gebhart/patrepeval huggingface dataset:
Functional Annotation of LigU as a 1,3-Allylic Isomerase during the Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway from the Soil Bacterium <i>Sphingobium</i> sp. SYK-6 (2018)

Sphingobium sp. SYK-6 is a Gram-negative soil bacterium that contributes to the degradation of lignin. Lignin provides structural support and protection to plants as a complex aromatic heteropolymer. The lignin degradation pathway of guaiacyl moieties leads to the intermediate, protocatechuate (PCA), which is further degraded via the 4,5-cleavage pathway in which PCA is ultimately metabolized to pyruvate and oxaloacetate. In this pathway, LigI has been shown to catalyze the hydrolysis of 2-pyrone-4,6-dicarboxylate to (4 E)-oxalomesaconate (OMA). Here we have demonstrated, using <sup>1</sup>H and <sup>13</sup>C nuclear magnetic resonance spectroscopy, that LigU catalyzes the isomerization of the double bond between C4 and C5 in (4 E)-OMA to (3 Z)-2-keto-4-carboxy-3-hexenedioate (KCH), where the double bond has migrated to be between C3 and C4 via a 1,3-allylic isomerization. LigU is most closely related in amino acid sequence to methylaconitate isomerase (PrpF) from Shewanella oneidensis and methylitaconate-Δ-isomerase (Mii) from Eubacterium barkeri. The kinetic constants for the isomerization of OMA to KCH by LigU at pH 8.0 were determined to be 1300 ± 120 s<sup>-1</sup> and (7.7 ± 1.5) × 10<sup>6</sup> M<sup>-1</sup> s<sup>-1</sup> for k<sub>cat</sub> and k<sub>cat</sub>/ K<sub>m</sub>, respectively. We have also shown that the product of the LigU-catalyzed reaction is the preferred substrate for the LigJ hydratase. In this reaction, LigJ catalyzes the hydration of KCH to 4-carboxy-4-hydroxy-2-oxoadipate.
DeepBase: Deep Inspection of Neural Networks (2018)

Although deep learning models perform remarkably well across a range of tasks such as language translation and object recognition, it remains unclear what high-level logic, if any, they follow. Understanding this logic may lead to more transparency, better model design, and faster experimentation. Recent machine learning research has leveraged statistical methods to identify hidden units that behave (e.g., activate) similarly to human understandable logic, but those analyses require considerable manual effort. Our insight is that many of those studies follow a common analysis pattern, which we term Deep Neural Inspection. There is opportunity to provide a declarative abstraction to easily express, execute, and optimize them. This paper describes DeepBase, a system to inspect neural network behaviors through a unified interface. We model logic with user-provided hypothesis functions that annotate the data with high-level labels (e.g., part-of-speech tags, image captions). DeepBase lets users quickly identify individual or groups of units that have strong statistical dependencies with desired hypotheses. We discuss how DeepBase can express existing analyses, propose a set of simple and effective optimizations to speed up a standard Python implementation by up to 72x, and reproduce recent studies from the NLP literature.
Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems (2008)

Cellular uptake of therapeutic oligonucleotides and subsequent intracellular trafficking to their target sites represents the major technical hurdle for the biological effectiveness of these potential drugs. Accordingly, laboratories worldwide focus on the development of suitable delivery systems. Among the different available non-viral systems like cationic polymers, cationic liposomes and polymeric nanoparticles, cell-penetrating peptides (CPPs) represent an attractive concept to bypass the problem of poor membrane permeability of these charged macromolecules. While uptake per se in most cases does not represent the main obstacle of nucleic acid delivery in vitro, it becomes increasingly apparent that intracellular trafficking is the bottleneck. As a consequence, in order to optimize a given delivery system, a side-by-side analysis of nucleic acid cargo internalized and the corresponding biological effect is required to determine the overall efficacy. In this review, we will concentrate on peptide-mediated delivery of siRNAs and steric block oligonucleotides and discuss different methods for quantitative assessment of the amount of cargo taken up and how to correlate those numbers with biological effects by applying easy to handle reporter systems. To illustrate current limitations of non-viral nucleic acid delivery systems, we present own data as an example and discuss options of how to enhance trafficking of molecules entrapped in cellular compartments.
Use of Therapeutic Hypothermia After In-Hospital Cardiac Arrest* (2013)

After in-hospital cardiac arrest, therapeutic hypothermia was used rarely. Once initiated, the target temperature was commonly not achieved. The frequency of use increased over time but remained low. Factors associated with therapeutic hypothermia use included patient age, time and location of occurrence, and type of hospital.
Early Onset Scoliosis (2007)

Thompson, George H. MD; Lenke, Lawrence G. MD; Akbarnia, Behrooz A. MD; McCarthy, Richard E. MD; Campbell, Robert M. Jr. MD Author Information
A Modern Condition Monitoring and Gas Turbine Control System (1984)

For plants with multiple gas turbines, a second generation integrated plant condition monitoring and control system combines prime mover and driven load controls with process controls for the balance of plant. Projected applications include electric power generation, cogeneration, combined cycle plants, and gas compression plants. The system offers redundant distributed control, with diagnostics, repair, and return to original fault tolerance levels. This forms the basis for projections of high control availability. Two data highways drastically reduce plant wiring while improving availability of communications. Color graphic plots of any parameter can be displayed, along with analysis of the condition of the plant components. The system can interface with dispatching telemetery systems.
Multimodal Affective Computing to Enhance the User Experience of Educational Software Applications (2018)

Affective computing is becoming more and more important as it enables to extend the possibilities of computing technologies by incorporating emotions. In fact, the detection of users’ emotions has become one of the most important aspects regarding Affective Computing. In this paper, we present an educational software application that incorporates affective computing by detecting the users’ emotional states to adapt its behaviour to the emotions sensed. This way, we aim at increasing users’ engagement to keep them motivated for longer periods of time, thus improving their learning progress. To prove this, the application has been assessed with real users. The performance of a set of users using the proposed system has been compared with a control group that used the same system without implementing emotion detection. The outcomes of this evaluation have shown that our proposed system, incorporating affective computing, produced better results than the one used by the control group.
5-N-Acetylardeemin, a novel heterocyclic compound which reverses multiple drug resistance in tumor cells. II. Isolation and elucidation of the structure of 5-N-acetylardeemin and two congeners. (1993)

A family of novel compounds has been detected and isolated following an assay for the attenuation of multiple drug resistance in tumor cells from the fermentation broth and mycelia of a strain of Aspergillus fischeri which we have designated var. brasiliensis. The structures of three components were determined employing 1-D and 2-D homonuclear and heteronuclear NMR spectroscopy and mass spectrometry. The structure of 5-N-acetylardeemin was confirmed by single crystal X-ray diffraction. These compounds are most closely structurally related to asperlicin E1).
Human circadian pacemaker is sensitive to light throughout subjective day without evidence of transients (1997)

Fifty-six resetting trials were conducted across the subjective day in 43 young men using a three-cycle bright-light (approximately 10,000 lx). The phase-response curve (PRC) to these trials was assessed for the presence of a "dead zone" of photic insensitivity and was compared with another three-cycle PRC that had used a background of approximately 150 lx. To assess possible transients after the light stimulus, the trials were divided into 43 steady-state trials, which occurred after several baseline days, and 13 consecutive trials, which occurred immediately after a previous resetting trial. We found that 1) bright light induces phase shifts throughout subjective day with no apparent dead zone; 2) there is no evidence of transients in constant routine assessments of the fitted temperature minimum 1-2 days after completion of the resetting stimulus; and 3) the timing of background room light modulates the resetting response to bright light. These data indicate that the human circadian pacemaker is sensitive to light at virtually all circadian phases, implying that the entire 24-h pattern of light exposure contributes to entrainment.
Multi-${V}_{\text{th}}$ Strategies of 7-nm node Nanosheet FETs With Limited Nanosheet Spacing (2018)

In this paper, multi-threshold voltage ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) scheme of 7-nm node nanosheet FETs (NSFETs) with narrow NS spacing were successfully achieved by metal-gate work function (WF) and channel doping ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ch</sub> ) using fully calibrated 3-D TCAD simulations. The limited NS spacing, which allows TiN capping layer only, makes different WF between the edge and the middle part of NS circumference. Unfortunately, this causes non-linear Vth shifts and dc performance degradation as a function of WF due to one-side turn-on phenomena between the edge and the middle part. Furthermore, the fixed WF of TiN capping layer limits Vth shifts toward ultra-low-power applications. To enable multi-Vth of NSFETs, several possible solutions are addressed: changing the Nch and the WF of TiN capping layer. The higher <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ch</sub> enables lower off-state current while 50-nm-wide three-stacked NS decreases dc performance variations effectively. Changing the WF of TiN capping layer can extend <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> margins, but degrade DC performance as a trade-off. Nonetheless, 7-nm node NSFETs adopting these techniques have multi- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> options to satisfy wide ranges from ultra-low-power to high-performance applications.
Do [<i>all</i>]-<i>S</i>,<i>S</i>′-Dioxide Oligothiophenes Show Electronic and Optical Properties of Oligoenes and/or of Oligothiophenes? (2010)

A comprehensive photophysical and spectroscopic (electronic and Raman) study guided by density functional theory, DFT, CIS, and correlated ab initio calculations has been performed on a series of fully oxidized oligothiophenes with variable chain length, and up to four rings. A comparison with the properties of oligoenes and oligothiophenes is proposed. Absorption, fluorescence, lifetimes, flash-photolysis, phosphorescence, two-photon absorption, Raman, resonance Raman, and thermospectroscopy data are collected and interpreted according to the obtained theoretical results. The interest is focused on the ground electronic state and in the low-lying excited electronic states. Full oxygenation of the sulfur atoms of oligothiophenes results in: (i) restricted inter-ring isomerization such as observed from the absorption spectra; (ii) an effective quenching of fluorescence, and (iii) the appearance of dual emission. The emission features are explained by the interference of a dipole-allowed and a dipole-forbidden singlet excited states leading to simultaneous lighting from a local Frenkel and an intramolecular charge transfer photon-releasing configurations. These two excited states contribute to the broadening of the light emission spectrum. These properties highlight the similarity of these samples to that of oligoenes with comparable number of pi-electrons.
Photoinduced Electron Transfer in an Oligodeoxynucleotide Duplex:  Observation of the Electron-Transfer Intermediate (2000)

Kinetics of a photoinduced electron-transfer reaction between phenothiazine (PTZ) and Ru(bpy)2(4-m-4‘-pa-bpy)2+ [bpy = 2,2‘-bipyridine and 4-m-4‘-pa-bpy = 4-methyl-4‘-carbonylpropargylamine] covalently bound to a DNA duplex is investigated by transient absorption spectroscopy. The electron donor, PTZ, is attached to the 5‘ terminal of one oligodeoxynucleotide strand, and the chromophore, Ru(bpy)2(4-m-4‘-pa-bpy)2+, is covalently linked to a uridine of the complementary strand. Electron transfer between the donor, PTZ, and photoexcited acceptor, *Ru(bpy)2(4-m-4‘-pa-bpy)2+, occurs, and the product of the forward electron-transfer reaction, PTZ+•, is observed. The rate of the back electron-transfer reaction (kb = 3.94 × 106 s-1; ΔG ∼ 2.0 eV) is determined by monitoring the decay of the electron-transfer intermediate, PTZ+•, by transient absorption spectroscopy.
The NSR processor (2002)

The NSR processor is a general-purpose computer structured as a collection of self-timed blocks. These blocks operate concurrently and cooperate by communicating with other blocks using self-timed communication protocols. The blocks that make up the NSR processor correspond to standard synchronous pipeline stages such as instruction fetch, instruction decode, execute, memory interface and register file, but each operates concurrently as a separate self-timed process. In addition to being internally self-timed, the units are decoupled through self-timed first-in first-out (FIFO) queues between each of the units which allows a high degree of overlap in instruction execution. Branches, jumps, and memory accesses are also decoupled through the use of additional FIFO queues which can hide the execution latency of these instructions. A prototype implementation of the NSR processor has been constructed using Actel FPGAs (field programmable gate arrays).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Junction size effect on switching current and thermal stability in CoFeB/MgO perpendicular magnetic tunnel junctions (2011)

Junction size dependence of critical current (IC0) for spin transfer torque switching and thermal stability factor (E/kBT) was examined in CoFeB/MgO perpendicular magnetic tunnel junctions (p-MTJs). The IC0 increased with increasing recording layer area (Srec). On the other hand, the E/kBT showed almost constant values even though the Srec was increased from ∼1500 nm2 (44 nmφ) to ∼5000 nm2 (76 nmφ). Both IC0 and E/kBT behavior can be explained with assuming that the nucleation type magnetization reversal takes place in CoFeB/MgO p-MTJs.
Inhibition of SUV39H1 Methyltransferase Activity by DBC1 (2009)

SUV39H1 is a histone H3K9-specific methyltransferase important for heterochromatin formation, regulation of gene expression, and induction of senescence in premalignant cells. SUV39H1 forms a complex with SirT1, and its activity is stimulated by SirT1 binding. Here we present evidence that the product of the DBC1 (deleted in breast cancer 1) gene disrupts the SUV39H1-SirT1 complex. Furthermore, DBC1 binds to the SUV39H1 catalytic domain and inhibits its ability to methylate histone H3 in vitro and in vivo. Knockdown of endogenous DBC1 increased the level of cellular H3K9 methylation. As expected, DBC1 also binds to SirT1 and inhibits the deacetylase activity of SirT1. These results identify DBC1 as a novel cellular inhibitor of SUV39H1 activity. DBC1 may be an important regulator of heterochromatin formation and genomic stability by disrupting the SUV39H1-SirT1 complex and inactivating both enzymes.
Low-power microwave plasma source based on a microstrip split-ring resonator (2003)

Microplasma sources can be integrated into portable devices for applications such as bio-microelectromechanical system sterilization, small-scale materials processing, and microchemical analysis systems. Portable operation, however, limits the amount of power and vacuum levels that can be employed in the plasma source. This paper describes the design and initial characterization of a low-power microwave plasma source based on a microstrip split-ring resonator that is capable of operating at pressures from 0.05 torr (6.7 Pa) up to one atmosphere. The plasma source's microstrip resonator operates at 900 MHz and presents a quality factor of Q=335. Argon and air discharges can be self-started with less than 3 W in a relatively wide pressure range. An ion density of 1.3/spl times/10/sup 11/ cm/sup -3/ in argon at 400 mtorr (53.3 Pa) can be created using only 0.5 W. Atmospheric discharges can be sustained with 0.5 W in argon. This low power allows for portable air-cooled operation. Continuous operation at atmospheric pressure for 24 h in argon at 1 W shows no measurable damage to the source.
Extraction of cartilage protein–polysaccharides with inorganic salt solutions (1973)

1. Bovine nasal cartilage was extracted with inorganic salt solutions of various ionic strengths. The efficiency of extraction of protein-polysaccharide from the tissue was determined for each extraction. The results confirm and enlarge earlier observations (Sajdera & Hascall, 1969). 2. The chloride salts of lanthanide metals extract high yields of protein-polysaccharide from the tissue at much lower concentrations than was achieved with univalent and bivalent salts. 3. The lanthanum salt of extracted protein-polysaccharide precipitates when the concentration of LaCl(3) is decreased. Precipitation is complete in the presence of 0.05m-LaCl(3). This finding is relevant to the interpretation of earlier observations on the effect of LaCl(3) on elastic recovery of articular cartilage after compression (Sokoloff, 1963). 4. A linear relationship was found between the concentration at which a particular salt is maximally effective in solubilizing protein-polysaccharide from the tissue and the enthalpy of hydration of the cation of the salt. On the basis of this relationship a hypothesis is proposed to explain the characteristic protein-polysaccharide-extraction profiles exhibited by inorganic salt solutions.
Missing data techniques for robust speech recognition (2002)

In noisy listening conditions, the information available on which to base speech recognition decisions is necessarily incomplete: some spectro-temporal regions are dominated by other sources. We report on the application of a variety of techniques for missing data in speech recognition. These techniques may be based on marginal distributions or on reconstruction of missing parts of the spectrum. Application of these ideas in the resource management task shows a performance which is robust to random removal of up to 80% of the frequency channels, but falls off rapidly with deletions which more realistically simulate masked speech. We report on a vowel classification experiment designed to isolate some of the RM problems for more detailed exploration. The results of this experiment confirm the general superiority of marginals-based schemes, demonstrate the viability of shared covariance statistics, and suggest several ways in which performance improvements on the larger task may be obtained.
IFN‐α/β enhances BCR‐dependent B cell responses (2002)

Type I interferon (IFN-I) is constitutively produced in the bone marrow (BM), and induced at sites of inflammation and following infection by viruses or microorganisms. We have previously shown that IFN-I regulates the generation and selection of normal B cell populations in the BM. In the present work, we assess the effects of IFN-I on mature B cell function by monitoring the responses of IFN-alpha/beta-treated murine splenic B cells to apoptotic, mitogenic and activating stimuli. A similar analysis is performed on BM mature B cells obtained from wild-type or IFN-I receptor-deficient mice. IFN-alpha/beta is shown to induce B cells to a state of partial activation characterized by the up-regulation of CD69, CD86 and CD25 molecules in the absence of either proliferation or terminal differentiation. B cells treated with IFN-alpha/beta show an increased survival and resistance to Fas-mediated apoptosis. IFN-alpha/beta also enhances B cell responses to BCR ligation such as calcium fluxes, IgM internalization, induction of activation markers and proliferation. These results indicate that in addition to its inhibitory effect on viral replication and T cell apoptosis, IFN-alpha/beta plays an essential role during an inflammatory response by lowering the threshold for B cell induction, thereby promoting fast and polyclonal antibody responses.
Lightweight Dependency Checking for Parallelizing Loops with Non-Deterministic Dependency on GPU (2016)

General-purpose GPUs have been prevalent for a decade. Nevertheless, GPU programming remains an onerous job practically exclusive to veteran developers who must know both domain-specific knowledge and GPU architecture well. Although current parallelizing compilers that automatically parallelize and offload sizable loops onto the GPU have helped in unfettering the power of the GPU with minimal programming effort, there are still a family of loops that carry statically non-deterministic data dependencies and cannot be parallelized. To tackle this issue, we propose two lightweight dependency checking schemes that are very different from existing conservative compilers to assist parallelizing loops with non-deterministic data dependencies. Our schemes feature linear work complexity for memory operations, lower memory consumption compared to previous work, and minimal false positives by leveraging the lockstep execution on the GPU's SIMD lanes. Experiments done using microbenchmarking and real-life applications on the latest advanced AMD discrete GPUs show that our schemes can achieve 2.2 × speedup over existing solutions in dependency-free cases while only taking about 20% of time compared to existing solutions in the case with statically unproven loop-carried dependencies.