gebhart/patrepeval huggingface dataset:
Dasatinib (BMS-354825) inhibits Stat5 signaling associated with apoptosis in chronic myelogenous leukemia cells (2007)

Dasatinib (BMS-354825) is a novel, oral, potent, multi-targeted kinase inhibitor of Bcr-Abl and Src family kinases (SFK) and is a promising cancer therapeutic agent. Preclinical data indicate that dasatinib is 325-fold more potent than imatinib against cells expressing wild-type Bcr-Abl, and that dasatinib is active against 18 of 19 Bcr-Abl mutations known to cause imatinib resistance. Phase I clinical data show that dasatinib is well tolerated and highly effective for the treatment of imatinib-resistant/imatinib-intolerant chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive acute lymphoblastic leukemia. However, the molecular mechanism of action of dasatinib is not fully understood. In this study, we confirm that dasatinib inhibits tyrosine phosphorylation of SFKs, including Src, Hck, and Lyn, in K562 human CML cells. Significantly, downstream signal transducer and activator of transcription 5 (Stat5) signaling is also blocked by dasatinib as shown by decreases in levels of phosphorylated Stat5 and Stat5 DNA-binding activities. In addition, dasatinib down-regulates expression of Stat5 target genes, including Bcl-x, Mcl-1, and cyclin D1. Consistent with these results, blockade of Stat5 signaling by dasatinib is accompanied by inhibition of cell proliferation and induction of apoptosis. Surprisingly, Stat5 DNA-binding activities are enhanced with increasing cell density, which is associated with resistance to apoptosis by dasatinib. Our findings indicate that inhibition of Stat5 signaling downstream of Bcr-Abl/SFKs contributes to the action of dasatinib, and, conversely, that increasing cell density up-regulates Stat5 activation and confers resistance to dasatinib. Moreover, the level of phosphorylated Stat5 in CML cells represents a mechanistically relevant biomarker for monitoring inhibition of Bcr-Abl signaling by dasatinib in CML patients using convenient immunocytochemical assays.
Origin and Effects of Negative Ions in the Sputtering of Intermetallic Compounds (1977)

An unexpected etching phenomenon during the sputtering of rare earth-gold alloys has been found to be caused by a large flux of negative gold ions from the sputtering target. We find this effect to occur in a range of intermetallic compounds. A model is presented which predicts when negative ion formation will be important. Effects of negative ions on sputter deposition of thin films include reduced deposition rate or substrate etching, and changes in film composition and other properties. Negative ion formation must also be taken into account for accurate quantitative analysis by Secondary Ion Mass Spectrometry (SIMS).
Engineering multiple biological functional motifs into a blank collagen‐like protein template from <i>Streptococcus pyogenes</i> (2013)

Bacterially derived triple-helical, collagen-like proteins are attractive as potential biomedical materials. The collagen-like domain of the Scl2 protein from S. pyogenes lacks any specific binding sites for mammalian cells yet possesses the inherent structural integrity of the collagen triple-helix of animal collagens. It can, therefore, be considered as a structurally-stable "blank slate" into which various defined, biological sequences, derived from animal collagens, can be added by substitutions or insertions, to enable production of novel designed materials to fit specific functional requirements. In the present study, we have used site directed mutagenesis to substitute two functional sequences, one for heparin binding and the other for integrin binding, into different locations in the triple-helical structure. This provided three new constructs, two containing the single substitutions and one containing both substitutions. The stability of these constructs was marginally reduced when compared to the unmodified sequence. When compared to the unmodified bacterial collagen, both the modified collagens that contain the heparin binding site showed marked binding of fluorescently labeled heparin. Similarly, the modified collagens from both constructs containing the integrin binding site showed significant adhesion of L929 cells that are known to possess the appropriate integrin receptor. C2C12 cells that lack any appropriate integrins did not bind. These data show that bacterial collagen-like sequences can be modified to act like natural extracellular matrix collagens by inserting one or more unique biological domains with defined function.
Identification of CDCA1‐derived long peptides bearing both CD4<sup>+</sup> and CD8<sup>+</sup> T‐cell epitopes: CDCA1‐specific CD4<sup>+</sup> T‐cell immunity in cancer patients (2013)

We recently identified a novel cancer-testis antigen, cell division cycle associated 1 (CDCA1) using genome-wide cDNA microarray analysis, and CDCA1-derived cytotoxic T lymphocyte (CTL)-epitopes. In this study, we attempted to identify CDCA1-derived long peptides (LPs) that induce both CD4+ helper T (Th) cells and CTLs. We combined information from a recently developed computer algorithm predicting HLA class II-binding peptides with CDCA1-derived CTL-epitope sequences presented by HLA-A2 (A*02:01) or HLA-A24 (A*24:02) to select candidate CDCA1-LPs encompassing both Th cell epitopes and CTL-epitopes. We studied the immunogenicity of CDCA1-LPs and the cross-priming potential of LPs bearing CTL-epitopes in both human in vitro and HLA-class I transgenic mice in vivo. Then we analyzed the Th cell response to CDCA1 in head-and-neck cancer (HNC) patients before and after vaccination with a CDCA1-derived CTL-epitope peptide using IFN-γ enzyme-linked immunospot assays. We identified two CDCA1-LPs, CDCA1(39–64)-LP and CDCA1(55–78)-LP, which encompass naturally processed epitopes recognized by Th cells and CTLs. CDCA1-specific CTLs were induced through cross-presentation of CDCA1-LPs in vitro and in vivo. In addition, CDCA1-specific Th cells enhanced induction of CDCA1-specific CTLs. Furthermore, significant frequencies of CDCA1-specific Th cell responses were detected after short-term in vitro stimulation of peripheral blood mononuclear cells (PBMCs) with CDCA1-LPs in HNC patients (CDCA1(39–64)-LP, 74%; CDCA1(55–78)-LP, 68%), but not in healthy donors. These are the first results demonstrating the presence of CDCA1-specific Th cell responses in HNC patients and underline the possible utility of CDCA1-LPs for propagation of both CDCA1-specific Th cells and CTLs.
Comparison of phase‐contrast and fluorescence digital autofocus for scanning microscopy (1994)

Reliable autofocus is required to obtain accurate measurements of fluorescent stained cellular components from a system capable of scanning multiple microscope fields. Autofocus could be performed directly with fluorescence images, but due to photobleaching and destructive fluorescence by-products, it is best to minimize fluorescence exposure for photosensitive specimens and live cells. This exposure problem could be completely avoided by using phase-contrast microscopy, implemented through the same optics as fluorescence microscopy. The purpose of this work was to evaluate functions for both phase-contrast and fluorescence autofocus and determine the suitability of phase-contrast autofocus for fluorescence microscopy. Eleven autofocus functions were independently evaluated for fluorescence and phase-contrast microscopy. The most suitable functions were then chosen from these and phase-contrast and fluorescence autofocus were compared on scans each comprising more than 1,000 microscope fields. Autofocus standard deviation (S.D.) of better than 100 nm was achieved for both phase contrast and fluorescence. There was a measurable difference between the best focus positions in the two modes, but the difference was constant enough to be measured and corrected, suggesting the possibility of using phase contrast to predict best focus in fluorescence microscopy. The scanning experiments also showed that autofocus can be performed at least as fast as 0.25 s/field without loss of precision.
Design of a high-quality audio-specific DSP core (2006)

This paper proposes a specialized DSP architecture and their instructions, which efficiently support MPEG-2/4 AAC high-quality audio algorithms. The proposed architecture is specially designed and optimized for the IMDCT (inverse modified discrete cosine transform), Huffman decoding, etc. Performance comparisons show significant improvement compared with TMS320C62x and ASDSP21060 for the IMDCT computation. Furthermore, the dedicated Huffman accelerator performs the decoding process in only 2 cycles. The proposed DSP has been synthesized using the Samsung SEC 0.18 /spl mu/m standard cell library. The proposed DSP core consists of 120,283 gates and runs at 200 MHz.
The L1014F Point Mutation in the House Fly Vssc1 Sodium Channel Confers Knockdown Resistance to Pyrethroids (1997)

Voltage-sensitive sodium channels encoded by a full-length cDNA corresponding to the Vssc1 gene of the house fly (Musca domestica) were expressed in Xenopus laevis oocytes either alone or in combination with the tipE gene product of Drosophila melanogaster and were characterized by two-electrode voltage clamp. Vssc1 cRNA alone produced very small (50-150 nA) sodium currents, whereas the combination of Vssc1 and tipE cRNAs produced robust (0.5-3 microA), rapidly inactivating sodium currents. The pyrethroid insecticide cismethrin prolonged the sodium current carried by Vssc1/tipE sodium channels during a depolarizing pulse and induced a tail current after repolarization. The Vssc1 cDNA was specifically mutated to substitute phenylalanine for leucine at position 1014 of the inferred amino acid sequence (L1014F), a polymorphism shown previously to be associated with the kdr (knockdown resistance) trait of the house fly. The L1014F substitution reduced the sensitivity of expressed house fly sodium channels to cismethrin at least 10-fold and increased the rate of decay of pyrethroid-induced sodium tail currents. These results demonstrate that the resistance-associated L1014F mutation confers a reduction in the sensitivity of house fly sodium channels to pyrethroids that is sufficient to account for the kdr resistance trait.
An In-Situ Galvanically Coupled Multielectrode Array Sensor for Localized Corrosion (2002)

A localized corrosion sensor consisting of multiple, corrodible, miniature electrodes was tested in different chemical environments. The miniature electrodes were coupled together by connecting each of them to a common joint through independent resistors, with each electrode simulating an area of a corroding metal. In a localized corrosion environment, anodic currents flow into the more corroding electrode, and cathodic currents flow out of the less or noncorroding electrodes. These currents are measured from the voltages across the resistors. The variation among the galvanic currents measured from the miniature electrodes responded well to changes in the environment with respect to localized corrosion. It was demonstrated that statistical parameters derived from the currents flowing through the miniature electrodes, such as the standard deviation or the 90th percentile anodic value, can be used as effective indictors for localized corrosion. Measurement showed the following order of corrosiveness of the environment for UNS S30400 stainless steel: deionized water &lt; saturated potassium chloride (KCl) &lt; 1 M sodium nitrate (NaNO3) + 0.25 M ferric chloride (FeCl3) &lt; 0.0025 M FeCl3 &lt; 0.25 M FeCl3. It was also shown that the penetration rate of localized corrosion may be estimated from either the measured maximum or the standard deviation of the anodic current densities, and the cumulative penetration may be estimated from either the measured maximum or the standard deviation of the cumulative anodic charges through the electrodes.
Ink‐Jet Printing of Metallic Nanoparticles and Microemulsions (2005)

Abstract Summary: Two types of ink‐jet inks are presented: ink containing an aqueous dispersion of silver nanoparticles and an oil‐in‐water microemulsion‐based ink. The metallic ink contains nanoparticles of silver, which are formed in the presence of an ionic polymeric stabilizer. Sintering of the printed image obtained with the use of such silver‐based inks at temperatures as low as 300 °C results in formation of patterns possessing noticeable conductivity. The microemulsion inks are based on a thermodynamically stable microemulsion, in which the dispersed oil phase is a volatile solvent containing a water‐insoluble colorant. After contact of the jetted ink droplets with a substrate, nanodroplets of the microemulsion are converted into nanoparticles of the solubilized colorant. In some cases, it was found that the evaporation of microemulsion ink droplets leads to formation of rings composed of ordered nanoparticles. Scheme of ink‐jet printing of an oil‐in‐water microemulsion followed by conversion of the nanodroplets into nanoparticles, caused by quick evaporation of the solvent within the microemulsion droplets. Therefore, the ink behaves as a dye‐based ink prior to printing, but after printing it behaves like a pigment‐based ink. magnified image Scheme of ink‐jet printing of an oil‐in‐water microemulsion followed by conversion of the nanodroplets into nanoparticles, caused by quick evaporation of the solvent within the microemulsion droplets. Therefore, the ink behaves as a dye‐based ink prior to printing, but after printing it behaves like a pigment‐based ink.
YAG laser direct writing of copper from copper formate films (1990)

Very thin copper lines for seeding of chemical copper deposition have been deposited by laser direct writing techniques, using water soluble precursor films from copper formate. Writing speeds of up to 50 mm/s could be reached. The deposition process has a strong influence on the substrate surface, thereby achieving a very stable film adhesion.
Fabrication of X-Ray Masks Using the Silicon Direct Write Electron-Beam Lithography Process and Complementary Electron-Sensitive Resists (2002)

In order to meet the long term goals of the International Technology Roadmap for Semiconductors, it is important to demonstrate that X-ray masks can be fabricated at resolutions well below the 100 nm barrier. This paper presents results on the use of conventional electron-sensitive resists and the silicide direct write electron beam lithography process (SiDWEL) for the fabrication of X-ray masks with sub-100 nm resolution. By optimizing the deposition of the thin films using conventional evaporators, the SiDWEL process was able to achieve linewidths of less than 40 nm and line spacing of less than 100 nm. The silicide patterns formed by the SiDWEL process are sufficiently resistant to plasma etching to directly transfer the patterns to the tantalum absorber. To improve the turnover time for mask fabrication, different writing schemes were studied, including combining the SiDWEL process with QSR-4, a novel negative resist designed specifically for this application.
Design and quantitative evaluation of a stance-phase controlled prosthetic knee joint for children (2005)

The aims of this study were to demonstrate a theoretical basis for the design of a stance-phase controlled paediatric prosthetic knee joint, clinically test prototypes of the knee, and use a questionnaire to evaluate its efficacy. Biomechanical models were used to analyze the stance-phase control characteristics of the proposed knee, and those of three other commonly prescribed paediatric knee joint mechanisms, which were also the conventional knee joints used by the six participants of this study (mean age 10.8 years). A questionnaire pertaining to stance-phase control was designed and administered twice to each child; once for the evaluation of the prototype knee joint and once for the conventional knee joint. Stance-phase modeling results indicated decreased zones of instability for the new knee as compared to other paediatric knee joints. Questionnaire results revealed a decrease in the frequency of falls with the prototype compared to other knees, especially in highly active children. The children also reported worrying less about the knee collapsing during walking. No differences were evident for stance-phase stability during running, walking on uneven terrain, ambulating up and down stairs and inclines, fatigue, and types of activities performed.
Multi-scale dictionaries based fingerprint orientation field estimation (2016)

Orientation field estimation is significantly important for fingerprint recognition. Dictionary based algorithm and its variant, localized dictionaries based algorithm have shown promising performance. In this paper, we extend the original dictionary based algorithm to a multi-scale version. The motivation is that small scale dictionary is more accurate while large scale dictionary is more robust against image noise. Hence information from orientation fields of different scales can be integrated to obtain better results. A multi-layer MRF model is used to formulate and solve the proposed problem. Experimental results on challenging latent fingerprint database demonstrate the advantages of the proposed algorithm.
Fault-tolerant meshes and hypercubes with minimal numbers of spares (1993)

This paper presents several techniques for tolerating faults in d-dimensional mesh and hypercube architectures. The approach consists of adding spare processors and communication links so that the resulting architecture will contain a fault-free mesh or hypercube in the presence of faults. The authors optimize the cost of the fault-tolerant architecture by adding exactly k spare processors (while tolerating up to k processor and/or link faults) and minimizing the maximum number of links per processor. For example, when the desired architecture is a d-dimensional mesh and k=1, they present a fault-tolerant architecture that has the same maximum degree as the desired architecture (namely, 2d) and has only one spare processor. They also present efficient layouts for fault-tolerant two- and three-dimensional meshes, and show how multiplexers and buses can be used to reduce the degree of fault-tolerant architectures. Finally, they give constructions for fault-tolerant tori, eight-connected meshes, and hexagonal meshes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Seam-carving based anonymization against image &amp; video source attribution (2013)

As image source attribution techniques have become significantly sophisticated and are now becoming commonplace, there is a growing need for capabilities to anonymize images and videos. Focusing on the photo response non-uniformity noise pattern based sensor fingerprinting technique, this work evaluates the effectiveness of well-established seam carving method to defend against sensor fingerprint matching. We consider ways in which seam-carving based anonymization can be countered and propose enhancements over conventional seam carving method. Our results show that applying geometrical distortion in addition to seam carving will make counter attack very ineffective both in terms of computational complexity and accuracy.
Aperture weighted cardiac reconstruction for cone-beam CT (2006)

Multi-row detectors together with fast rotating gantries made cardiac imaging possible for CT. Due to the cardiac motion, ECG gating has to be integrated into the reconstruction of the data measured on a low pitch helical trajectory. Since the first multi-row scanners were introduced, it has been shown that approximative true cone-beam reconstruction methods are most suitable for the task of retrospectively gated cardiac volume CT. In this paper, we present the aperture weighted cardiac reconstruction (AWCR), which is a three-dimensional reconstruction algorithm of the filtered back-projection type. It is capable of handling all illumination intervals of an object point, which occur as a consequence of a low pitch helical cone-beam acquisition. Therefore, this method is able to use as much redundant data as possible, resulting in an improvement of the image homogeneity, the signal to noise ratio and the temporal resolution. Different optimization techniques like the heart rate adaptive cardiac weighting or the automatic phase determination can be adopted to AWCR. The excellent image quality achieved by AWCR is presented for medical datasets acquired with both a 40-slice and a 64-slice cone-beam CT scanner.
Organic field-effect bipolar transistors (1996)

Organic field-effect transistors (FETs) which employ two carefully selected active materials can function as n channel, p channel, or both n- and p-channel devices. It is shown that under an appropriate set of bias conditions the channel current in FETs with α-hexathienylene (α-6T) and C60 active layers consist of electron and hole components that are injected from the source and drain contacts into the C60 and α-6T layers, respectively.
A global passive sampling technique for high-speed switched-capacitor time-interleaved ADCs (2000)

In this paper, we present a passive sampling technique for time-interleaved switched capacitor analog-to-digital converters (ADCs). The purpose of the proposed sampling technique is to reduce the effect of delay skews between the sample and hold (SCH) circuits in the parallel channels, which limits the performance at high signal frequencies. If designed properly, the circuit can reduce the delay-skew related distortion by 10-20 dB compared to an architecture without a global input S/H circuit. Since no op amp needs to work at the full speed of the ADC, the circuit is suitable for high-speed and consumes less power than an architecture with an active input S/H circuit.
PlyPH, a Bacteriolytic Enzyme with a Broad pH Range of Activity and Lytic Action against <i>Bacillus anthracis</i> (2006)

We have cloned a lytic enzyme, PlyPH, with a specific lytic effect on Bacillus anthracis strains. PlyPH remains active between pH 4 and 10.5, and a single dose rescued a significant percentage of mice infected intraperitoneally with an attenuated B. anthracis strain. We propose PlyPH as a novel therapeutic agent.
Poly(vinyl alcohol) hydrogels as soft contact lens material (1994)

A new type of soft contact lens was developed from the poly(vinyl alcohol) (PVA) hydrogel prepared by a low temperature crystallization technique using a water-dimethyl sulfoxide mixed solvent. The PVA contact lens materials had a water content of 78% and a tensile strength of 50 kg/cm2, five times as strong as that of commercial poly(2-hydroxyethyl methacrylate) soft contact lens. The amount of proteins adsorbed to the PVA soft hydrogel material was half to one thirtieth of that of conventional soft contact lenses. Histological and scanning electron microscopic observation of rabbit eyes which had worn the PVA soft contact lens for 12 weeks showed no difference in corneal epithelium and cell arrangement in the corneal epithelium from the non-wearing eyes.
Hardware-efficient random circuits to classify noise in a multiqubit system (2021)

In this work, we extend a multiqubit benchmarking technique known as the binned output generation (BOG) in order to discriminate between coherent and incoherent noise sources in the multiqubit regime. While methods exist to discriminate coherent from incoherent noise at the single and few-qubit level, these methods scale poorly beyond a few qubits or must make assumptions about the form of the noise. On the other end of the spectrum, system-level benchmarking techniques exist, but they fail to discriminate between coherent and incoherent noise sources. We experimentally verify the BOG against randomized benchmarking (RB) (the industry standard benchmarking technique) in the two-qubit regime, then apply this technique to a six-qubit linear chain, a regime currently inaccessible to RB. In this experiment, we inject an instantaneous coherent $Z$-type noise on each qubit and demonstrate that the measured coherent noise scales correctly with the magnitude of the injected noise, while the measured incoherent noise remains unchanged as expected. This demonstrates a robust technique to measure coherent errors in a variety of hardware.