gebhart/patrepeval huggingface dataset:
FAST: FPGA-based Acceleration of Genomic Sequence Trimming (2022)

The sheer amount of genomic sequencing data generated daily that requires time-sensitive processing for downstream analysis calls for accelerating the bioinformatics pipelines. Previous studies mainly have attempted accelerating the alignment stage, leaving the other pipeline stages as performance bottlenecks. In this work, we propose the first FPGA-based framework dubbed FAST to accelerate the stages that deal with sequence trimming, in particular adapter and primer removal. FAST supports a comprehensive set of functionalities and is convenient to use by operating on standard genomics data formats. The proposed framework is fully configurable and supports variety of runtime settings. It surpasses the state-of-the-art widely-used adapter trimmer (fastp) by 4.7×–29.4× speed-up, with 10.1×–54.9 less energy, respectively. For clipping primers, which with current existing tool (iVar) accounts for ∼50% of SARS-CoV-2 analysis pipeline, FAST achieves up to 62× speed-up in trimming the virus sequences with a low FPGA resource utilization of 12%.
Industrial Hydrogen Production from Hydrocarbon Fuels and Biomass (2016)

This chapter summarizes the most relevant state-of-the-art technologies for the industrial production of hydrogen from hydrocarbon fuels and biomass. All processes treated in this chapter generate in their first step synthesis gas (syngas), a mixture of hydrogen and carbon monoxide. The latter is further processed by water–gas shift reaction, CO2-removal, CO methanization and/or pressure swing adsorption to finally produce pure hydrogen. While catalytic steam reforming is the key process to transform methane into syngas, non-catalytic partial oxidation processes prevail for coal or biomass. The main reason for using different process options for the different feedstock lies in the sensitivity of the reforming catalyst to sulfur and other impurities that are present in coal and biomass. In contrast to natural gas where desulfurization is technically feasible this option does not exist for solid, heavy and biogenic feedstock making a catalytic treatment of the latter technically impossible.
Lp85 calpain is an enzymatically active rodent-specific isozyme of lens Lp82 (2000)

Lp85 is a newly classified, lens- and rodent-specific, enzymatically active, member of the AX1 (alternative exon 1) subclass of calpains. In conjunction with Lp82 and m-calpain in lens, Lp85 may be responsible for proteolysis during normal lens development and maturation or during cataract formation in young rodents.
A Naphtho-p-quinodimethane Exhibiting Baird’s (Anti)Aromaticity, Broken Symmetry, and Attractive Photoluminescence (2017)

We report a novel reductive desulfurization reaction involving π-acidic naphthalene diimides (NDI) 1 using thionating agents such as Lawesson's reagent. Along with the expected thionated NDI derivatives 2-6, new heterocyclic naphtho-p-quinodimethane compounds 7 depicting broken/reduced symmetry were successfully isolated and fully characterized. Empirical studies and theoretical modeling suggest that 7 was formed via a six-membered ring oxathiaphosphenine intermediate rather than the usual four-membered ring oxathiaphosphetane of 2-6. Aside from the reduced symmetry in 7 as confirmed by single-crystal XRD analysis, we established that the ground state UV-vis absorption of 7 is red-shifted in comparison to the parent NDI 1. This result was expected in the case of thionated polycyclic diimides. However, unusual low energy transitions originate from Baird 4nπ aromaticity of compounds 7 in lieu of the intrinsic Hückel (4n + 2)π aromaticity as encountered in NDI 1. Moreover, complementary theoretical modeling results also corroborate this change in aromaticity of 7. Consequently, photophysical investigations show that, compared to parent NDI 1, 7 can easily access and emit from its T<sub>1</sub> state with a phosphorescence <sup>3</sup>(7a)* lifetime of τ<sub>P</sub> = 395 μs at 77 K indicative of the formation of the corresponding "aromatic triplet" species according to the Baird's rule of aromaticity.
Comparative Studies of Scintillation Properties of Tl-based Crystals (2020)

Tl-based crystalline scintillators, such as Tl 2 ZrCl 6 , TlMgCl 3 , TlCdCl 3 , TlSrCl 3 , and TlBaCl 3, were synthesized by the Bridgeman method. The scintillation light yields of these materials were evaluated under 137 Cs -ray irradiation. The relationship between the photoabsorption peak channel and -ray energy was evaluated using various radioisotopes. Furthermore, the same relationship for energy resolution was also investigated.
Perturbations in travel time and ray geometry due to mesoscale disturbances: A comparison of exact and approximate calculations (1983)

Exact calculations of the changes in eigenray travel time and geometry, due to range-dependent mesoscale disturbances, are compared to three approximations. In the first approximation, the sound-speed perturbation is integrated along the unperturbed path. In the second approximation, the range average of the sound-speed perturbation is integrated along the unperturbed path. The third approximation uses the range-average raytrace to estimate changes of travel time and geometry. Calculations made both for a measured section through a mesoscale eddy and for a simplified model of an eddy (with variable strength, position, and boundary width) suggest that: (i) while none of the approximations tested is uniformly the best, the first approximation is to be preferred ; (ii) the eddy position relative to the ray path is quite significant; and (iii) the exact travel-time perturbations are not sensitive to whether the eddy boundaries are assumed sharp or gradual. For an eddy perturbation of ±9 m/s (±1.9 °C or Rossby wave displacement of about ∓200 m) at 700-m depth, the travel-time approximations are typically in error by 10%–20%. The associated change in turning depth from the unperturbed state to either the perturbed or the range-average state is typically ±100–200 m. These errors are significant, but not large, and suggest that it will be beneficial to iterate linear inverse schemes used to estimate sound-speed perturbations from travel-time perturbations.
3P-081 Creation of TNFR1-selective mutant lymphotoxin alpha using phage display system(The 46th Annual Meeting of the Biophysical Society of Japan) (2008)

AnalytsibandprediLtionefpretem"olub]1ityShmLhT Ibrose(iV Ktyenebu }2)kotafly "laeki Ci)shtmaC2) lhshihumt KL-tamuraav thhr"
Percolated (yellow) and discrete (colored by size) clusters of ions in different types of ionic polymers. (2020)

Abstract not provided.
A Case of Myoclonus–Dystonia Responding to Low-frequency Pallidal Stimulation (2017)

Low-frequency pallidal stimulation provides an effective means of treating various dystonias, regardless of genetic status, as in our case, as it provides increased programming options with fewer adverse effects.
Electrochemical Investigation of Quaternary Ammonium/Aluminum Chloride Ionic Liquids (2004)

Quaternary ammonium salts have been studied as ionic liquids for electrochemical applications, including sodium batteries. Mixtures of benzyltrialkylammonium chlorides with chloroaluminate formed ionic liquids near room temperature. The maximum coulombic efficiency for the reduction and re-oxidation of sodium ions with benzyltriethylammonium chloride ionic liquid was over 91%. The self-discharge current for a sodium electrode in this ionic liquid was 32.7 and 18 μA/cm2 by chronopotentiometry at tungsten electrodes at 6.37 and 2.55 mA/cm2, respectively. These are comparable to values in 1-methyl-3-propylimidazolium chloride melt. Issues with the coulombic efficiencies and the self-discharge currents are discussed. © 2004 The Electrochemical Society. All rights reserved.
Effect of Electrode Material on Resistive Switching Characteristics in TaON Nonvolatile Memory Devices (2013)

The devices composed of Pt/TaON/TiN reveal bipolar switching behavior that shows excellent resistance ratio of 10 2 with operations over 100 DC cycles. The formation/disruption of conducting filaments by oxygen anions migration near/at the TiN electrode was applied to explain the switching behavior. In comparison with Pt/TaON/TiN device, the Cu/TaON/TiN device exhibits reversed bipolar resistive switching characteristic. The switching mechanism of Cu/TaON/TiN device is regarded as the Cu redox reaction and migration in the TaON film. Furthermore, the setting voltage of the Cu/TaON/TiN device is lower than that of the Pt/TaON/TiN device due to the confined conduction path by Cu filaments.
On LTE performance trade-off between connected and idle states with always-on type applications (2012)

In cellular networks it is envisioned an explosion of diverse data applications running in smart phones, which could increase significantly not only user plane but also control plane load in the network. Smart phones and their always-on applications introduce several challenges: From the network perspective, an increased amount of UEs/applications can increase the signaling load due to frequent state transitions and handover signaling. From the UE perspective, challenges of power consumption are evident, since UE would increasingly be in connected state. In this article we study the trade-off between releasing the UE into idle state vs. keeping the UE in connected state, in a LTE system. The results indicate that optimum performance can be achieved using UE specific RRC release timer and DRX configurations by taking advantage of traffic characteristics and UE mobility.
Modeling of thermo-mechanical behavior of Ti-Ni shape memory alloy foils embedded in carbon fiber reinforced plastic laminates (2005)

Ti-Ni shape memory alloy (SMA) foils are embedded into carbon fiber reinforced plastic (CFRP) cross-ply laminates in order to suppress the occurrence and progress of the transverse cracks in the laminates. When the pre-strained SMA foil is heated, the shape memory effect produces appropriate recovery compressive stress in the direction to suppress transverse cracks. However, Ti-Ni SMA foil has these specific characteristics due to the existence of a rhombohedral phase (R-phase). Thus, in this research, in order to use this SMA foil as an actuator, an extended Brinson model was proposed to clarify complicated behaviors of SMA. Then, for the determination of the parameters in the constitutive equation in this model, experimental tests were performed for the SMA foils. Using this model, several simulations were conducted and compared with experimental results. The agreement indicated that this model could express the thermo-mechanical behavior of the Ti-Ni SMA foil adequately. Finally, the behavior of the SMA foil during the CFRP manufacturing process was calculated on the basis of this model. The calculation results proved that the recovery stress already existed after the manufacturing process and the embedment of 4% pre-strained SMA into CFRP cross-ply laminate had the effect of suppressing the occurrence of transverse cracks.
Rate-Splitting Multiple Access for Multi-antenna Downlink Communication Systems: Spectral and Energy Efficiency Tradeoff (2020)

Rate-splitting (RS) has recently been recognized as a promising physical-layer technique for multi-antenna broadcast channels (BC). Due to its ability to partially decode the interference and partially treat the remaining interference as noise, RS is an enabler for a powerful multiple access, namely rate-splitting multiple access (RSMA), that has been shown to achieve higher spectral efficiency (SE) and energy efficiency (EE) than both space division multiple access (SDMA) and non-orthogonal multiple access (NOMA) in a wide range of user deployments and network loads. As SE maximization and EE maximization are two conflicting objectives, the study of the tradeoff between the two criteria is of particular interest. In this work, we address the SE-EE tradeoff by studying the joint SE and EE maximization problem of RSMA in multiple input single output (MISO) BC with rate-dependent circuit power consumption at the transmitter. To tackle the challenges coming from multiple objective functions and rate-dependent circuit power consumption, we first propose two methods to transform the original problem into a single-objective problem, namely, weighted-sum method and weighted-power method. A successive convex approximation (SCA)-based algorithm is then proposed to jointly optimize the precoders and RS message split of the transformed problem. Numerical results show that our algorithm converges much faster than existing algorithms. In addition, the performance of RS is superior to or equal to non-RS strategy in terms of both SE and EE and their tradeoff.
Integration of Bass Enhancement and Active Noise Control System in Automobile Cabin (2008)

With the advancement of digital signal processing technologies, consumers are more concerned with the quality of multimedia entertainment in automobiles. In order to meet this demand, an audio enhancement system is needed to improve bass reproduction and cancel engine noise in the cabins. This paper presents an integrated active noise control system that is based on frequency‐sampling filters to track and extract the bass information from the audio signal, and a multifrequency active noise equalizer to tune the low‐frequency engine harmonics to enhance the bass reproduction. In the noise cancellation mode, a maximum of 3 dB bass enhancement can be achieved with significant noise suppression, while higher bass enhancement can be achieved in the bass enhance mode. The results show that the proposed system is effective for solving both the bass audio reproduction and the noise control problems in automobile cabins.
Improving efficiency of dye-sensitized solar cells (DSCs) with energy relay dyes and light trapping (2010)

Cadaveric canine intestinal specimens tested immediately after collection or after chilling for 24 hours should be recommended for ex vivo burst pressure assessment in dogs. Additional studies to evaluate loss in testing viability of chilled intestinal specimens are warranted to help govern experimental methodologies.
Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence (2014)

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence-rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
Patterning performance of hyper NA immersion lithography for 32nm node logic process (2008)

We have developed the lithography process for 32nm node logic devices under the 1.35NA single-exposure conditions. In low-k1 generation, we have to consider the minimum pitch resolution and two-dimensional pattern fidelity at the same time. Although strong RET (Resonance Enhancement Technique) can achieve the high image contrast, it has negative effects like line end shortening and resist pattern collapse. Moderate RET such as annular illumination can combine the minimum pitch resolution and two-dimensional pattern fidelity with hyper NA illumination condition. The simulation and experimental results indicate that the minimum pitches should be determined as 100nm for line pattern and 110nm for contact hole pattern, respectively. The isolated contact hole needs SRAF and focus drift exposure to improve DOF. Embedded SRAM cell of 0.125&mgr;m2 area is clearly resolved across exposure and focus window.
ChemInform Abstract: Catalysis Using Multifunctional Organosiliceous Hybrid Materials (2013)

Abstract Review: 82 refs.
Measurement of Parts per Million Level Gaseous Concentration of Hydrogen Sulfide by Ultraviolet Spectroscopy using 1,1,1,5,5,5-Hexafluoropentan-2,4-dione as a Derivative by Reaction of Cu(hfac)(1,5-Cyclooctadiene) (2009)

Hydrogen sulfide reacts rapidly and quantitatively at ppm levels with cycloocta-1,5-diene-1,1,1,5,5,5-hexafluoropentan-2,4-dionatocopper(I) (Cu(hfac)(COD)) to yield 1,1,1,5,5,5-hexafluoropentan-2,4-dione (Hhfac) having a strong ultraviolet absorption at 268 nm, and which can be used without interference as a derivative in the continuous, fast online spectroscopic determination of the H(2)S concentration. The analytical method has excellent selectivity and can be used in the presence of N(2), H(2), CO, COS, SO(2), moist air, CH(3)OH, C(2)H(4), C(6)H(6), and light alkanes including fuel gases. Using a standard spectrometer, the level of detection is about 10 ppb. Concentrations down to 1 ppm H(2)S can be analyzed readily, usually with an error in the range 0 to -7% dependent largely on the sorption characteristics of the apparatus. These are systematic errors due to adsorption; however, the analytical apparatus was very stable, and relative standard deviations as low as 0.1% of the mean can be obtained. The method can also be applied to the analysis of methanethiol.
Effects of interconfiguration fluctuations upon the far-infrared and dc-transport properties of the thulium-chalcogenides (1977)

The far-infrared reflectivity and dc resistivity of $\mathrm{Tm}X(X=\mathrm{T}\mathrm{e},\phantom{\rule{0ex}{0ex}}\mathrm{S}\mathrm{e},\phantom{\rule{0ex}{0ex}}\mathrm{S})$ were measured as a function of temperature from 1 K to room temperature; the Hall constant of TmSe was also measured. Most of the properties of TmTe were semiconductorlike with a reststrahlen band at 120 ${\mathrm{cm}}^{\ensuremath{-}1}$. However, the low-temperature resistivity could not be fit by a thermal activation model and weak, sample-dependent structure appeared in the reflectivity above the reststrahlen band above 2.5 K. Interconfiguration fluctuations are suggested as the cause. The reflectivities of TmSe and TmS are much more metallic; TmS shows a possible weak reststrahlen band at \ensuremath{\sim} 190 ${\mathrm{cm}}^{\ensuremath{-}1}$. The dc transport properties are not like those of a simple metal in their temperature dependences, but may be explained by Kondo scattering from ${\mathrm{Tm}}^{3+}$ ions in the temperature range studied.
Association Study of the Chromosomal Region Containing the FCER2 Gene Suggests It Has a Regulatory Role in Atopic Disorders (2000)

On the basis of studies with animal models, the gene for the low-affinity receptor for immunoglobulin E (IgE) (FCER2, CD23) has been implicated as a candidate for IgE-mediated allergic diseases and bronchial hyperreactivity, or related traits. Given evidence for genetic complexity in atopic disorders, we sought to study two European subpopulations, Finnish and Catalonian. We studied three phenotypic markers: (1) total serum IgE level; (2) asthma; and (3) specific IgE level for a mixture of the most common aeroallergens in Finland. Altogether, eight polymorphic markers spanning a region of 10 cM around the FCER2 gene on chromosome 19p13 were analyzed in 124 families. The physical order of the markers and the location of the FCER2 gene were confirmed by using radiation hybrids. The allele and haplotype association study showed a suggestive haplotype association (significance of p </= 0.03 based on a permutation test) for a high serum IgE response. In a subset of chromosomes segregating with asthma in families with two or more affected members, a single haplotype was found to be highly enriched (p = 8.3 x 10(-6)). However, sequence polymorphisms, which would verify structural differences in the FCER2 gene, were not detected in the coding region of the receptor. Our results suggest that chromosome 19p13 might harbor a genetic determinant of IgE-related traits. Studies in other population samples are needed to verify this finding.
Fractional-N frequency synthesizer design at the transfer function level using a direct closed loop realization algorithm (2003)

A new methodology for designing fractional-N frequency synthesizers and other phase locked loop (PLL) circuits is presented. The approach achieves direct realization of the desired closed loop PLL transfer function given a set of user-specified parameters and automatically calculates the corresponding open loop PLL parameters. The algorithm also accomodates nonidealities such as parasitic poles and zeros. The entire methodology has been implemented in a GUI-based software package, which is used to verify the approach through comparison of the calculated and simulated dynamic and noise performance of a third order fractional-N frequency synthesizer.
Molecular features of primary mediastinal B‐cell lymphoma: involvement of p16INK4A, p53 and c‐myc (1999)

Primary mediastinal B-cell lymphoma (PMBL) shows chromosome 9p anomalies in 50% of cases. Based on reports that p16INK4A gene, located on this chromosomal arm, is frequently altered in aggressive lymphomas, we analysed for alterations of this gene in 27 cases of PMBL, which were part of a series of 32 PMBL cases that have been characterized for alterations in c-myc, p53, N-ras, bcl-1, bcl-2, bcl-6 and for Epstein-Barr virus (EBV) infection. Four cases showed p16INK4A gene anomalies, including three with promoter methylation and one homozygous deletion. Eight PMBLs showed c-myc rearrangements. Three additional cases showed sequence variations in the c-myc P2 promoter, two of which consisted of the same germline variation involving a novel polymorphic XhoI site. Four tumours contained p53 gene mutations and three had clonal EBV infection. One case had a bcl-6 rearrangement. In conclusion, our study shows that p16INK4, c-myc and p53 alterations occur in 15%, 25% and 13% of PMBLs, respectively. EBV monoclonality was found in 9% of cases, whereas no abnormality was detected in bcl-1, bcl-2 and N-ras. Thus, none of the common genetic aberrations seen in other types of non-Hodgkin's lymphomas appears to be stringently involved in the pathogenesis of this unique lymphoma type.
Haptic Feedback Enhances Force Skill Learning (2007)

This paper explores the use of haptic feedback to teach an abstract motor skill that requires recalling a sequence of forces. Participants are guided along a trajectory and are asked to learn a sequence of one-dimensional forces via three paradigms: haptic training, visual training, or combined visuohaptic training. The extent of learning is measured by accuracy of force recall. We find that recall following visuohaptic training is significantly more accurate than recall following visual or haptic training alone, although haptic training alone is inferior to visual training alone. This suggests that in conjunction with visual feedback, haptic training may be an effective tool for teaching sensorimotor skills that have a force-sensitive component to them, such as surgery. We also present a dynamic programming paradigm to align and compare spatiotemporal haptic trajectories