gebhart/patrepeval huggingface dataset:
Complex assembly mechanism and an RNA‐binding mode of the human p14‐SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses (2007)

The spliceosomal protein p14, a component of the SF3b complex in the U2 small nuclear ribonucleoprotein (snRNP), is essential for the U2 snRNP to recognize the branch site adenosine. The elucidation of the dynamic process of the splicing machinery rearrangement awaited the solution structural information. We identified a suitable complex of human p14 and the SF3b155 fragment for the determination of its solution structure by NMR. In addition to the overall structure of the complex, which was recently reported in a crystallographic study (typical RNA recognition motif fold beta1-alpha1-beta2-beta3-alpha2-beta4 of p14, and alphaA-betaA fold of the SF3b155 fragment), we identified three important features revealed by the NMR solution structure. First, the C-terminal extension and the nuclear localization signal of p14 (alpha3 and alpha4 in the crystal structure, respectively) were dispensable for the complex formation. Second, the proline-rich segment of SF3b155, following betaA, closely approaches p14. Third, interestingly, the beta1-alpha1 loop and the alpha2-beta4 beta-hairpin form a positively charged groove. Extensive mutagenesis analyses revealed the functional relevance of the residues involved in the protein-protein interactions: two aromatic residues of SF3b155 (Phe408 and Tyr412) play crucial roles in the complex formation, and two hydrophobic residues (Val414 and Leu415) in SF3b 155 serve as an anchor for the complex formation, by cooperating with the aromatic residues. These findings clearly led to the conclusion that SFb155 binds to p14 with three contact points, involving Phe408, Tyr412, and Val414/Leu415. Furthermore, to dissect the interactions between p14 and the branch site RNA, we performed chemical-shift-perturbation experiments, not only for the main-chain but also for the side-chain resonances, for several p14-SF3b155 complex constructs upon binding to RNA. These analyses identified a positively charged groove and the C-terminal extension of p14 as RNA-binding sites. Strikingly, an aromatic residue in the beta1-alpha1 loop, Tyr28, and a positively charged residue in the alpha2-beta4 beta-hairpin, Agr85, are critical for the RNA-binding activity of the positively charged groove. The Tyr28Ala and Arg85Ala point mutants and a deletion mutant of the C-terminal extension clearly revealed that their RNA binding activities were independent of each other. Collectively, this study provides details for the protein-recognition mode of p14 and insight into the branch site recognition.
Electromigration Performance Improvement of Metal Heaters for Si Photonic Ring Modulators (2022)

Ring-based, resonant Si photonic (SiPho) devices are temperature sensitive and require thermal tuning for stable operation, which is accomplished with integrated metallic heaters. This paper investigates the combined electromigration (EM) and thermal performance of tungsten (W) heaters using calibrated electro-thermal finite element models. The current injectors that are used to supply the current to the heater are a known weak spot for electromigration. The presented modelling study shows the conflicting design requirements for optimal thermal performance and optimal EM performance, which results in the need of a careful trade-off, supported by experimental reliability data. Based on modelling results, new device designs are proposed with significant performance increase. Lastly, a new methodology is introduced which allows to predict the lifetime of the W-heaters, given specific operating conditions such as ambient temperature and required phase shift.
Aframodial and other bioactive diterpenoids from Aframomum species (1994)

Abstract
Diffraction-based overlay metrology from visible to infrared wavelengths using a single sensor (2022)

Background: Integrated circuits are fabricated layer by layer. It is crucial to their performance that these layers are well aligned to each other, and any undesired translation of a layer is called overlay. Thus far, overlay measurements have been limited to visible wavelengths, but the use of materials that are opaque to visible wavelengths necessitates measurements using infrared light.&#13;\\n&#13;\\nAim: We set out to demonstrate that an overlay sensor based on digital holographic microscopy can perform such overlay measurement at infrared wavelengths, while maintaining functionality at visible wavelengths.&#13;\\n&#13;\\nApproach: This was done by constructing a breadboard setup that is capable of measuring overlay at wavelengths ranging from 400 to 1100 nm.&#13;\\n&#13;\\nResults: Using the setup, we demonstrated good linearity between an applied amount of overlay and the measured amount. In addition, we demonstrated that the setup is only sensitive to structures at the top of the wafer. Measurements are therefore unaffected by the fact that Si is transparent at 1100 nm.&#13;\\n&#13;\\nConclusions: These results demonstrate the viability of an overlay sensor that is sensitive to visible and infrared light, allowing more freedom in choice of materials for integrated circuits.
Fast image recovery using dynamic load balancing in parallel architectures, by means of incomplete projections (2001)

This paper formulates an incomplete projection algorithm that is applied to the image recovery problem. The algorithm allows an easy implementation of dynamic load balancing for parallel architectures. Furthermore, the local computation-communication load ratio can be adjusted, since each processor performs a finite number of iterations of any projection-type technique, and this number can be provided as a parameter of the algorithm. Numerical results compare favorably with those obtained by the extrapolated method of parallel subgradient projections.
Modeling the effect of fuel ethanol concentration on cylinder pressure evolution in Direct-Injection Flex-Fuel engines (2009)

A physics-based lumped-parameter model for the cylinder pressure evolution during the compression stroke in Flex-Fuel Direct-Injection (DI) engines is developed in this paper. The proposed model captures the fuel vaporization process for ethanol-gasoline fuel blends and the associated charge cooling effect. In addition, a detection residue is introduced to process cylinder pressure measurements under two different fuel injection patterns and extract the charge cooling effect caused by fuel vaporization during the compression stroke. The residues calculated from the proposed model were validated with those generated from experimental cylinder pressure for different gasoline-ethanol blends and various speeds and loads on a 2.0 L Turbocharged Spark Ignited Direct Injection (SIDI) engine with Variable Valve timing (VVT). Residues generated from both measured and modeled cylinder pressure exhibit a monotonic correlation with the fuel ethanol content for all the tested engine operating conditions. The promising results point to the potential of the proposed model to be integrated with the residue generation algorithm into a real-time model-based scheme for ethanol detection.
QoE-Based Cross-Layer Optimization of Wireless Video with Unperceivable Temporal Video Quality Fluctuation (2011)

This paper proposes a novel approach for Quality of Experience (QoE) driven cross-layer optimization for wireless video transmission. We formulate the cross-layer optimization problem with a constraint on the temporal fluctuation of the video quality. Our objective is to minimize the temporal change of the video quality as perceivable quality fluctuations negatively affect the overall quality of experience. The proposed QoE scheme jointly optimizes the application layer and the lower layers of a wireless protocol stack. It allocates network resources and performs rate adaptation such that the fluctuations lie within the range of unperceivable changes. We determine corresponding perception thresholds via extensive subjective tests and evaluate the proposed scheme using an OPNET High Speed Downlink Packet Access (HSDPA) emulator. Our simulation results show that the proposed approach leads to a noticeable improvement of overall user satisfaction for the provided video delivery service when compared to state-of-the-art approaches.
Chemical Synthesis of L‐Fucose Derivatives for Acceptor Specificity Characterisation of Plant Cell Wall Glycosyltransferases (2017)

Abstract Seven derivatives of L‐fucose: methyl α‐L‐fucopyranoside, methyl 2‐ O ‐methyl‐α‐L‐fucopyranoside, methyl 3‐ O ‐methyl‐α‐L‐fucopyranoside, methyl 4‐ O ‐methyl‐α‐L‐fucopyranoside, α‐L‐fucopyranosyl‐(1→4)‐α/β‐L‐rhamnopyranose, methyl α‐L‐fucopyranosyl‐(1→4)‐α‐L‐rhamnopyranoside and methyl α‐L‐fucopyranosyl‐(1→4)‐β‐L‐rhamnopyranoside, were chemically synthesized and characterized. The derivatives of L‐fucose were designed to mimic the L‐fucose moieties present in the A‐chain of pectic rhamnogalacturonan‐II and used to investigate the regiospecificity of three heterologously expressed xylosyltransferases from Arabidopsis thaliana . The monosaccharide methyl α‐L‐fucopyranoside was the most efficient acceptor, 30 fold more effective than methyl 4‐ O ‐methyl‐α‐L‐fucopyranoside. O ‐methylation in position 2 or 3 abolished acceptor function. The efficiencies of the disaccharides as acceptors were methyl α‐L‐fucopyranosyl‐(1→4)‐β‐L‐rhamnopyranoside &gt; α‐L‐fucopyranosyl‐(1→4)‐α/β‐L‐rhamnopyranose &gt; methyl α‐L‐fucopyranosyl‐(1→4)‐α‐L‐rhamnopyranoside. These findings demonstrate the utility of acceptor derivatives as probes of glycosyltransferase regiospecificity.
3.4-Inch Quarter High Definition Flexible Active Matrix Organic Light Emitting Display with Oxide Thin Film Transistor (2011)

In this paper, we report a 3.4-in. flexible active matrix organic light emitting display (AMOLED) display with remarkably high definition (quarter high definition: QHD) in which oxide thin film transistors (TFTs) are used. We have developed a transfer technology in which a TFT array formed on a glass substrate is separated from the substrate by physical force and then attached to a flexible plastic substrate. Unlike a normal process in which a TFT array is directly fabricated on a thin plastic substrate, our transfer technology permits a high integration of high performance TFTs, such as low-temperature polycrystalline silicon TFTs (LTPS TFTs) and oxide TFTs, on a plastic substrate, because a flat, rigid, and thermally-stable glass substrate can be used in the TFT fabrication process in our transfer technology. As a result, this technology realized an oxide TFT array for an AMOLED on a plastic substrate. Furthermore, in order to achieve a high-definition AMOLED, color filters were incorporated in the TFT array and a white organic light-emitting diode (OLED) was combined. One of the features of this device is that the whole body of the device can be bent freely because a source driver and a gate driver can be integrated on the substrate due to the high mobility of an oxide TFT. This feature means "true" flexibility.
CeON/CERMINE: CERMINE 1.13 (2017)

Content ExtRactor and MINEr
Large language models encode clinical knowledge (2023)

Large language models (LLMs) have demonstrated impressive capabilities, but the bar for clinical applications is high. Attempts to assess the clinical knowledge of models typically rely on automated evaluations based on limited benchmarks. Here, to address these limitations, we present MultiMedQA, a benchmark combining six existing medical question answering datasets spanning professional medicine, research and consumer queries and a new dataset of medical questions searched online, HealthSearchQA. We propose a human evaluation framework for model answers along multiple axes including factuality, comprehension, reasoning, possible harm and bias. In addition, we evaluate Pathways Language Model<sup>1</sup> (PaLM, a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM<sup>2</sup> on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA<sup>3</sup>, MedMCQA<sup>4</sup>, PubMedQA<sup>5</sup> and Measuring Massive Multitask Language Understanding (MMLU) clinical topics<sup>6</sup>), including 67.6% accuracy on MedQA (US Medical Licensing Exam-style questions), surpassing the prior state of the art by more than 17%. However, human evaluation reveals key gaps. To resolve this, we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, knowledge recall and reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLMs for clinical applications.
Masking Effects on Visual Target Detection and Tracking. (1982)

Abstract : Since eye movements are required for the detection and tracking of a point target, their concomitant signal can provide physiological objective measures of performance in target acquisition tasks. Saccadic latency, misses, and false alarm rate were used in assessing and comparing the effects of static and dynamic masks on target detection and tracking. A point target with an effective diameter of 0.4 degrees was displayed in either of two fixed positions separated by 18 degrees symmetrically with respect to the egocentric axis. Timing of target displacement was either periodic, or aperiodic. The masking field was generated by projection of a polarized texture pattern, characterized by a spectrum below 1 cpd, superimposed on the visual axis via a beam splitter. Masking dynamics were generated by a rotating polarizer situated in front of the masking field projector. As target luminance decreased from 11 to 6 ft-L, reaction time measured as saccadic latency, increased. This effect of target luminance was further substantiated once static masking was introduced. Aperiodic target displacements resulted in false alarm saccades to the right position. It was found that dynamic mask of the same spatial spectrum and contrast had a significantly more detrimental effect on subject performance.
La famille des récepteurs de la dopamine (1993)

Cinq genes codant pour les recepteurs de la dopamine sont aujourd'hui connus, correspondant a une diversite supplementaire de transcrits et de proteines du fait de phenomenes surajoutes d'epissages alternatifs. Les recepteurs peuvent etre classes en deux groupes, de type D 1 (recepteurs D 1 et D 5 ), couples a l'activation de l'adenylate cyclase par une proteine G s , et du type D 2 (D 2 , D 3 et D 4 ), couples a l'inhibition de l'adenylate cyclase par des proteines G i ou G o . De plus, ces recepteurs peuvent egalement etre couples a l'activation des phospholipases C et A, ou au controle de canaux ioniques
Using Deep Learning Based Approaches for Bearing Fault Diagnosis with AE Sensors (2016)

In the age of Internet of Things and Industrial 4.0, the prognostic and health management (PHM) systems are used to collect massive real-time data from mechanical equipment. Mechanical big data has the characteristics of large-volume, diversity and high-velocity. Effectively mining features from such data and accurately identifying the machinery health conditions with new advanced methods become new issues in PHM. A major problem of using the existing PHM methods for machinery fault diagnosis with big data is that the features are manually extracted relying on much prior knowledge about signal processing techniques and diagnostic expertise, limiting their capability in fault diagnosis with big data. This paper presents a deep learning based approach for bearing fault diagnosis using acoustic emission (AE) sensors with big data. Different from widely used shallow neural network architecture with only one hidden layer, the branch of machine learning methods with multiple hidden layers are regarded as deep learning method. The presented approach pre-processes AE signals using short time Fourier transform (STFT) and extract features. Based on the simply processed AE features, an optimized deep learning structure, large memory storage retrieval neural network (LAMSTAR) is used to perform bearing fault diagnosis. The unique structure of LAMSTAR enables it to establish more efficient and sparse distributed feature maps than traditional neural networks. By leveraging the labelled information via supervised learning, the trained network is endowed with discriminative ability to classify bearing faults. The AE signals acquired from a bearing test rig are used to validate the presented method. The test results show the accurate classification performance on various fault types under different working conditions, namely input shaft rotating speeds. It also proves to be effective on diagnosing bearing faults with relatively low rotating speeds.
Comparison of 2D and 3D unsteady effects of a pair of opposed confined impinging jets (2010)

The unsteady laminar flow and heat transfer characteristics for a pair of opposed confined impinging air jets in 2D and 3D were studied numerically. The present study continues the authors' earlier work [1] and identifies the main similarities and differences arising from the expansion to the third dimension. For comparison purposes, the space and time-averaged heat transfer coefficients for a pair of heat sources arranged at different locations on opposite target walls were determined together with the oscillating jet frequency. The authors' previous investigation found that opposite confined jets remain steady at Reynolds numbers that make the parallel (side-by-side) jets highly unsteady. The nature of the unsteadiness depends on the proximity of the jet inlets, the channel dimensions and the jet Reynolds number. The unsteadiness causes the stagnation point locations to sweep back and forth over the impingement region, causing the jets to "wash" a larger surface area on the target wall. Depending on the proximity of the jet inlets, a fixed stagnation "bubble" is formed between the two jets, leading to a quasi-independence of the local heat transfer on flow conditions. The study focuses on the flow field unsteadiness and associated heat transfer coefficients when varying the distance between the chips placed on the target walls for a flow at Re = 750. The relevant trends for the 2D and 3D jet hydrodynamic and thermal fields are documented. Although similar in nature, the unsteady 3D opposite jets produce results that deviate from the 2D unsteady opposite jets. The complex vortex patterns resulting from the jet interaction at the higher Reynolds number is investigated and its impact on electronics component cooling are documented.
Safety and Feasibility of Open Chest Epicardial Mapping and Ablation of Ventricular Tachycardia During the Period of Left Ventricular Assist Device Implantation (2015)

Open-chest hybrid epicardial mapping and ablation for recurrent VT is feasible and can be considered in select patients during the period of LVAD implantation.
Progesterone induces porcine sperm release from oviduct glycans in a proteasome-dependent manner (2021)

In mammals, the oviduct retains sperm, forming a reservoir from which they are released in synchrony with ovulation. However, the mechanisms underlying sperm release are unclear. Herein, we first examined in greater detail the release of sperm from the oviduct reservoir by sex steroids, and secondly, if the ubiquitin-proteasome system (UPS) mediates this release in vitro. Sperm were allowed to bind to oviductal cells or immobilized oviduct glycans, either bi-SiaLN or a suLeX, and channeled with steroids in the presence or absence of proteasome inhibitors. Previously, we have demonstrated progesterone-induced sperm release from oviduct cells and immobilized glycans in a steroid-specific manner. Herein, we found that the release of sperm from an immobilized oviduct glycan, a six-sialylated branched structure, and from immobilized fibronectin was inhibited by the CatSper blocker NNC 055-0396, akin to the previously reported ability of NNC 055-0396 to inhibit sperm release from another oviduct glycan, sulfated Lewis-X trisaccharide. Thus, CatSper may be required for release of sperm from a variety of adhesion systems. One possible mechanism for sperm release is that glycan receptors on sperm are degraded by proteasomes or shed from the sperm surface by proteasomal degradation. Accordingly, the inhibition of proteasomal degradation blocked sperm release from oviduct cell aggregates both immobilized oviduct glycans as well as fibronectin. In summary, progesterone-induced sperm release requires both active CatSper channels and proteasomal degradation, suggesting that hyperactivation and proteolysis are vital parts of the mechanism by which sperm move from the oviduct reservoir to the site of fertilization.
Survival and Prognostic Factors in Thyroid Carcinoma (1986)

A multivariate analysis of prognostic factors and survival was carried out in a series of 200 patients with thyroid carcinoma. The cumulative survival rate corrected for intercurrent deaths was higher for papillary carcinoma than for follicular carcinoma both at 5 years (92% vs 74%) and at ten years (87% vs 66%) after the diagnosis. Seventeen of the eighteen patients with anaplastic carcinoma died within 24 months after the diagnosis. The most important independent prognostic factor in patients with papillary or follicular carcinoma, by multivariate analysis, was age at time of diagnosis, followed by tumor penetration beyond the thyroid capsule and follicular histologic type. When different types of treatment were included in the analysis, age at diagnosis still remained the most important prognostic factor. Misdiagnosed intercurrent deaths in the elderly did not explain the negative effect of age on survival.
Libraries of green fluorescent protein fusions generated by transposition in vitro (1998)

Two artificial transposons have been constructed that carry a gene encoding Green Fluorescent Protein and can be used for generating libraries of GFP fusions in a gene of interest. One such element, AT2GFP, can be used to generate GFP insertions in frame with the amino acid sequence of the protein of interest, with a stop codon at the end of the GFP coding sequence; AT2GFP also contains a selectable marker that confers trimethoprim resistance in bacteria. The second element, GS, can be used to generate tribrid GFP fusions because there is no stop codon in the GFP transposon, and the resulting fusion proteins contain the entire amino acid sequence encoded by the gene. The GS element consists of a gfp open reading frame and a supF amber suppressor tRNA gene; the supF portion of the GS transposon can be utilized as a selectable marker in bacteria. Its sequence contains a fortuitous open reading frame, and thus it can be translated continuously with the gfp amino acid sequence. As a target for GFP insertions, we used a plasmid carrying the native Ty1 retrotransposon of the yeast Sacharomyces cerevisiae. The resulting multiple GFP fusions to Ty1 capsid protein Gag and Ty1 integrase were useful in determining the cellular localization of these proteins. Libraries of GFP fusions generated by transposition in vitro represent a novel and potentially powerful method to study the cell distribution and cellular localization signals of proteins.
ChemInform Abstract: Synthesis, Characterization, and Computation of Catalysts at the Center for Atomic‐Level Catalyst Design (2014)

Abstract Review: 229 refs.