gebhart/patrepeval huggingface dataset:
NPM1 mutations and cytoplasmic nucleophosmin are mutually exclusive of recurrent genetic abnormalities: a comparative analysis of 2562 patients with acute myeloid leukemia (2008)

Acute myeloid leukemia carrying NPM1 mutations and cytoplasmic nucleophosmin (NPMc(+) acute myeloid leukemia) represents one-third of adult AML (50-60% of all acute myeloid leukemia with normal karyotype) and shows distinct biological, pathological and clinical features. We confirm in 2562 patients with acute myeloid leukemia our previous observation that NPM1 mutations and cytoplasmic nucleophosmin are mutually exclusive of recurrent genetic abnormalities. Taken together, these findings make NPMc+ acute myeloid leukemia a good candidate for inclusion in the upcoming World Health Organization classification.
Recent results from thin-film-coated semiconductor neutron detectors (2003)

Semiconductor based thermal neutron detectors provide a compact technology for neutron detection and imaging. Such devices can be produced by externally coating semiconductor charged particle detectors with neutron reactive films that convert free neutrons into charged-particle reaction products. Commonly used films for such devices utilize the <sup>10</sup>B(n,a)<sup>7</sup>Li reaction or the <sup>6</sup>Li(n,a)<sup>3</sup>H reaction, which are attractive due to the relatively high energies imparted to the reaction products. Unfortunately, thin film or "foil" type thermal neutron detectors suffer from self-absorption effects that ultimately limit neutron detection efficiency. Design considerations that maximize the efficiency and performance of such devices are discussed. Linear arrays fabricated from thin-film-coated pixel detectors are presented with results.
Long-Term Evaluation of Low-Density Cement: Laboratory Studies and Field Application (2007)

Abstract Cementing a string in one stage is a challenging task, especially in the presence of weak formations. Cement slurry losses during placement is highly possible in S-1 (sandstone) and S-2 (carbonate) formations, if the equivalent circulating density (ECD) exceeds 11 lb/gal during placement. A conventional method to overcome this challenge is to use multi-stage cementing by setting the stage tool above the loss circulation zone. However, the success of this tool is limited. A second method is to use low density cement. In this study, we present extensive lab work evaluation of a low density cement system based on the use of hollow microspheres at field conditions. The tests included shrinkage, compressive strength development, porosity, gas and brine permeability. Data generated during three months supported the use the cement examined. The hollow microspheres cement was applied in several gas wells. The technical objective of the cement job was to achieve zonal isolation across the weak S-1 & S-2 formations. The operation objective was to cement the casing to the surface in one stage without using stage tools. This paper will discuss case histories that include job design, execution, and evaluation of the hollow microspheres cement. Field treatments were conducted without encountering any operational problems. The treatment was successful and maintained isolation for more than three years which confirmed the effectiveness of this cement system.
A biomimetic controller for a multifinger prosthesis (1999)

A novel controller for a multifinger hand prosthesis was developed and tested to measure its accuracy and performance in transducing volitional signals for individual "phantom" fingers. Pneumatic sensors were fabricated from open-cell polymeric foam, and were interposed between the prosthetic socket and superficial extrinsic tendons associated with individual finger flexion. Test subjects were prompted to move individual fingers or combinations thereof to execute either taps or grasps. Sensor outputs were processed by a computer that controlled motions of individual fingers on a mechanical prosthesis. Trials on three upper-limb amputees showed that after brief training sessions, the TAP controller was effective at producing voluntary flexions of individual fingers and grasping motions. Signal energies were between 5 and 25 dB relative to noise from all sources, including adjacent sensors, indicating high degrees of both sensitivity and specificity for tendon-associated transduction. Finger flexions at up to three repetitions per second, and rhythmic tapping of sequential fingers were readily transduced. One amputee subject was able to play a short piano piece with three fingers, at approximately one-quarter normal tempo. TAP sensors responded linearly to graded forces from individual fingers, indicating proportional force control. Our results demonstrate the feasibility of restoring some degree of finger dexterity by noninvasive sensing of extrinsic tendons.
Advanced Macro-block Entropy Coding in H.264 (2007)

Existing video encoders, such as MPEG4, H.263 and H.264, adopt variable length coding (VLC) as entropy coding method, focusing on residue data coding. In low bit-rate video coding, larger quantization parameters are used to give a smaller number of bits spent on residue data. As a result, the header overhead is a dominant factor of yielding the overall bit rates. In this paper, macro-block (MB) header behavior is investigated. It is found that the relative percentage of the number of bits of MB header increases with quantization parameter (QP) and header correlation between neighboring MBs is high. Based on these MB header properties, we propose an advanced coding algorithm for entropy coding of MB header. The experimental results suggest that our proposed algorithm achieves lower total number of encoded bits over JM10.2, up to 10% bit reduction, with the same PSNR quality. At the same bit rates, our algorithm has about 0.3-0.4 dB PSNR gain.
Ion-selective sensors incorporating strongly adhesive polymeric membranes (1990)

Chemical-selective membranes having matrices of polyvinyl chloride (PVC)/(hydroxylated PVC), polyurethane/(hydroxylated PVC), and moisture-curable silicone rubber are compared to conventional PVC membranes in terms of adhesion to silicon nitride. A well-controlled peel test, developed for this evaluation, yields repeatable, quantitative results for both wet and dry membranes. Polyurethane and silicon membranes have much better adhesion to the sensor surface than do PVC or hydroxylated PVC. The hydroxylated PVC- and polyurethane-based membranes have electrochemical performance equivalent to that of PVC membranes in terms of slope, detection limit, and selectivity. Though the electrochemical properties of the silicone-matrix membrane are degraded somewhat by its high resistance, it has extremely good adhesion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Crucial Role of 3-Bromoethyl in Removing the Estrogenic Activity of 17β-HSD1 Inhibitor 16β-(<i>m</i>-Carbamoylbenzyl)estradiol (2011)

17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) represents a promising therapeutic target for breast cancer treatment. To reduce the undesirable estrogenic activity of potent 17β-HSD1 inhibitor 16β-(m-carbamoylbenzyl)estradiol (1) (IC(50) = 27 nM), a series of analogues with a small functionalized side chain at position 3 were synthesized and tested. The 3-(2-bromoethyl)-16β-(m-carbamoylbenzyl)-estra-1,3,5(10)-trien-17β-ol (5) was found to be a potent inhibitor (IC(50) = 68 nM) for the transformation of estrone (E1) into estradiol (E2) and, most importantly, did not stimulate the proliferation of estrogen-sensitive MCF-7 cells, suggesting no estrogenic activity. From these results, the crucial role of a bromoalkyl side chain at carbon 3 was identified for the first time. Thus, this new inhibitor represents a good candidate with an interesting profile suitable for further studies including pharmacokinetic and in vivo studies.
Narrative review of urinary glycan biomarkers in prostate cancer (2021)

Prostate cancer (PC) is the second most common cancer in men worldwide. The application of the prostate-specific antigen (PSA) test has improved the diagnosis and treatment of PC. However, the PSA test has become associated with overdiagnosis and overtreatment. Therefore, there is an unmet need for novel diagnostic, prognostic, and predictive biomarkers of PC. Urinary glycoproteins and exosomes are a potential source of PC glycan biomarkers. Urinary glycan profiling can provide noninvasive monitoring of tumor heterogeneity and aggressiveness throughout a treatment course. However, urinary glycan profiling is not popular due to technical disadvantages, such as complicated structural analysis that requires specialized expertise. The technological development of glycan analysis is a rapidly advancing field. A lectin-based microarray can detect aberrant glycoproteins in urine, including PSA glycoforms and exosomes. Glycan enrichment beads can enrich the concentration of <i>N</i>-linked glycans specifically. Capillary electrophoresis, liquid chromatography-tandem mass spectrometry, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry can detect glycans directory. Many studies suggest potential of urinary glycoproteins, exosomes, and glycosyltransferases as a biomarker of PC. Although further technological challenges remain, urinary glycan analysis is one of the promising approaches for cancer biomarker discovery.
An Image Processing Algorithm to Find New and Old Bruises (1995)

Abstract. Stored Red Delicious apples can have old and new bruises. Previous studies have shown the near-infrared (NIR) reflection of bruised tissue with respect to unbruised tissue to be darker in new (24 h) bruises and lighter in old (four to six weeks) bruises. An algorithm was developed to identify both old and new bruises in the same NIR image. Apple images were low pass filtered to remove small surface characteristics (lenticels) and normalized. Absolute difference between these images and a standard (delrin sphere) representing unbruised tissue were also low pass filtered. A binary image of bruised/unbruised tissue was formed based upon a user defined threshold level. Shapes of the bruised areas were evaluated and, based upon a shape factor, either dismissed or counted as bruised areas. The algorithm detected both old and new bruises except for large 25 to 35 mm (0.98 to 1.38 in.) diameter old bruises. These bruises had areas within their boundaries where NIR reflectance had not changed completely from darker to lighter than unbruised tissue. This patterning altered the bruise shape causing the algorithm to discount them.
Silicon photonic integrated devices for optical interconnects (2013)

We present our latest update on key components in the integrated Si photonic interconnect system, including hybrid Si microring lasers, Si microring modulators, hybrid Si photodetector and passive waveguide devices.
Abstract 2106: Focal gene expression profiling of counterstained FFPE with correlation to morphology using TempO-Seq (2018)

Abstract We previously reported on use of the whole transcriptome TempO-Seq® assay to profile gene expression from 1 mm2 focal areas of 5 µm thick FFPE sections of normal and cancerous tissue to identify disease biomarkers and mechanistic pathways. We are now presenting data demonstrating that the TempO-Seq assay can be performed as an “in situ” assay on slides by an automated slide stainer, followed by counterstaining. Then, using an automated digital imaging platform, areas as small as 30 μm in diameter within the FFPE section can be profiled, permitting the gene expression data to be correlated directly to the specific morphology of that focal area. The pathologist uses a computer interface to select areas for profiling during the course of the histologic examination of the section, and then the TempO-Seq probes are automatically recovered from those region(s) of interest. After depositing them into PCR tubes, the assay is completed with PCR amplification and sample barcoding before pooling the samples into a library for sequencing. Analysis of the sequencing data is carried out automatically to report results. There is no use of laser capture or destruction of the tissue. The TempO-Seq processed slides can be archived and additional areas may be sampled at a later date. In this study, we sample replicate areas of matched normal vs. cancerous tissue, measuring gene biomarkers of clinical utility, gene fusions, and SNPs. We present gene expression profiles for replicate areas of pure stroma, single normal glands, single high-grade PIN glands, and single cancerous glands from prostate FFPE, demonstrating the statistical power of the TempO-Seq in situ assay as well as the correlation to focal histology and the use of focal differential expression to elucidate molecular pathways involved in the transition from normal tissue to cancer. We report measurements of clinically relevant biomarkers and signatures from clinical FFPE samples, plus therapeutic targets and drug resistance genes. This new approach demonstrates that complex molecular tests can be carried out by any pathologist in their own lab, and makes moot the issues of “% cancer” and amount of tissue required for testing. The approach we present brings extraction-free complex molecular testing of FFPE into the pathology lab and takes molecular pathology to a new level of simplicity, focal precision and correlation to morphology. Citation Format: Elliot Imler, Milos Babic, Deanna Adams, Peter Shepard, Joanne Yeakley, Raymond B. Nagle, Bruce Seligmann. Focal gene expression profiling of counterstained FFPE with correlation to morphology using TempO-Seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2106.
TIE Breaking: Tunable Interdomain Egress Selection (2007)

In a large backbone network, the routers often have multiple egress points they could use to direct traffic toward an external destination. Today's routers select the ldquoclosestrdquo egress point, based on the intradomain routing configuration, in a practice known as early-exit or hot-potato routing. In this paper, we argue that hot-potato routing is restrictive, disruptive, and convoluted and propose an alternative called TIE (Tunable Interdomain Egress selection). TIE is a flexible mechanism that allows routers to select the egress point for each destination prefix based on both the intradomain topology and the goals of the network administrators. In fact, TIE is designed from the start with optimization in mind, to satisfy diverse requirements for traffic engineering and network robustness. We present two example optimization problems that use integer-programming and multicommodity-flow techniques, respectively, to tune the TIE mechanism to satisfy networkwide objectives. Experiments with traffic, topology, and routing data from two backbone networks demonstrate that our solution is both simple (for the routers) and expressive (for the network administrators).
Analysis of the Expression of Peptide–Major Histocompatibility Complexes Using High Affinity Soluble Divalent T Cell Receptors (1997)

Understanding the regulation of cell surface expression of specific peptide-major histocompatibility complex (MHC) complexes is hindered by the lack of direct quantitative analyses of specific peptide-MHC complexes. We have developed a direct quantitative biochemical approach by engineering soluble divalent T cell receptor analogues (TCR-Ig) that have high affinity for their cognate peptide-MHC ligands. The generality of this approach was demonstrated by specific staining of peptide-pulsed cells with two different TCR-Ig complexes: one specific for the murine alloantigen 2C, and one specific for a viral peptide from human T lymphocyte virus-1 presented by human histocompatibility leukocyte antigens-A2. Further, using 2C TCR- Ig, a more detailed analysis of the interaction with cognate peptide-MHC complexes revealed several interesting findings. Soluble divalent 2C TCR-Ig detected significant changes in the level of specific antigenic-peptide MHC cell surface expression in cells treated with gamma-interferon (gamma-IFN). Interestingly, the effects of gamma-IFN on expression of specific peptide-MHC complexes recognized by 2C TCR-Ig were distinct from its effects on total H-2 Ld expression; thus, lower doses of gamma-IFN were required to increase expression of cell surface class I MHC complexes than were required for upregulation of expression of specific peptide-MHC complexes. Analysis of the binding of 2C TCR-Ig for specific peptide-MHC ligands unexpectedly revealed that the affinity of the 2C TCR-Ig for the naturally occurring alloreactive, putatively, negatively selecting, complex, dEV-8-H-2 Kbm3, is very low, weaker than 71 microM. The affinity of the 2C TCR for the other naturally occurring, negatively selecting, alloreactive complex, p2Ca-H-2 Ld, is approximately 1000-fold higher. Thus, negatively selecting peptide-MHC complexes do not necessarily have intrinsically high affinity for cognate TCR. These results, uniquely revealed by this analysis, indicate the importance of using high affinity biologically relevant cognates, such as soluble divalent TCR, in furthering our understanding of immune responses.
Detecting Double JPEG Compression With the Same Quantization Matrix (2010)

Detection of double joint photographic experts group (JPEG) compression is of great significance in the field of digital forensics. Some successful approaches have been presented for detecting double JPEG compression when the primary compression and the secondary compression have different quantization matrixes. However, when the primary compression and the secondary compression have the same quantization matrix, no detection method has been reported yet. In this paper, we present a method which can detect double JPEG compression with the same quantization matrix. Our algorithm is based on the observation that in the process of recompressing a JPEG image with the same quantization matrix over and over again, the number of different JPEG coefficients, i.e., the quantized discrete cosine transform coefficients between the sequential two versions will monotonically decrease in general. For example, the number of different JPEG coefficients between the singly and doubly compressed images is generally larger than the number of different JPEG coefficients between the corresponding doubly and triply compressed images. Via a novel random perturbation strategy implemented on the JPEG coefficients of the recompressed test image, we can find a “proper” randomly perturbed ratio. For different images, this universal “proper” ratio will generate a dynamically changed threshold, which can be utilized to discriminate the singly compressed image and doubly compressed image. Furthermore, our method has the potential to detect triple JPEG compression, four times JPEG compression, etc.
Situation awareness and security risk mitigation for integrated energy systems with the inclusion of power‐to‐gas model (2020)

Power‐to‐gas (P2G) and gas‐fired generation units (GFGUs) enable the bidirectional energy flow of integrated energy systems (IESs). The static security of IES should be analysed considering the interdependence between energy systems. In this study, the static security of IES is analysed, and a novel static security control strategy to improve the security of IES after N −1 contingency is proposed considering P2G. First, electricity–gas IES model is presented, and the multi‐energy flow of IES is solved by the Newton–Raphson method. Then, N − 1 static security analysis is carried out for the electricity system and natural gas system. Based on the obtained Jacobian matrix during the energy flow calculation process after N − 1 contingency, variable sensitivity matrixes of voltage, gas pressure, branch power flow and pipeline flow to control variables are derived. Furthermore, a static security control strategy for IES based on the sensitivity matrices is developed to regulate operation statuses of P2G and GFGU and compressor outlet pressure to mitigate the violation of security constraints. The performance of the proposed analysis method and control strategy is evaluated by IES 4‐12 and IES 118‐48 test systems. The results demonstrate that the proposed control strategy can mitigate security risks of IES after N − 1 contingencies.
Moir&#x00E9; reflecting Bragg gratings recorded in photo-thermo-refractive glass (2009)

Over the last 15 years, a new photosensitive glass called photo-thermo-refractive (PTR) glass has been developed for the recording of volume holographic elements such as volume Bragg gratings. Main advantage of such elements is that they allow obtaining narrowband filters in both spectral and angular spaces [1]. However, the further decrease of the spectral bandwidth of volume Bragg gratings represents a technological issue and is thus limited to values between 50 and 100 pm depending on their central wavelength. For some applications such as LIDARS or the longitudinal mode selection of Nd:YAG lasers [2], bandwidth in the range of a few picometers or tens of picometers would be required. Hence, new technology must be developed in order to achieve ultra-narrowband selectivity. In this paper we present the fabrication of so-called Moiré reflecting Bragg gratings (Moiré RBG), resulting from the recording of two reflecting Bragg gratings with shifted periods (figure 1). Such structure was widely investigated in the past in germanium doped silica fibers [3]. However, due to the unavailability of bulk photosensitive materials, no experimental demonstration of Moiré RBG was performed. PTR glass allows recording of high efficiency reflecting Bragg gratings in a few millimeters glass samples and losses can be kept low below 1%. Hence, PTR glass makes an ideal candidate for the recording of Moiré RBG with very high transmission at resonance.
EFFECTS OF TEMPERATURE SENSOR PLACEMENT ON PERFORMANCE OF TEMPERATURE-CONTROLLED ABLATION (1995)

The significant changes in power with tissue-electrode angle suggested that the lesions were more predictable when ablating with temperature-based RF generators, rather than non-temperature systems. The maximal tissue temperature was reached at locations within the tissue a fraction of a millimeter away from the ablation electrode surface. The mors in tissue temperature prediction introduced by temperature sensors placed inside the electrode changed with blood flow rate and tissue-electrode angle. This study shows that to reduce tissue temperature prediction errors, during temperature-controlled ablation it was better to use a temperature ksor placed at the tip rather than at the center of the ablation electrode. I. INTRODUCTION RF catheter ablation is becoming fkquently used for the therapy of various cardiac arrhythmias. To be therapeutically effective, the ablation volume must include the targeted region and extend as little as possible beyond it. This is a difficult goal to achieve, since the desired lesion geometries vary with the intended therapy. For example, it is hypothesized that long thin lesions may be desired for curing atrial fibrillation, whereas deep and wide lesions are more effective for curing monomorphic ventricular tachycardia ( 1,2). To avoid charring and tissue &siccaridexplosion, it is very important to maintain the tissue temperature below 100°C (3). Given these considerations, it has been shown (3) that temperature-based RF ablation systems can generate more predictable lesions than non-temperature systems. The temperature-based systems intend to either monitor the tissue temperature or to use it to control the amount of delivered RF energy. However, due to temperature gradients, the tempemure sensors carried by ablation electrodes usually do not measure precisely the highest temperature of the tissue. As a consequence, improper temperature sensor placement can affect negatively the performance of the ablation system. The goal of this study was to determine the effects of tissue- electrode relative position and temperature sensor placement on the accuracy of tissue temperature monitofing by sensors placed inside the ablation electrode.