gebhart/patrepeval huggingface dataset:
Genetic Variants in <i>CCNB1</i> Associated With Differential Gene Transcription and Risk of Coronary In-Stent Restenosis (2014)

Allele-dependent transcriptional regulation of CCNB1 associated with rs350099, rs350104, and rs164390 affects the risk of in-stent restenosis. These findings reveal these common genetic variations as attractive diagnostic tools in risk stratification for restenosis.
Detection of IFN-γ Secretion by T Cells Collected Before and After Successful Treatment of Early Lyme Disease (2016)

Our findings suggest that measurement of IFN-γ after incubating blood with Borrelia antigens could be useful in the laboratory diagnosis of early Lyme disease. Also, after antibiotic treatment, this response appears to be short lived.
PD-L1 expression in Epstein-Barr virus-infected gastric cancers. (2016)

4052 Background: Gastric cancer (GC) is a deadly disease with limited treatment options. Recent studies with PD-1 inhibitor Pembrolizumab have shown promising results in GC. Key questions remain which GC subclass may respond best. In a comprehensive molecular analysis of gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) we identified that 15% of Epstein Barr Virus (EBV)+ GCs have amplification of chromosomal region 9p24.1, the locus of PD-1 ligands PD-L1 and PD-L2. As EBV+ cancers have multiple mechanisms to induce PD-L1 expression, we hypothesize that PD-L1 status may differ specifically in EBV+ GCs, regardless of 9p24.1 status, indicating a broader potential role for PD-1 blockade in this GC subtype. Methods: PD-L1 expression was analyzed with immunohistochemistry (IHC) using whole tissues slides of EBV+ (n = 32) and EBV negative (n = 49) GCs. The transcriptional landscape of EBV+ and EBV negative GCs was determined using mRNA sequencing results from the TCGA study. Results: With IHC we showed that EBV+ GCs have PD-L1 expression in tumor and immune cells in 50% (16/32) and 94% (30/32) of GCs respectively. This in contrast to EBV negative GCs that have PD-L1+ tumor and immune cells in only 10% (5/49) and 39% (19/49) of cases respectively (P< 0.001). Furthermore, PD-L1+ immune cells infiltrated the center of the majority of EBV+ GCs, while in EBV negative GCs PD-L1+ immune cells remained at the invasive margin (P = 0.007). mRNA sequencing analyses of 12 EBV+ GCs and 10 EBV- GCs showed that PD-L1+/EBV+ GCs have enrichment of an interferon-γ driven gene signature. Single-sample gene set enrichment analyses on a bigger series of 214 individual GCs demonstrated that besides EBV+ GCs (n = 19), microsatellite instable (MSI) GCs (n = 47) have strong enrichment of IFN-γ response gene expression, in contrast to genomic stable (GS) (n = 42) and chromosomal instable (CIN) (n = 106) gastric cancer subtypes (P< 0.001). Conclusions: As the presence of PD-L1+ tumor and/or tumor infiltrating immune cells as well as an interferon-mediated adaptive immune response are associated with PD-1 blockade vulnerability in other cancers, we here provide a strong rationale for testing of PD-1 blockade in EBV+ GC and for evaluating EBV and MSI status as variables for response.
Low complexity algorithm for the decoding of convolutional codes of any rate (2004)

It is well known that convolutional codes can be optimally decoded by using the Viterbi algorithm (VA). A decoding technique where the VA is applied to identify the error vector rather than the information message is proposed. We previously focused on convolutional coders of rate 1/2 . The method to codes of any rate is generalized and shows that, with the proposed type of decoding, the exhaustive computation of a vast majority of state to state iterations is unnecessary. Hence, performance close to optimum is achievable with a significant reduction of complexity. The higher the SNR, the greater the improvement for reduction in complexity. For instance, for SNR greater than 3 dB, a five fold reduction in complexity for the computation of ACS (add compare select) is achieved.
Parallel Burst Correction of Cyclic Codes (2009)

In this paper, a method to perform parallel decoding of the errors within a burst is presented for cyclic codes. It is shown that O(L) operations per position are sufficient to estimate each error of a burst of length L in parallel.
Simple method for measuring the thermal conductivity of a thin plate (1993)

A simple technique is described for measuring the thermal conductivity of a plate of material, with heat flowing parallel to the plane of the plate. The design is aimed at rapid and accurate measurement. Results on copper and diamond indicate an uncertainty of ∼5%.
Analytical validation of protein biomarkers for risk of spontaneous preterm birth (2017)

Presented are the validation results of a second-generation assay for determining the relative abundances of two protein biomarkers found in maternal serum that predict an individual's risk of spontaneous preterm birth. The sample preparation workflow is complex, consisting of immuno-depletion of high-abundance serum proteins, tryptic digestion of the immuno-depleted fraction to generate surrogate peptide analytes, and detection by tandem mass spectrometry. The method was determined to be robust on observation of the following characteristics: classifier peptide detection precision was excellent; results were accurate when compared to a reference method; results were linear over a clinically relevant range; the limits of quantitation encompassed the range of expected results; and the method demonstrated analytical specificity and resilience to differences in patient serum and common endogenous interferents.
Timing slack aware incremental register placement with non-uniform grid generation for clock mesh synthesis (2011)

A novel clock mesh network synthesis approach is proposed in this paper which generates an improved mesh size with registers placed incrementally considering the timing slack on the data paths and the non-uniform grid wire placement. The primary objective of the method is to reduce the power dissipation without a global skew degradation, which is achieved through a sparse and non-uniform mesh implementation with registers incrementally placed in close vicinity to the mesh grids. The incremental register placement is based on the timing information in order to preserve the timing slack of the circuit. Experimental results show that the total wirelength (mesh grid wires and stub wires) as well as the power dissipation is reduced significantly on the clock mesh network. Specifically, the wirelength of the mesh network and the power dissipation of the clock network are reduced by 52% and 48% on average, respectively. Moreover, the global clock skew and the non-negative timing slack are preserved.
Segmentation of three-dimensional intravascular ultrasound images using spectral analysis and a dual active surface model (2005)

Intravascular ultrasound (IVUS) imaging provides detailed assessment of the coronary anatomy and can be used as at quantitative tool for tracking the progression of atherosclerotic disease. The geometric information also provides evaluation of positive remodeling, a phenomenon linked to the likelihood of plaque rupture. To provide this valuable information, luminal and medial-adventitial borders must be identified in the sequence of IVUS images, a problem traditionally approached using gray-scale intensity based algorithms. However, by acquiring the radiofrequency (RF) IVUS data, the frequency information that is typically ignored can be used to improve segmentation algorithms.
Learning Multiple Sound Source 2D Localization (2020)

In this paper, we propose novel deep learning based algorithms for multiple sound source localization. Specifically, we aim to find the 2D Cartesian coordinates of multiple sound sources in an enclosed environment by using multiple microphone arrays. To this end, we use an encoding-decoding architecture and propose two improvements on it to accomplish the task. In addition, we also propose two novel localization representations which increase the accuracy. Lastly, new metrics are developed relying on resolution-based multiple source association which enables us to evaluate and compare different localization approaches. We tested our method on both synthetic and real world data. The results show that our method improves upon the previous baseline approach for this problem.
Malolactic fermentation by engineered Saccharomyces cerevisiae as compared with engineered Schizosaccharomyces pombe (1996)

The ability of yeast strains to perform both alcoholic and malolactic fermentation in winemaking was studied with a view to achieving a better control of malolactic fermentation in enology. The malolactic gene of Lactococcus lactis (mleS) was expressed in Saccharomyces cerevisiae and Schizosaccharomyces pombe. The heterologous protein is expressed at a high level in cell extracts of a S. cerevisiae strain expressing the gene mleS under the control of the alcohol dehydrogenase (ADH1) promoter on a multicopy plasmid. Malolactic enzyme specific activity is three times higher than in L. lactis extracts. Saccharomyces cerevisiae expressing the malolactic enzyme produces significant amounts of L-lactate during fermentation on glucose-rich medium in the presence of malic acid. Isotopic filiation was used to demonstrate that 75% of the L-lactate produced originates from endogenous L-malate and 25% from exogenous L-malate. Moreover, although a small amount of exogenous L-malate was degraded by S. cerevisiae transformed or not by mleS, all the exogenous degraded L-malate was converted into L-lactate via a malolactic reaction in the recombinant strain, providing evidence for very efficient competition of malolactic enzyme with the endogenous malic acid pathways. These results indicate that the sole limiting step for S. cerevisiae in achieving malolactic fermentation is in malate transport. This was confirmed using a different model, S. pombe, which efficiently degrades L-malate. Total malolactic fermentation was obtained in this strain, with most of the L-malate converted into L-lactate and CO2. Moreover, L-malate was used preferentially by the malolactic enzyme in this strain also.
Studies on organic fluorine compounds. XXXIX. Studies on steroids. LXXIX. Synthesis of 1.ALPHA.,25-dihydroxy-26,26,26,27,27,27-hexafluorovitamin D3. (1982)

1α, 25-Dihydroxy-26, 26, 26, 27, 27, 27-hexafluorocholesterol was synthesized by two procedures. Cholenic acid was converted to the 1α-hydroxy-24-sulfone derivative and hexafluoroacetone was reacted with the lithiated 24-sulfone. Subsequent removal of the sulfonyl group afforded the hexafluoro-1α, 25-dihydroxy compound. An alternative process consists of construction of the hexafluoro-25-hydroxy part on the side chain followed by the introduction of a hydroxy group at the 1α-position. The hexafluoro derivative was converted to the vitamin D form, 1α, 25-dihydroxyhexafluorovitamin D3, via the corresponding 5, 7-diene.
Integrated optical and charged particle inspection apparatus : Corrected version (2013)

The invention relates to an apparatus for inspecting a sample, equipped with a charged particle column for producing a focused beam of charged particles to observe or modify the sample, and an optical microscope to observe a region of interest on the sample as is observed by the charged particle beam or vice versa, the apparatus accommodated with a processing unit adapted and equipped for representing an image as generated with said column and an image as generated with said microscope, the unit further adapted for performing an alignment procedure mutually correlating a region of interest in one of said images wherein the alignment procedure involves detecting a change in the optical image as caused therein by the charged particle beam.
High-output-power polarization-insensitive semiconductor optical amplifier (2003)

A high-output-power 1550 nm polarization-insensitive semiconductor optical amplifier (SOA) was developed for use as a compact in-line optical amplifier. A very thin tensile-strained bulk structure was used for the active layer and active width-tapered spot-size converters (SSCs) were integrated on both input and output sides. The SOA module exhibited a high saturation output power of +17 dBm together with a low noise figure of 7 dB, large gain of 19 dB, and low polarization sensitivity of 0.2 dB for optical signals of 1550 nm wavelength. For the amplification of optical signals modulated at 10 Gb/s in the nonreturn-to-zero (NRZ) format, a good eye pattern without waveform distortion due to the pattern effect was obtained at an average output power of up to +12 dBm. Additionally, good amplification characteristics were demonstrated for the signal wavelength range corresponding to the C-band.
Liquid-Phase Sensors Based on Acoustic Plate Mode Devices (1989)

The response of piezoelectric devices propagating shear horizontal acoustic plate modes (SH-APMs) has been modeled and experimentally characterized for variations in surface mass, liquid rheological properties, and solution dielectric coefficient and electrical conductivity. The nature of the SH-APM and its propagation characteristics are outlined and used to describe a range of interactions at the solid/liquid interface. Sensitivity to sub-monolayer mass changes is demonstrated and a Cu2+ sensor is described. The APM device is compared to the surface acoustic wave device and the quartz crystal microbalance for liquid sensing applications.
Localizing Ground Penetrating RADAR: A Step Toward Robust Autonomous Ground Vehicle Localization (2015)

Autonomous ground vehicles navigating on road networks require robust and accurate localization over long-term operation and in a wide range of adverse weather and environmental conditions. GPS/INS (inertial navigation system) solutions, which are insufficient alone to maintain a vehicle within a lane, can fail because of significant radio frequency noise or jamming, tall buildings, trees, and other blockage or multipath scenarios. LIDAR and camera map-based vehicle localization can fail when optical features become obscured, such as with snow or dust, or with changes to gravel or dirt road surfaces. Localizing ground penetrating radar (LGPR) is a new mode of a priori map-based vehicle localization designed to complement existing approaches with a low sensitivity to failure modes of LIDAR, camera, and GPS/INS sensors due to its low-frequency RF energy, which couples deep into the ground. Most subsurface features detected are inherently stable over time. Significant research, discussed herein, remains to prove general utility. We have developed a novel low-profile ultra-low power LGPR system and demonstrated real-time operation underneath a passenger vehicle. A correlation maximizing optimization technique was developed to allow real-time localization at 126 Hz. Here we present the detailed design and results from highway testing, which uses a simple heuristic for fusing LGPR estimates with a GPS/INS system. Cross-track localization accuracies of 4.3 cm RMS relative to a “truth” RTK GPS/INS unit at speeds up to 100 km/h (60 mph) are demonstrated. These results, if generalizable, introduce a widely scalable real-time localization method with cross-track accuracy as good as or better than current localization methods.
Activity-based diubiquitin probes for elucidating the linkage specificity of deubiquitinating enzymes (2013)

We report a new class of deubiquitinating enzyme (DUB) probes that resemble the native diubiquitin with a same linkage size and contain a Michael addition acceptor for trapping the DUB active-site cysteine. Both K63- and K48-linked diubiquitin probes were generated using a facile chemical ligation method. The diUb probes were demonstrated to label DUBs from different families and revealed intrinsic linkage specificities of DUBs.
Metal–Organic Frameworks as Platforms for the Controlled Nanostructuring of Single-Molecule Magnets (2015)

The prototypical single-molecule magnet (SMM) molecule [Mn12O12(O2CCH3)16(OH2)4] was incorporated under mild conditions into a highly porous metal-organic framework (MOF) matrix as a proof of principle for controlled nanostructuring of SMMs. Four independent experiments revealed that the SMM clusters were successfully loaded in the MOF pores, namely synchrotron-based powder diffraction, physisorption analysis, and in-depth magnetic and thermal analyses. The results provide incontrovertible evidence that the magnetic composite, SMM@MOF, combines key SMM properties with the functional properties of MOFs. Most importantly, the incorporated SMMs exhibit a significantly enhanced thermal stability with SMM loading advantageously occurring at the periphery of the bulk MOF crystals with only a single SMM molecule isolated in the transverse direction of the pores.
A FEASIBILITY ANALYSIS OF A NOVEL APPROACH FOR THE CONVERSION OF XYLOSE TO ETHANOL (1992)

Economic production of ethanol from plant biomass could be significantly increased if the feedstock for the fermentation is more completely utilized. Currently, simple sugars (mostly D-glucose and D-xylose) can be recovered from lignocellulose by enzymatic or acid hydrolysis. However, while glucose can be readily converted to ethanol by yeasts, the xylose is not fermentable by many of the same species of yeasts that are able to convert glucose into ethanol. Nevertheless, xylose can be converted to its ketose isomer, xylulose, by the enzyme xylose isomerase and this isomer can be converted to ethanol. A major obstacle, however, in converting the xylose to xylulose and then simultaneously converting the xylulose to ethanol is that the pH at which xylose isomerase displays its optimal activity (pH of 7.0-8.0) is much different from the pH at which the fermentation of the xylulose and glucose is best carried out (pH of 4.0-5.0). Herein we propose a novel scheme to provide a means by which the isomerization and the fermentation can both take place simultaneously. The xylose isomerase is immobilized in a porous polymer pellet and this pellet is then coated with an additional layer in which the enzyme urease is immobilized. These bilayered pellets are dispersed in a fermentation broth which contains a prespecified concentration of urea in addition to all the other necessary ingredients. The xylose isomerase, immobilized in the core region of the pellet, catalyses the conversion of xylose to xylulose, and this latter substrate at the same time also becomes available for the fermentation reaction immediately. It is also possible to sustain the necessary spatial pH gradient between the bulk liquid phase and the core region of the pellet, because as hydrogen ions diffuse into the pellet they are neutralized by the ammonia produced in the outer layer of the pellet by the hydrolysis of urea by urease. A mathematical model is developed to demonstrate that the required pH gradient can be achieved. The model evaluates the effect of pellet design parameters (enzyme loading and thickness of the outer layer) and reactor conditions (bulk concentration of urea, and the effect of weak acids) on the ability to generate the required pH gradient across the outer layer of the pellet.
Receptor‐coupled Amyloid Precursor Protein Processing<sup>a</sup> (1993)

The family of beta-amyloid protein precursors (APP) can be processed via several alternative proteolytic pathways. Some generate potentially amyloidogenic APP derivatives, whereas others preclude the formation of such fragments. The cellular mechanisms regulating the relative activities of these pathways are thus important in determining the factors contributing to the formation of amyloidogenic APP derivatives. In order to investigate whether cell-surface receptor activity can regulate APP processing, HEK 293 cell lines stably expressing human muscarinic acetylcholine receptors (mAChR; subtypes m1, m2, m3, m4) were stimulated with the muscarinic agonist carbachol, and the release of APP derivatives was measured. Carbachol increased the release of large amino-terminal APP-fragments 4- to 6-fold in cell lines expressing the m1 or m3 receptors but not in those expressing m2 or m4 subtypes. This increase was blocked by various protein kinase inhibitors and mimicked by phorbol esters, indicating that it is mediated by protein kinase activation, presumably by protein kinase C (PKC). To determine whether additional cell-surface receptor types linked to this signal transduction pathway could also regulate APP processing, we stimulated differentiated PC-12 cells with bradykinin and found that this neuropeptide also increased the secretion of amino-terminal APP derivatives. We next investigated the possibility that neuronal depolarization might affect APP processing in mammalian brain. Electrically stimulated rat hippocampal slices released two times more amino-terminal APP derivatives than unstimulated control slices. This release increased with increasing stimulation frequencies in the physiological firing range of hippocampal pyramidal cells, and was blocked by tetrodotoxin. These results suggest that, in brain, APP processing is regulated by neuronal activity.
Compactor independent direct diagnosis (2005)

In scan test environment, designs with embedded compression techniques can achieve dramatic reduction in test data volume and test application time. However, performing fault diagnosis with the reduced test data becomes a challenge. In this paper, we provide a general methodology based on circuit transformation technique that can be applied for performing fault diagnosis in the context of any compression technique. The proposed methodology enables seamless reuse of the existing standard ATPG based diagnosis infrastructure with compressed test data. Experimental results indicate that the diagnostic resolution of devices with embedded compression is comparable with that of devices without embedded compression.
Test cost reduction using partitioned grid random access scan (2006)

The random access scan (RAS) has the ability to address major problems associated with serial-scan method. A practically implementable RAS test architecture called progressive random access scan (PRAS) was introduced earlier. This paper proposes a generalized architecture for the PRAS. We show that the generalized PRAS architecture offers two orders of magnitude gains in test application time over traditional serial scan and is superior to multiple serial scan in terms of the use of tester channels.
Long-wavelength erbium-doped fiber amplifier gain enhanced by ASE end-reflectors (1998)

We use for what we believe is the first time narrow-band end-reflectors to reduce losses through short-wavelength amplified stimulated emission (ASE) in silica-based erbium-doped fiber amplifiers operating at wavelengths above 1570 mm. The end-reflectors feed a small fraction of the ASE, up to a few tenths of a milliwatt, back into the amplifying fiber. The reflected ASE compresses the short-wavelength gain and thus reduces the ASE-losses, from, e,g., 50 mW for a launched pump power of 110 mW at 980 nm without end-reflector to 10 mW with an optimized end-reflector. We investigate possible improvements of gain (around 5 dB) and output power (up to 17 mW), and the influence of the amount and wavelength of the feedback.