gebhart/patrepeval huggingface dataset:
Variations in the bitterness perception-related genes TAS2R38 and CA6 modify the risk for colorectal cancer in Koreans (2017)

Bitterness perception is known to be an important factor in individuals' dietary behaviors and is also associated with the sensing of nutritious/noxious molecules for subsequent metabolic responses in multiple organs. Therefore, the genetic variation in bitterness sensing may be associated with diet-related diseases, including colorectal cancer (CRC). We investigated the influence of variations in the bitterness-sensing genes taste receptor type 2 member 38 (TAS2R38) and carbonic anhydrase 6 (CA6) on the consumption of food, tobacco and alcohol and the risk of CRC in Koreans. The study population consisted of 681 cases and 1361 controls, and their intake of vegetables, fruits, fiber, fat-food and sweets was analyzed. The genotypes for TAS2R38 A49P, V262A and I296V and CA6 rs2274333 A/G were assessed using the MassArray technique. Our findings suggested that the TAS2R38 diplotype, CA6 rs2274333 and their combined genotype had a negligible influence on dietary and alcohol intake. The combined TAS2R38-CA6 AVI/AVI-AA genotype was associated with higher tobacco consumption than the other genotypes in CRC cases only. However, the genetic variations were a significant risk factor for CRC. The TAS2R38 AVI/AVI diplotype and CA6 G allele were associated with a reduced risk of CRC. Moreover, when the combined genotypes of the subjects were analyzed, possessing both the variant diplotype/variant allele (AVI/AVI+G*) was associated with a greater reduction in the risk of CRC (adjusted OR = 0.49; 95%CI: 0.34-0.74). In summary, variations in the bitterness perception genes TAS2R38 and CA6 did not influence the examined food intake in Koreans. However, those genetic variants were a decisive modifying factor of CRC susceptibility.
Metabolic syndrome and chronic hepatitis B: is the evidence enough? (2010)

We appreciated the interest and comment of Li and colleagues on our recent publication.1 We would like to acknowledge the results from the Taiwanese longitudinal studies concerning the effect of fatty liver, obesity and type 2 diabetes on the risk of liver cirrhosis and hepatocellular carcinoma (HCC) in chronic hepatitis B (CHB) patients. This evidence echoed the conclusion of the present study that metabolic syndrome increased the risk of liver cirrhosis in CHB.

In the present cross-sectional study, the causal …
Breaking the Ice: Navigating in the Arctic (2011)

Arctic navigation is becoming increasingly important, because oil exploration and normal shipping in the region are both on the rise. Navigation integrity is particularly important, because an accident could be very damaging to the sensitive Arctic environment. Thus, this article investigates the Arctic extension of space-based augmentation systems (SBAS) such as WAAS, EGNOS, and MSAS. More specifically, it analyzes the potential benefit of adding new SBAS reference stations for the far North, use of Iridium satellites to broadcast integrity information to the users, and multi-constellation GNSS to improve vertical performance.
Data from Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History (2023)

&lt;div&gt;Abstract&lt;p&gt;While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones &lt;i&gt;in vivo&lt;/i&gt;. We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics.&lt;/p&gt;Significance:&lt;p&gt;Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as &lt;i&gt;in vivo&lt;/i&gt; barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Hilton and Scott, p. 2965&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 2945&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Selecting Patients with Favorable Risk, Grade Group 2 Prostate Cancer for Active Surveillance—Does Magnetic Resonance Imaging Have a Role? (2020)

Combining multiple magnetic resonance imaging modalities (multiparametric magnetic resonance imaging) provides a more accurate prediction of the risk presented by prostate cancer than current prediction methods. In this study, positive magnetic resonance imaging results approximately doubled the chances that a patient with favorable risk prostate cancer would be found to have adverse pathology when their prostate was removed. Thus, multiparametric magnetic resonance imaging could help select patients with favorable risk cancer who may be good candidates for active surveillance, and help guide biopsy and surveillance strategies for such patients.
DeepSeg: Deep Segmental Denoising Neural Network for Seismic Data (2022)

Noise attenuation is a crucial phase in seismic signal processing. Enhancing the signal-to-noise ratio (SNR) of registered seismic signals improves subsequent processing and, eventually, data analysis and interpretation. In this work, a novel noise reduction framework based on an intelligent deep convolutional neural network is proposed that works on segments of the time-frequency domain and, hence named as DeepSeg. The proposed network is efficient in learning sparse representation of the data simultaneously in the time-frequency domain and adaptively capturing seismic signals corrupted with noise. DeepSeg is able to achieve impressive denoising performance even when seismic signal shares common frequency band with noise. The proposed approach properly tackles a variety of correlated (color) and uncorrelated noise, and other nonseismic signals. DeepSeg can boost the SNR considerably even in extremely noisy environments with minimal changes to the signal of interest. The effectiveness of the proposed methodology is demonstrated in enhancing passive seismic event detection/denoising. However, there are other obvious applications of the DeepSeg in active and passive seismic fields, e.g., seismic imaging, preprocessing of ambient noise data, and microseismic event monitoring. It is worth pointing out here that the deep neural network is trained exclusively using synthetic seismic data, negating the need for real data during the training phase. Furthermore, the proposed setup is general and its potential applications are not confined to passive event denoising or even seismic. The method proposed is also adaptable to other diverse signals in different settings, like medical images/signals [magnetic resonance imaging (MRI), electroencephalogram (EEG) signals, electrocardiograms (ECG) signals, and retinal images, to name a few], radar signals, speech signals, fault detection in electrical/mechanical systems, daily life images, etc. Experiments on synthetic and real seismic data reveal the efficacy and supremacy of the proposed method in terms of SNR improvement and required training data when compared to the state-of-the-art deep neural network-based denoising technique.
Fast parametric image reconstruction for FDG using dynamic PET data (2002)

Measurement of the rate constant parameters of the tracer /sup 18/F-FDG, used with positron emission tomography (PET) to determine the local cerebral metabolic rate of glucose (LCMRGlc), can provide a clear understanding of the physiological processes in the human brain. At present, the methods that are widely used to obtain LCMRGlc, such as nonlinear least squares (NLS), first require the reconstruction of a time sequence of images. The reconstruction of these images requires a large amount of computation, especially in 3D-PET, and the nonlinear based methods also require a large amount of computation. Here, the authors propose a fast parametric image reconstruction method for /sup 18/F-FDG dynamic PET studies. In their method a deconvolving process is first employed on the time sequential projection data to remove the effect of the measured plasma time activity. The deconvolved terms are integrated over three different time intervals and the parameters for determining LCMRGlc can be obtained analytically. The authors' method requires only three reconstructing processes and reduces the computational demand to estimate LCMRGlc. The algorithm performance is evaluated using a digital phantom and a clinical data set and the results show that the proposed method produces images with the same or better quality as the images form the NLS method, with much less computation compared to the NLS method.
Computationally efficient modeling of structural inhomogeneities by analytical/numerical matching (1999)

Solving structural acoustic problems in the mid-frequency range is a challenging task. Computation is expensive due to both the large well-coupled nature of the domain and resolution constraints such as small flexural wavelength. In addition, discrete structural elements such as ribs and stiffeners cause localized high-resolution content that requires much greater resolution than would be otherwise warranted. A method called analytical/numerical matching (ANM) alleviates this additional computational burden. The ANM method captures the particular influence of the inhomogeneity on the structure in an analytically expressed local solution. The governing equation is then used to show that the extraction of this local solution by superposition amounts to replacing the original discrete influence of the inhomogeneity by a smoothed forcing derived from the local solution. The result is a smoother problem that can be computed more efficiently and without the loss of any information. The method has been demonstrated for several configurations of increasing complexity in the process of its development as a useful tool for efficiently solving realistic problems of engineering interest. These problems have shown the usefulness, accuracy, and efficiency of the method. Examples will be presented, including recent work on implementation within a finite element analysis.
Parallel optical interconnections development at HP Labs (2002)

Bandwidth and distance needs continue to increase as we enter this ever-growing information age. To satisfy this need, Hewlett Packard as well as other fiber-optic component suppliers have begun to develop parallel optical interconnections. Initial markets requiring multigigabit/sec bandwidths include: large symmetric multiprocessors, telecom central switches, and high resolution video at a distance. The key to being successful in these markets is affordability and availability of actual parallel optical interconnection links. HP has been working towards both of these goals while maintaining a clear performance advantage over electrical interconnection solutions.
Development of a Hydraulically Expanded Metal Internal Casing Patch (2005)

This paper details the technical development & implementation of a Coiled Tubing (CT) deployed, expandable internal metal casing patch. The driver for the development of the technology was to introduce an internal casing patch system for deployment in 7
On the high temperature crack propagation in the nickel-based superalloy AD730TM (2019)

International audience
Cooperative hydrogen bonding and yttrium(iii) complexation in the assembly of molecular capsules (2000)

A combination of hydrogen bonding and metal coordination leads to the formation of the new solid state molecular capsule [{18-crown-6}⊂{(Y(H2O)73+ )1.33(p-sulfonatocalix[4]arene4− )}2] at pH between 1.0 and 4.0.
Refractive index and birefringence of In x Ga 1– x N films grown by MOCVD (2005)

The refractive index and birefringence of InxGa1–xN films grown on GaN layers were measured by prism coupling used in conjunction with multilayer optical waveguide analysis. Samples with x = 0.036, 0.049, 0.060, and 0.066 were examined at the separate wavelengths of 442, 457.9, 476.5, 488, 514.5, 532, and 632.8 nm. The In fraction x was determined by Rutherford backscattering spectroscopy. Separate measurements of the film thicknesses were performed by cross-sectional field-emission scanning electron microscopy (FESEM). Film thickness information was required in order to constrain the numerical simulation used to solve for the ordinary (no) and extraordinary (ne) refractive indices. We found that no is a weak function of both x and wavelength for the InGaN layers and could only be well distinguished from GaN (x = 0) for the two shortest wavelengths used. On the other hand, ne for the InGaN layers was resolved from GaN for all the wavelengths and x values. The measurements for ne are limited by optical scattering observed at the shortest wavelengths and the higher values of x. Cross-sectional FESEM reveals that a source of this scattering is most likely triangular pits at the InGaN/GaN upper interface. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Adenoviral RB2/p130 Gene Transfer Inhibits Smooth Muscle Cell Proliferation and Prevents Restenosis After Angioplasty (1999)

Smooth muscle cell (SMC) proliferation that results in neointima formation is implicated in the pathogenesis of atherosclerotic plaques and accounts for the high rates of restenosis that occur after percutaneous transluminal coronary angioplasty, a widespread treatment for coronary artery disease. Endothelial lesions trigger intense proliferative signals to the SMCs of the subintima, stimulating their reentry into the cell cycle from a resting G(0) state, resulting in neointima formation and vascular occlusion. Cellular proliferation is negatively controlled by growth-regulatory or tumor-suppressor genes, or both, such as the retinoblastoma gene family members (RB/p105, p107, RB2/p130). In the present study, we show that RB2/p130 inhibited SMC proliferation in vitro and in vivo. We used the rat carotid artery model of restenosis to demonstrate that adenovirus-mediated localized arterial transduction of RB2/p130 at the time of angioplasty significantly reduced neointimal hyperplasia and prevented restenosis. Furthermore, the ability of pRb2/p130 to block proliferation correlated with its ability to bind and sequester the E2F family of transcription factors, which are important mediators of cell cycle progression. These results imply that RB2/p130 could be an important target for vascular gene therapy.
Understanding the Exceptional Performance of Lithium‐Ion Battery Cathodes in Aqueous Electrolytes at Subzero Temperatures (2018)

Abstract Lithium‐ion batteries with aqueous electrolytes can be excellent candidates for battery applications at low temperatures. In contrast to a common misconception, aqueous lithium ion batteries can operate at several tens of degrees below the freezing point of water when high concentration electrolyte solutions are utilized. Furthermore, it is reported here that the performance of intercalation cathodes in aqueous electrolytes is quite remarkable and superior to that in common organic electrolytes at very low temperatures down to about −40 °C. Here in the performance of water‐based electrolyte solutions‐based on three low‐cost inorganic salts (LiNO 3 , Li 2 SO 4 , and LiCl) and that of the corresponding aqueous battery systems is studied in order to understand the rate‐limiting step at sub‐zero temperatures. It is found that the charge transfer resistance is the largest impedance contributor at low temperatures. However, layered cathodes in aqueous electrolytes do not exhibit a significant increase in the charge‐transfer resistance, or a reduction in the accessible capacity during charging until the temperature is close to the solution freezing point. This is in sharp contrast to their behavior in organic electrolytes that do not support any performance below −20 °C. This different behavior explains the dramatically superior performance of lithium ion battery cathodes in water‐based electrolytes at lower temperatures.
3D routing (2010)

A 3D underlay routing protocol, for scenarios with device and networking technology heterogeneity is presented. It provides mechanisms for the seamless interoperation of dynamic, heterogeneous ad hoc networks. This underlay protocol aggregates and exchanges device context information, such as hardware resources, channel state information and network interfaces to build its routing decisions. 3D Routing considers the following fundamental emergency networking aspects: the bootstrapping process of the network(s) and nodes, the building and spreading of context information between the nodes, and the assignment of roles to particular nodes. To this end, we discuss how these ideas are designed and implemented in order to provide seamless interoperability for this type of emerging networking scenarios.
Data from Development and Validation of a Gene Profile Predicting Benefit of Postmastectomy Radiotherapy in Patients with High-Risk Breast Cancer: A Study of Gene Expression in the DBCG82bc Cohort (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To identify genes predicting benefit of radiotherapy in patients with high-risk breast cancer treated with systemic therapy and randomized to receive or not receive postmastectomy radiotherapy (PMRT).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The study was based on the Danish Breast Cancer Cooperative Group (DBCG82bc) cohort. Gene-expression analysis was performed in a training set of frozen tumor tissue from 191 patients. Genes were identified through the Lasso method with the endpoint being locoregional recurrence (LRR). A weighted gene-expression index (DBCG-RT profile) was calculated and transferred to quantitative real-time PCR (qRT-PCR) in corresponding formalin-fixed, paraffin-embedded (FFPE) samples, before validation in FFPE from 112 additional patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Seven genes were identified, and the derived DBCG-RT profile divided the 191 patients into “high LRR risk” and “low LRR risk” groups. PMRT significantly reduced risk of LRR in “high LRR risk” patients, whereas “low LRR risk” patients showed no additional reduction in LRR rate. Technical transfer of the DBCG-RT profile to FFPE/qRT-PCR was successful, and the predictive impact was successfully validated in another 112 patients.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; A DBCG-RT gene profile was identified and validated, identifying patients with very low risk of LRR and no benefit from PMRT. The profile may provide a method to individualize treatment with PMRT. &lt;i&gt;Clin Cancer Res; 20(20); 5272–80. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis (2007)

The data obtained by TRAC supported the usefulness of focused and intensive transcriptional analysis in monitoring of biotechnical processes providing thus tools for process optimisation purposes.
Use of Corrosion Inhibitors in GMR Biosensor (2010)

Abstract not Available.
Effect of bacterial extracellular polymers on the saturated hydraulic conductivity of sand columns (1992)

Columns were packed with clean quartz sand, sterilized, and inoculated with different strains of bacteria, which multiplied within the sand at the expense of a continuous supply of fresh nutrient medium. The saturated hydraulic conductivity (HCsat) of the sand was monitored over time. Among the four bacterial strains tested, one formed a capsule, one produced slime layers, and two did not produce any detectable exopolymers. The last two strains were nonmucoid variants of the first two. Only one strain, the slime producer, had a large impact on the HCsat. The production of exopolymers had no effect on either cell multiplication within or movement through the sand columns. Therefore, the HCsat reduction observed with the slime producer was tentatively attributed to the obstruction of flow channels with slime. Compared with the results with Arthrobacter sp. strain AK19 used in a previous study, there was a 100-fold increase in detachment from the solid substratum and movement through the sand of the strains used in this study. All strains induced severe clogging when they colonized the inlet chamber of the columns. Under these conditions, the inlet end was covered by a confluent mat with an extremely low HCsat.
RNase III: Genetics and Function; Structure and Mechanism (2013)

RNase III is a global regulator of gene expression in Escherichia coli that is instrumental in the maturation of ribosomal and other structural RNAs. We examine here how RNase III itself is regulated in response to growth and other environmental changes encountered by the cell and how, by binding or processing double-stranded RNA (dsRNA) intermediates, RNase III controls the expression of genes. Recent insight into the mechanism of dsRNA binding and processing, gained from structural studies of RNase III, is reviewed. Structural studies also reveal new cleavage sites in the enzyme that can generate longer 3' overhangs.
Purification, crystallization and preliminary X-ray diffraction study of human ribosomal protein L10 core domain (2007)

Eukaryotic ribosomal protein L10 is an essential component of the large ribosomal subunit, which organizes the architecture of the aminoacyl-tRNA binding site. The human L10 protein is also called the QM protein and consists of 214 amino-acid residues. For crystallization, the L10 core domain (L10CD, Phe34-Glu182) was recombinantly expressed in Escherichia coli and purified to homogeneity. A hexagonal crystal of L10CD was obtained by the sitting-drop vapour-diffusion method. The L10CD crystal diffracted to 2.5 A resolution and belongs to space group P3(1)21 or P3(2)21.
Optical Tuning of Fano Resonances in Dielectric Metasurfaces. (2020)

Abstract not provided.
Automated Luminescence-Based Cytochrome P450 Profiling Using a Simple, Elegant Robotic Platform (2010)

The determination of inhibitory effects that lead compounds have on cytochrome P450 (CYP) enzymes is an important part of today's drug discovery process. Assays can be performed early in the discovery process to predict adverse drug-drug interactions caused by CYP inhibition and to minimize the costs associated with terminating candidates in late stage development or worse, removing a drug from the market after launch. For early discovery work, testing substantial numbers of compounds is desirable, thus automated "mix and read" assays are beneficial. Here, we demonstrate the automation of the CYP profiling process using a simple, yet robust robotic platform. Compound titration, as well as transfer of compounds and assay components was performed by the same automated pipetting system. IC(50)s of small molecule drugs were determined using recombinant CYP enzymes, CYP3A4, -2C9, and -2D6 and luminogenic substrates specific to each. Compounds were profiled against all three enzymes on the same 384-well assay plate.