gebhart/patrepeval huggingface dataset:
Nucleoside Antiviral Agents for HCV (2020)

Hepatitis C virus (HCV) persists asymptomatically in the majority of infected individuals and is strongly associated with chronic hepatitis, hepatic steatosis, cirrhosis, and hepatocellular carcinoma. Unlike interferon or ribavirin, direct-acting antivirals specifically target nonstructural proteins, such as the NS3/NS4A serine protease, the nonstructural protein 5A (NS5A), or the HCV polymerase (NS5B), leading to inhibition of HCV RNA replication and infection. NS5A has been implicated as a modulator of critical viral functions including facilitation of viral RNA replication, virus assembly, transport and release, as well as regulator of the antiviral interferon response. Clinically relevant NS5B inhibitors are classified as non-nucleoside inhibitors and nucleotide inhibitors that act at distinct stages of RNA synthesis. Finally, sofosbuvir and other nucleoside HCV polymerase inhibitors have been shown to inhibit replication of various viruses such as zika, dengue, and norovirus.
Associations between complications and health‐related quality of life in individuals with diabetes (2012)

Quality of life in patients with diabetes is affected mainly by presence of complications, and not diabetes per se. Peripheral neuropathy was associated with the greatest reduction in quality of life. Improved management to prevent or delay onset of complications may reduce the effect on quality of life in patients with diabetes.
Clusterin is not essential for androgen-regulated involution and regeneration of the normal mouse prostate (2006)

Clusterin is not critical for normal prostate development or androgen-regulated involution and regrowth of the mouse prostate gland, suggesting that clusterin may have distinct functions in malignant versus normal prostatic epithelial cells.
Towards Wave-Domain Adaptive Filtering for Multichannel Acoustic Echo Cancellation in Higher-Order Ambisonics Systems (2021)

The concept of wave-domain adaptive filtering (WDAF) is a powerful technique in the field of massive-multichannel acoustic system identification. By using fundamental solutions of the wave-equation for signal representation the wave-domain system model exhibits desirable properties in suitable setups. This allows efficient approximations of the model or can improve the convergence of an adaptive filter. The applicability of the WDAF technique to higher-order Ambisonics systems and three-dimensional wave fields was often mentioned in literature, but conducted experiments were always limited to two-dimensional setups. This paper investigates the WDAF technique in a new context of practical Ambisonics systems, aiming at acoustic echo cancellation for immersive telepresence systems. Experiments are conducted with simulated and measured room impulse responses in ideal and non-ideal loudspeaker setups. Furthermore different Ambisonics decoding methods are investigated and compared. The transferability of previously proposed WDAF approaches is examined and the results show the general applicability of these approaches, but with some limitations for real-world problems.
A 28-GHz CMOS Phased-Array Beamformer Supporting Dual-Polarized MIMO with Cross-Polarization Leakage Cancellation (2020)

This paper introduces a CMOS 28-GHz phased-array beamformer chip supporting dual-polarized MIMO (DP-MIMO) operation. A cross-pol. leakage cancellation technique is implemented for improving the degraded cross-pol. isolation caused by the antennas and the propagation. More than 40-dB cross-pol. isolation is maintained along the TX array to the RX array. This work also adopts a compact neutralized bidirectional architecture to minimize the chip manufacturing cost. The bi-directional PA-LNA realizes a peak PAE of 33.1% in PA mode and an NF of 5.4dB in LNA mode. With the improved cross-pol. isolation, 2×2 DP-MIMO communication with two 5G NR OFDMA-mode streams in 256QAM is achieved in the OTA measurement. The corresponding TX-to-RX EVM is 3.3%. The power consumptions for each antenna path are 181mW in TX mode and 88mW in RX mode.
Biomolecular Engineering of Biosensing Molecules &mdash;The Challenges in Creating Sensing Molecules for Glycated Protein Biosensing&mdash; (2012)

Ever since Clark and Lyons introduced the first enzyme sensor five decades ago, extensive studies have been carried out to develop a range of biosensors employing the combination of biosensing molecules and transducers. The evolution from the early generation through to the current generation of biosensor research has witnessed the appearance of a number of very diversified biosensing molecules. In this review, we summarize the biomolecular engineering technology underlying the development of biosensing molecules. Among the various biosensor research targets, we focused on the development of glycated protein sensing technology. Glycated protein sensing is one of the most emergent and focused on technology in the field of diabetes diagnosis. We especially focused on the recent advances in the development of fructosyl amino acid/fructosyl peptide oxidases, which are the key enzymes in the biochemical measurement of glycated proteins, as the representative biosensing molecules to acknowledge the rewards of the current advanced biomolecular engineering technology.
Short Tandem Repeat stutter_model_inferred from direct measurement of in vitro stutter noise (2016)

Abstract Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise during in vitro amplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naïve STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.
Enhancement of Third Order Nonlinearity Calculated for Two-Dimensional Photonic Crystal (2003)

Using the finite difference time domain method, we calculated light propagation characteristics in a two dimensional photonic crystal, which is composed of triangular lattice airholes in a third-order nonlinear medium. The results showed the characteristic change of the transmission spectrum resulting in the strong saturation of the response, and the sufficiently low transmission loss with the help of projection-type airholes at input and output interfaces. The three-dimensional calculation also indicated the low transmission loss obtained in a realistic photonic crystal slab. Such characteristics are expected in a continuous spectral range near the Γ point of the second photonic band, owing to an overlap of two bands, which is unique in the two-dimensional lattice. It is applicable for an all-optical switch, an optical power limiter, a pulse reshaping device, and so forth.
Identification of genetic heterogeneity in the Cryptosporidium parvum ribosomal repeat (1996)

Oocysts of the protozoan parasite Cryptosporidium parvum are found in most surface waters and can contaminate municipal water supplies, as demonstrated by recent outbreaks of cryptosporidiosis. A method capable of fingerprinting C. parvum isolates from the environment would facilitate the study of epidemiology and transmission cycles and aid in the implementation of preventive measures to reduce water contamination by oocytes. In this study, we report polymorphism in C. parvum isolates on the basis of analysis of random amplified polymorphic DNA and nucleotide sequences in a region of the 18S rRNA and the internal transcribed spacer 1. Isolate-specific primers for these two regions were designed, and PCR tests capable of discriminating between isolates were developed. In both PCR assays, the five C. parvum isolates analyzed segregated into two subgroups. One group consisted of isolates that originated directly from human patients, and the other group had various host origins and had been propagated in laboratory animals. These results demonstrate the feasibility of distinguishing C. parvum isolates by sequence-specific PCR tests.
Portable and scalable FPGA-based acceleration of a direct linear system solver (2008)

FPGAs are becoming an attractive platform for accelerating many computations including scientific applications. However, their adoption has been limited by the large development cost and short life span of FPGA designs. We believe that FPGA-based scientific computation would become far more practical if there were hardware libraries that were portable to any FPGA with performance that could scale with the resources of the FPGA. To illustrate this idea we have implemented one common supercomputing library function: the LU factorization method for solving linear systems. This paper discusses issues in making the design both portable and scalable. The design is automatically generated to match the FPGA’s capabilities and external memory through the use of parameters. We compared the performance of the design on the FPGA to a single processor core and found that it performs 2.2 times faster, and that the energy dissipated per computation is a factor 5 times less.
Clinical Significance of Intermediate-Density Lipoprotein Cholesterol Determination as a Predictor for Coronary Heart Disease Risk in Middle-Aged Men (2021)

<b>Background:</b> Not only low-density lipoprotein (LDL) cholesterol but also non-high-density lipoprotein cholesterol (non-HDL-C), very low-density lipoprotein (VLDL) cholesterol (VLDL-C), and intermediate-density lipoprotein (IDL) cholesterol (IDL-C) are reported to be significant risk markers for coronary heart disease (CHD). We reported the relevance of IDL-C to Framingham risk score (F-score), but the present study addressed the relevance of IDL-C to Suita score (S-score), a risk score for coronary heart disease (CHD) developed for the Japanese individuals in addition to F-score. <b>Methods:</b> The cholesterol levels of lipoproteins, including triglyceride (TG)-rich lipoproteins (IDL and VLDL), were measured by an anion exchange high-performance liquid chromatography (AEX-HPLC). This study enrolled 476 men, aged mean 51 years and free of CHD and stroke. <b>Results:</b> Non-HDL-C, IDL-C, and VLDL-C significantly correlated with F-score and S-score. In the multiple stepwise regression analysis, IDL-C as well as body mass index (BMI) significantly correlated with both F-score and S-score in both the total subjects and the subjects without drug therapy. The multivariate logistic analysis with the model composed of BMI and IDL-C as the predictor variables demonstrated that 1 SD increase in IDL-C was an independent predictor for 10-year CHD risk >10% of F-score (<i>OR</i> 1.534, 95% CI 1.266-1.859, <i>p</i> < 0001) and that of S-score (<i>OR</i> 1.372, 95% CI 1.130-1.667, <i>p</i> = 0.0014) in the total subjects. Even in the subjects without the drug therapy, the increased IDL-C, as well as BMI, were significant predictors for 10-year CHD risk >10% of S-score as well as F-score. <b>Conclusion:</b> These results suggest the significant relevance of the increased IDL-C for CHD risk scores in middle-aged men free of CHD and stroke. Further investigations are needed in women and elderly subjects.
Increased Levels of Soluble LR11 in Cerebrospinal Fluid of Patients with Alzheimer Disease (2010)

These results suggest that the quantification of CSF sLR11 may serve as a biomarker of AD, although the diagnostic value for individual patients is limited. An elevated CSF sLR11 level in AD patients may be relevant to AD pathogenesis.
Making biological knowledge useful for humans and machines (2022)

Standardized nomenclature for genes, gene products and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are FAIR (Findable, Accessible, Interoperable, and Reusable). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccahromyces pombe Model Organism Database. This update introduces nomenclature guidelines for non-coding RNA genes, following those set forth by the HUGO Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.
Rectangular 1014 element matrix array for transperineal imaging (2021)

We developed a 2D matrix array for later use in transperineal volumetric ultrasound imaging in the context of radiation dose monitoring. In the envisioned applications, radiation-sensitive microbubbles shall induce changes in the (spectral) reflection behavior of ultrasonic waves. To optimize both amplitude and spectral sensitivity, we developed an array with a footprint adapted on the transperineal window and focused on a high bandwidth. Our 1014 element rectangular footprint array ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$26\times 39$</tex> ) was characterized on phantoms and allows resolutions below 1 mm (FWHM of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$910\ \mu\mathrm{m}$</tex> ) even with the simplest possible reconstruction scheme (single transmit 0° plan wave) and DAS beamforming. To allow advanced research on volumetric beamforming schemes, 1 to 1 wiring of all elements to TX/RX channels of our 1024ch electronics has been implemented, introducing some significant challenges to the contacting scheme.
Resting- and postexercise-ECG findings in an adult Lapp population. (1983)

Resting electrocardiograms were recorded in 412 and postexercise-ECGs in 186 Lapp men and women over the age of 40. Abnormalities in the resting-ECG suggestive of old myocardial infarction by the Minnesota code were found in 7% of the men and in 1% of the women. ST-depression compatible with myocardial ischaemia in the resting-ECG were found in 3% of men aged 40-49 years and in 5% of women of the same age; and increased with age up to 11% and 24% in men and women, respectively, over the age of 60. Postexercise ST-depressions of "ischemic type" were found in 18% of the men and in 13% of the women, but there was no clear age dependence. The frequency of high amplitude R-waves of the left type was high compared with most normal populations, especially in men (29%). These prevalences were very similar to those previously reported in a Finnish population.
Design of selective divalent chain transfer agents for coordinative chain transfer polymerization of ethylene and its copolymerization with butadiene (2022)

A selective divalent chain transfer agent is designed to exclusively lead to polyolefin chain growth on a divalent pentanediyl moiety via coordinative chain transfer polymerization (CCTP).
Efficient Bit-Channel Reliability Computation for Multi-Mode Polar Code\n Encoders and Decoders (2017)

Polar codes are a family of capacity-achieving error-correcting codes, and\nthey have been selected as part of the next generation wireless communication\nstandard. Each polar code bit-channel is assigned a reliability value, used to\ndetermine which bits transmit information and which parity. Relative\nreliabilities need to be known by both encoders and decoders: in case of\nmulti-mode systems, where multiple code lengths and code rates are supported,\nthe storage of relative reliabilities can lead to high implementation\ncomplexity. In this work, observe patterns among code reliabilities. We propose\nan approximate computation technique to easily represent the reliabilities of\nmultiple codes, through a limited set of variables and update rules. The\nproposed method allows to tune the trade-off between reliability accuracy and\nimplementation complexity. An approximate computation architecture for encoders\nand decoders is designed and implemented, showing 50.7% less area occupation\nthan storage-based solutions, with less than 0.05 dB error correction\nperformance degradation.\n
Synthesis of 3β‐(4‐[125I]iodophenyl)tropane‐2‐β‐pyrrolidine carboxamide ([125I]RTI‐229) (1999)

A WIN 35,065-2 analog, 3β-(4-iodophenyl)tropane-2β-pyrrolidine carboxamide (RTI-229), has been radiolabelled with iodine-125 by radioiododestannylation of the corresponding trimethyltin derivative using carrier-free sodium iodide-125 as the isotope source. Purification by reversed-phase HPLC gives [125I]RTI-229 in good yield (89·4%) with high radiochemical purity (>99%) and high specific activity (2125 mCi/μmol, 78·6 GBq/μmol, based on the specific activity of the Na125I used). Copyright © 1999 John Wiley & Sons, Ltd.
Toughness of welded joint and crack arrestability of base plate in ultra low C-2.5%Ni steel produced by thermo-mechanical control process. (1987)

Using 2.5% Ni steel plates for LPG storage tanks, the effect of C content on crack initiation toughness of the fusion boundary of the MIG welded joint and the effects of processing conditions in controlled rolling and accelerated cooling on mechanical properties of base plate were investigated.The experimental results indicated that the minimum crack initiation toughness of the welded joint was improved by decreasing C content. Furthermore, the crack arrestability of the 0.01%C-2.5%Ni steel plate was improved by reducing ferrite grain diameter and decreasing solute Nb. The ferrite grain was refined by lowering the slab repeating temperature and increasing the cooling rate after hot rolling. Refinement of ferrite grain made by increasing the cooling rate after hot rolling improved carck arrestability, even though solute Nb increased. On the basis of these experimental results, a 0.01%C-2.5%Ni steel plate with good crack arrestability in base plate and also good initiation toughness in welded joint was produced for LPG storage tanks using the thermo-mechanical control process.
Search for high-mass diphoton resonances in proton–proton collisions at 13 TeV and combination with 8 TeV search (2017)

A search for the resonant production of high-mass photon pairs is presented. The search focuses on spin-0 and spin-2 resonances with masses between 0.5 and 4.5 TeV, and with widths, relative to the mass, between 1.4×10−4 and 5.6×10−2. The data sample corresponds to an integrated luminosity of 12.9fb−1 of proton–proton collisions collected with the CMS detector in 2016 at a center-of-mass energy of 13 TeV. No significant excess is observed relative to the standard model expectation. The results of the search are combined statistically with those previously obtained in 2012 and 2015 at s=8 and 13 TeV, respectively, corresponding to integrated luminosities of 19.7 and 3.3fb−1, to derive exclusion limits on scalar resonances produced through gluon–gluon fusion, and on Randall–Sundrum gravitons. The lower mass limits for Randall–Sundrum gravitons range from 1.95 to 4.45 TeV for coupling parameters between 0.01 and 0.2. These are the most stringent limits on Randall–Sundrum graviton production to date.
Electron backscatter diffraction applied to lithium sheets prepared by broad ion beam milling (2014)

Due to its very low hardness and atomic number, pure lithium cannot be prepared by conventional methods prior to scanning electron microscopy analysis. Here, we report on the characterization of pure lithium metallic sheets used as base electrodes in the lithium-ion battery technology using electron backscatter diffraction (EBSD) and X-ray microanalysis using energy dispersive spectroscopy (EDS) after the sheet surface was polished by broad argon ion milling (IM). No grinding and polishing were necessary to achieve the sufficiently damage free necessary for surface analysis. Based on EDS results the impurities could be characterized and EBSD revealed the microsctructure and microtexture of this material with accuracy. The beam damage and oxidation/hydration resulting from the intensive use of IM and the transfer of the sample into the microscope chamber was estimated to be <50 nm. Despite the fact that the IM process generates an increase of temperature at the specimen surface, it was assumed that the milling parameters were sufficient to minimize the heating effect on the surface temperature. However, a cryo-stage should be used if available during milling to guaranty a heating artefact free surface after the milling process.
<title>Accuracy of rendered depth in head-mounted displays: role of eyepoint location</title> (2000)

Eyetracking is typically not available in head-mounted displays, and eye motions are thus simply ignored when 2D virtual images are displayed, giving rise to rendered depth errors in generating stereoscopic image pairs in head- mounted displays. We present an investigation and quantification of rendered depth errors linked to natural eye movements in binocular head-mounted displays, or Albertian errors, for three possible eyepoint locations: the center of the entrance pupil, the nodal point, and the center of rotation. Theoretical computations based on the intersection of chief rays concluded that, while the center of rotation yields minimal depth errors if no eyetracking is used, rendered angular errors may in some cases be significant (i.e. up to six degrees). Based on the analysis presented in this paper, we suggest that the center of entrance pupil be chosen for far field applications. The center of rotation of the eye should be chosen for near field applications under the assumption that they emphasize position accuracy versus angular accuracy. Preventing or minimizing rendered depth errors may be required for some high accuracy tasks related, for example, to medical or military visualization.
Tapered and aperiodic silicon nanostructures with very low reflectance for solar hydrogen evolution (2012)

We introduce a facile method to generate silicon nanostructures with superior anti-reflectance (AR) properties. These nanostructures possess the ideal tapered structure and aperiodic distribution required for low reflectance over a broad range of wavelengths. Consideration of effective medium theories might explain the behavior between structure and reflectance, and suggest the advantage of aperiodicity in affording the material broadband AR properties. We then implemented these nanostructures as photocathodes to drive the hydrogen evolution reaction in AM 1.5 illumination. These nanostructures showed a significant improvement in photoelectrochemical performance over their planar counterpart, with the best performances corresponding to nanostructures which possessed AR properties matching the solar spectrum output.