of most characterized HPV types. In addition, these techniques have allowed the identification of potentially novel viral sequences in clinical specimens. These methods were used to determine the partial L1 nucleotide sequence (the region generated by L1 consensus primers MY09 and MY11) of four novel viruses. The prevalence of these viruses in cytologically normal and dysplastic cervical specimens and in invasive cervical cancer was also determined. The partial DNA sequences of W13B (MM4), PAP291 (MM7), PAP155 (MM8), and PAP238a (MM9) are most similar to HPV-51, -61, -61, and -34, respectively. Prevalence studies suggest that W13B and PAP238a are cancer-associated, while PAP155 and PAP291 appear to be lower-risk viruses.
<title>Effect of Cu at Al grain boundaries on electromigration behavior in Al thin films</title> (1991)

The distribution of copper in aluminum thin films is examined with respect to how the copper can influence electromigration behavior. Al-Cu thin films annealed in the single phase region, to just below the solvustemperature, have 0-phase Al2Cu precipitates at the aluminum grain boundaries. The grain boundaries between precipitates are depleted in copper. Al-Cu thin films heat treated at lower temperatures, within thetwo phase region, also have 0-phase precipitates at the grain boundaries but the aluminum grain boundariescontinuously become enriched in copper, perhaps due to the formation of a thin coating of 0-phase at the grain boundary. Here, it is proposed that electromigration behavior of aluminum is improved by addingcopper because the 0-phase precipitates may hinder aluminum diffusion along the grain boundaries. It was also found that resistivity of Al-Cu thin films decrease during accelerated electromigration testing prior to failure. Pure Al films did not exhibit this behavior. The decrease in resistivity is attributed to theredistribution of copper from the aluminum grain matrix to the 0-phase precipitates growing at the grain boundaries thereby reducing the number of defects in the microstructure.
Polyethylene Containing Triblock Copolymers Synthesized by Post-polymerization Functionalization (2020)

We report the synthesis of amphiphilic triblock copolymers containing a polyethylene block as the center block. The synthetic methodology consists of performing four consecutive post-polymerization reactions on polyethylene to yield a dihydroxyl-terminated polymer. First, a cross-metathesis reaction converts the olefinic end-group of the polyethylene into an α,β-unsaturated ester followed by isomerization of the double bond and then its hydroformylation. This sequence introduces an aldehyde group randomly distributed along the polymer backbone. Finally, the reduction of the aldehyde- and ester-functionalized polymer yields two terminal hydroxyl groups. The methodology was first established using low-molecular-weight model substrates before being performed on a polyethylene with a molecular weight of Mn = 13 kg mol–1. The functionalized polyethylene was used to initiate the ring-opening polymerizations of ε-caprolactone and tert-butyl glycidyl ether to yield the corresponding triblock copolymers. Subsequent hydrolysis of the tert-butyl groups in the polyether yielded an amphiphilic polymer that formed micelles in water.